I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 15 20:25:28 +14 2023
I: pbuilder-time-stamp: 1681539928
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [htsjdk_3.0.4+dfsg-2.dsc]
I: copying [./htsjdk_3.0.4+dfsg.orig.tar.xz]
I: copying [./htsjdk_3.0.4+dfsg-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Jan 24 17:26:04 2023 +14
gpgv:                using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./htsjdk_3.0.4+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting htsjdk in htsjdk-3.0.4+dfsg
dpkg-source: info: unpacking htsjdk_3.0.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking htsjdk_3.0.4+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 10-build.xml.patch
dpkg-source: info: applying 13-skip_network_tests
dpkg-source: info: applying 20-fix-version.patch
dpkg-source: info: applying 30-disable-scalatest.patch
dpkg-source: info: applying 40-fix-java9
dpkg-source: info: applying 60-enable-tests
dpkg-source: info: applying 70-removesometests-testng.patch
dpkg-source: info: applying 90-disable-testftp.patch
dpkg-source: info: applying 92-disable-testhttp.patch
dpkg-source: info: applying 100-fix-java11
dpkg-source: info: applying 110-debian-lib-version.patch
dpkg-source: info: applying disable-network-tests.diff
dpkg-source: info: applying 120-fix-build.patch
dpkg-source: info: applying 140-skip-testFlushNotSpammed.patch
dpkg-source: info: applying 150-use-rhino-as-JS-engine.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/D01_modify_environment starting
debug: Running on codethink10-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
lrwxrwxrwx 1 root root 4 Jan  6 03:20 /bin/sh -> dash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build'
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME='pbuilder2'
  BUILD_ARCH='arm64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
  DISTRIBUTION='bookworm'
  HOME='/var/lib/jenkins'
  HOST_ARCH='arm64'
  IFS=' 	
  '
  LANG='C'
  LANGUAGE='nl_BE:nl'
  LC_ALL='C'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='6123'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.DZeyy07G/pbuilderrc_fOwn --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.DZeyy07G/b2 --logfile b2/build.log --extrapackages usrmerge htsjdk_3.0.4+dfsg-2.dsc'
  SUDO_GID='117'
  SUDO_UID='110'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT-14'
  USER='root'
  USERNAME='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://192.168.101.16:3128'
I: uname -a
  Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Apr 15 02:48 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: default-jdk, javahelper, gradle-debian-helper, maven-repo-helper, debhelper-compat (= 13), libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-java, libmjson-java, librhino-java, libsnappy-java, libcommons-compress-java, libngs-java, default-jdk-doc, junit4, libcommons-lang3-java, libjimfs-java, scala-library
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on default-jdk; however:
  Package default-jdk is not installed.
 pbuilder-satisfydepends-dummy depends on javahelper; however:
  Package javahelper is not installed.
 pbuilder-satisfydepends-dummy depends on gradle-debian-helper; however:
  Package gradle-debian-helper is not installed.
 pbuilder-satisfydepends-dummy depends on maven-repo-helper; however:
  Package maven-repo-helper is not installed.
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-jexl2-java; however:
  Package libcommons-jexl2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however:
  Package libcommons-logging-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however:
  Package libjaxb-api-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-java; however:
  Package libjaxb-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmjson-java; however:
  Package libmjson-java is not installed.
 pbuilder-satisfydepends-dummy depends on librhino-java; however:
  Package librhino-java is not installed.
 pbuilder-satisfydepends-dummy depends on libsnappy-java; however:
  Package libsnappy-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-compress-java; however:
  Package libcommons-compress-java is not installed.
 pbuilder-satisfydepends-dummy depends on libngs-java; however:
  Package libngs-java is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk-doc; however:
  Package default-jdk-doc is not installed.
 pbuilder-satisfydepends-dummy depends on junit4; however:
  Package junit4 is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-lang3-java; however:
  Package libcommons-lang3-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjimfs-java; however:
  Package libjimfs-java is not installed.
 pbuilder-satisfydepends-dummy depends on scala-library; however:
  Package scala-library is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  adwaita-icon-theme{a} ant{a} ant-optional{a} antlr{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bnd{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} gradle{a} gradle-debian-helper{a} groff-base{a} groovy{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} ivy{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} libactivation-java{a} libantlr-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libbrotli1{a} libbsd0{a} libbsf-java{a} libbsh-java{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libdatrie1{a} libdbus-1-3{a} libdd-plist-java{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libeclipse-jdt-annotation-java{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexpat1{a} libfastinfoset-java{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfindbugs-java{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhawtjni-runtime-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libjansi-java{a} libjansi-native-java{a} libjansi1-java{a} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjcifs-java{a} libjcip-annotations-java{a} libjcommander-java{a} libjetty9-java{a} libjformatstring-java{a} libjgit-java{a} libjimfs-java{a} libjline2-java{a} libjna-java{a} libjna-jni{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-jquery-ui-theme-base{a} libjsch-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjzlib-java{a} libkryo-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm15{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libminlog-java{a} libmjson-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libnative-platform-java{a} libnative-platform-jni{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnekohtml-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-jni{a} libnpth0{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libpolyglot-maven-java{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libreadline8{a} libreflectasm-java{a} libregexp-ipv6-perl{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsimple-http-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libsub-quote-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxstream-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libyaml-snake-java{a} libz3-4{a} m4{a} man-db{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-doc{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} scala-library{a} sensible-utils{a} shared-mime-info{a} testng{a} unzip{a} wdiff{a} x11-common{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libbindex-java libdata-dump-perl libdistro-info-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpars-groovy-java libgpm2 libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libreflectasm-java-doc librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget xdg-user-dirs 
0 packages upgraded, 363 newly installed, 0 to remove and 0 not upgraded.
Need to get 473 MB of archives. After unpacking 1242 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 netbase all 6.4 [12.8 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-1 [1311 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 shared-mime-info arm64 2.2-1 [727 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-1+b1 [130 kB]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 gtk-update-icon-cache arm64 3.24.37-2 [42.7 kB]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 adwaita-icon-theme all 43-1 [5124 kB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 ca-certificates-java all 20230103 [11.4 kB]
Get: 42 http://deb.debian.org/debian bookworm/main arm64 java-common all 0.74 [6388 B]
Get: 43 http://deb.debian.org/debian bookworm/main arm64 libavahi-common-data arm64 0.8-9 [107 kB]
Get: 44 http://deb.debian.org/debian bookworm/main arm64 libavahi-common3 arm64 0.8-9 [40.3 kB]
Get: 45 http://deb.debian.org/debian bookworm/main arm64 libdbus-1-3 arm64 1.14.6-1 [191 kB]
Get: 46 http://deb.debian.org/debian bookworm/main arm64 libavahi-client3 arm64 0.8-9 [43.7 kB]
Get: 47 http://deb.debian.org/debian bookworm/main arm64 libcups2 arm64 2.4.2-3 [228 kB]
Get: 48 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB]
Get: 49 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB]
Get: 50 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB]
Get: 51 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 52 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB]
Get: 53 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB]
Get: 54 http://deb.debian.org/debian bookworm/main arm64 libnspr4 arm64 2:4.35-1 [105 kB]
Get: 55 http://deb.debian.org/debian bookworm/main arm64 libnss3 arm64 2:3.87.1-1 [1218 kB]
Get: 56 http://deb.debian.org/debian bookworm/main arm64 libasound2-data all 1.2.8-1 [20.5 kB]
Get: 57 http://deb.debian.org/debian bookworm/main arm64 libasound2 arm64 1.2.8-1+b1 [327 kB]
Get: 58 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB]
Get: 59 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB]
Get: 60 http://deb.debian.org/debian bookworm/main arm64 libpcsclite1 arm64 1.9.9-1 [60.4 kB]
Get: 61 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jre-headless arm64 17.0.6+10-1 [42.5 MB]
Get: 62 http://deb.debian.org/debian bookworm/main arm64 default-jre-headless arm64 2:1.17-74 [2932 B]
Get: 63 http://deb.debian.org/debian bookworm/main arm64 ant all 1.10.13-1 [2161 kB]
Get: 64 http://deb.debian.org/debian bookworm/main arm64 ant-optional all 1.10.13-1 [449 kB]
Get: 65 http://deb.debian.org/debian bookworm/main arm64 libantlr-java all 2.7.7+dfsg-12 [458 kB]
Get: 66 http://deb.debian.org/debian bookworm/main arm64 antlr all 2.7.7+dfsg-12 [14.3 kB]
Get: 67 http://deb.debian.org/debian bookworm/main arm64 at-spi2-common all 2.46.0-5 [162 kB]
Get: 68 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 69 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 70 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 71 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 72 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 73 http://deb.debian.org/debian bookworm/main arm64 unzip arm64 6.0-28 [157 kB]
Get: 74 http://deb.debian.org/debian bookworm/main arm64 java-wrappers all 0.4 [8916 B]
Get: 75 http://deb.debian.org/debian bookworm/main arm64 libhamcrest-java all 2.2-1 [121 kB]
Get: 76 http://deb.debian.org/debian bookworm/main arm64 junit4 all 4.13.2-3 [348 kB]
Get: 77 http://deb.debian.org/debian bookworm/main arm64 libfelix-framework-java all 4.6.1-2.1 [569 kB]
Get: 78 http://deb.debian.org/debian bookworm/main arm64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB]
Get: 79 http://deb.debian.org/debian bookworm/main arm64 libosgi-annotation-java all 8.1.0-1 [9436 B]
Get: 80 http://deb.debian.org/debian bookworm/main arm64 libosgi-core-java all 8.0.0-2 [182 kB]
Get: 81 http://deb.debian.org/debian bookworm/main arm64 libfelix-resolver-java all 1.16.0-1 [180 kB]
Get: 82 http://deb.debian.org/debian bookworm/main arm64 libhawtjni-runtime-java all 1.18-1 [36.3 kB]
Get: 83 http://deb.debian.org/debian bookworm/main arm64 libjansi-native-java all 1.8-1 [26.0 kB]
Get: 84 http://deb.debian.org/debian bookworm/main arm64 libjansi1-java all 1.18-3 [66.5 kB]
Get: 85 http://deb.debian.org/debian bookworm/main arm64 libjline2-java all 2.14.6-5 [151 kB]
Get: 86 http://deb.debian.org/debian bookworm/main arm64 libosgi-compendium-java all 7.0.0-1 [477 kB]
Get: 87 http://deb.debian.org/debian bookworm/main arm64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 88 http://deb.debian.org/debian bookworm/main arm64 libxz-java all 1.9-1 [143 kB]
Get: 89 http://deb.debian.org/debian bookworm/main arm64 libyaml-snake-java all 1.33-2 [321 kB]
Get: 90 http://deb.debian.org/debian bookworm/main arm64 bnd all 5.0.1-3 [9915 kB]
Get: 91 http://deb.debian.org/debian bookworm/main arm64 dctrl-tools arm64 2.24-3 [101 kB]
Get: 92 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 93 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 94 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 95 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 96 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 97 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 98 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 99 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 100 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 101 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 102 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 103 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 104 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 105 http://deb.debian.org/debian bookworm/main arm64 libgtk2.0-common all 2.24.33-2 [2700 kB]
Get: 106 http://deb.debian.org/debian bookworm/main arm64 libatk1.0-0 arm64 2.46.0-5 [47.4 kB]
Get: 107 http://deb.debian.org/debian bookworm/main arm64 libpixman-1-0 arm64 0.42.2-1 [470 kB]
Get: 108 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB]
Get: 109 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB]
Get: 110 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB]
Get: 111 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB]
Get: 112 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB]
Get: 113 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB]
Get: 114 http://deb.debian.org/debian bookworm/main arm64 libxcb-render0 arm64 1.15-1 [115 kB]
Get: 115 http://deb.debian.org/debian bookworm/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB]
Get: 116 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB]
Get: 117 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB]
Get: 118 http://deb.debian.org/debian bookworm/main arm64 libcairo2 arm64 1.16.0-7 [527 kB]
Get: 119 http://deb.debian.org/debian bookworm/main arm64 fontconfig arm64 2.14.1-4 [449 kB]
Get: 120 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB]
Get: 121 http://deb.debian.org/debian bookworm/main arm64 libthai-data all 0.1.29-1 [176 kB]
Get: 122 http://deb.debian.org/debian bookworm/main arm64 libdatrie1 arm64 0.2.13-2+b1 [42.6 kB]
Get: 123 http://deb.debian.org/debian bookworm/main arm64 libthai0 arm64 0.1.29-1 [56.2 kB]
Get: 124 http://deb.debian.org/debian bookworm/main arm64 libpango-1.0-0 arm64 1.50.12+ds-1 [200 kB]
Get: 125 http://deb.debian.org/debian bookworm/main arm64 libpangoft2-1.0-0 arm64 1.50.12+ds-1 [44.5 kB]
Get: 126 http://deb.debian.org/debian bookworm/main arm64 libpangocairo-1.0-0 arm64 1.50.12+ds-1 [32.0 kB]
Get: 127 http://deb.debian.org/debian bookworm/main arm64 libxcomposite1 arm64 1:0.4.5-1 [16.6 kB]
Get: 128 http://deb.debian.org/debian bookworm/main arm64 libxfixes3 arm64 1:6.0.0-2 [22.9 kB]
Get: 129 http://deb.debian.org/debian bookworm/main arm64 libxcursor1 arm64 1:1.2.1-1 [40.2 kB]
Get: 130 http://deb.debian.org/debian bookworm/main arm64 libxdamage1 arm64 1:1.1.6-1 [15.2 kB]
Get: 131 http://deb.debian.org/debian bookworm/main arm64 libxi6 arm64 2:1.8-1+b1 [82.3 kB]
Get: 132 http://deb.debian.org/debian bookworm/main arm64 libxinerama1 arm64 2:1.1.4-3 [17.8 kB]
Get: 133 http://deb.debian.org/debian bookworm/main arm64 libxrandr2 arm64 2:1.5.2-2+b1 [38.4 kB]
Get: 134 http://deb.debian.org/debian bookworm/main arm64 libgtk2.0-0 arm64 2.24.33-2 [1704 kB]
Get: 135 http://deb.debian.org/debian bookworm/main arm64 libglvnd0 arm64 1.6.0-1 [41.4 kB]
Get: 136 http://deb.debian.org/debian bookworm/main arm64 libdrm-common all 2.4.114-1 [7112 B]
Get: 137 http://deb.debian.org/debian bookworm/main arm64 libdrm2 arm64 2.4.114-1+b1 [36.7 kB]
Get: 138 http://deb.debian.org/debian bookworm/main arm64 libglapi-mesa arm64 22.3.6-1+deb12u1 [44.7 kB]
Get: 139 http://deb.debian.org/debian bookworm/main arm64 libx11-xcb1 arm64 2:1.8.4-2 [192 kB]
Get: 140 http://deb.debian.org/debian bookworm/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB]
Get: 141 http://deb.debian.org/debian bookworm/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB]
Get: 142 http://deb.debian.org/debian bookworm/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB]
Get: 143 http://deb.debian.org/debian bookworm/main arm64 libxcb-present0 arm64 1.15-1 [106 kB]
Get: 144 http://deb.debian.org/debian bookworm/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB]
Get: 145 http://deb.debian.org/debian bookworm/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB]
Get: 146 http://deb.debian.org/debian bookworm/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB]
Get: 147 http://deb.debian.org/debian bookworm/main arm64 libxshmfence1 arm64 1.3-1 [8712 B]
Get: 148 http://deb.debian.org/debian bookworm/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB]
Get: 149 http://deb.debian.org/debian bookworm/main arm64 libdrm-amdgpu1 arm64 2.4.114-1+b1 [20.4 kB]
Get: 150 http://deb.debian.org/debian bookworm/main arm64 libdrm-nouveau2 arm64 2.4.114-1+b1 [18.4 kB]
Get: 151 http://deb.debian.org/debian bookworm/main arm64 libdrm-radeon1 arm64 2.4.114-1+b1 [20.9 kB]
Get: 152 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB]
Get: 153 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB]
Get: 154 http://deb.debian.org/debian bookworm/main arm64 libllvm15 arm64 1:15.0.6-4+b1 [20.7 MB]
Get: 155 http://deb.debian.org/debian bookworm/main arm64 libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get: 156 http://deb.debian.org/debian bookworm/main arm64 libsensors5 arm64 1:3.6.0-7.1 [33.3 kB]
Get: 157 http://deb.debian.org/debian bookworm/main arm64 libgl1-mesa-dri arm64 22.3.6-1+deb12u1 [6278 kB]
Get: 158 http://deb.debian.org/debian bookworm/main arm64 libglx-mesa0 arm64 22.3.6-1+deb12u1 [146 kB]
Get: 159 http://deb.debian.org/debian bookworm/main arm64 libglx0 arm64 1.6.0-1 [30.8 kB]
Get: 160 http://deb.debian.org/debian bookworm/main arm64 libgl1 arm64 1.6.0-1 [90.2 kB]
Get: 161 http://deb.debian.org/debian bookworm/main arm64 libgif7 arm64 5.2.1-2.5 [46.7 kB]
Get: 162 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB]
Get: 163 http://deb.debian.org/debian bookworm/main arm64 libxtst6 arm64 2:1.2.3-1.1 [27.8 kB]
Get: 164 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jre arm64 17.0.6+10-1 [156 kB]
Get: 165 http://deb.debian.org/debian bookworm/main arm64 default-jre arm64 2:1.17-74 [1056 B]
Get: 166 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jdk-headless arm64 17.0.6+10-1 [219 MB]
Get: 167 http://deb.debian.org/debian bookworm/main arm64 default-jdk-headless arm64 2:1.17-74 [1108 B]
Get: 168 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jdk arm64 17.0.6+10-1 [4590 kB]
Get: 169 http://deb.debian.org/debian bookworm/main arm64 default-jdk arm64 2:1.17-74 [1068 B]
Get: 170 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 171 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 172 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui-theme-base all 1.12.1+dfsg-1.1 [44.3 kB]
Get: 173 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-doc all 17.0.6+10-1 [12.8 MB]
Get: 174 http://deb.debian.org/debian bookworm/main arm64 default-jdk-doc arm64 2:1.17-74 [3020 B]
Get: 175 http://deb.debian.org/debian bookworm/main arm64 libassuan0 arm64 2.5.5-5 [45.9 kB]
Get: 176 http://deb.debian.org/debian bookworm/main arm64 gpgconf arm64 2.2.40-1.1 [557 kB]
Get: 177 http://deb.debian.org/debian bookworm/main arm64 libksba8 arm64 1.6.3-2 [119 kB]
Get: 178 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB]
Get: 179 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB]
Get: 180 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB]
Get: 181 http://deb.debian.org/debian bookworm/main arm64 libnpth0 arm64 1.6-3 [18.6 kB]
Get: 182 http://deb.debian.org/debian bookworm/main arm64 dirmngr arm64 2.2.40-1.1 [770 kB]
Get: 183 http://deb.debian.org/debian bookworm/main arm64 gnupg-l10n all 2.2.40-1.1 [1093 kB]
Get: 184 http://deb.debian.org/debian bookworm/main arm64 gnupg-utils arm64 2.2.40-1.1 [880 kB]
Get: 185 http://deb.debian.org/debian bookworm/main arm64 gpg arm64 2.2.40-1.1 [903 kB]
Get: 186 http://deb.debian.org/debian bookworm/main arm64 pinentry-curses arm64 1.2.1-1 [75.2 kB]
Get: 187 http://deb.debian.org/debian bookworm/main arm64 gpg-agent arm64 2.2.40-1.1 [673 kB]
Get: 188 http://deb.debian.org/debian bookworm/main arm64 gpg-wks-client arm64 2.2.40-1.1 [532 kB]
Get: 189 http://deb.debian.org/debian bookworm/main arm64 gpg-wks-server arm64 2.2.40-1.1 [524 kB]
Get: 190 http://deb.debian.org/debian bookworm/main arm64 gpgsm arm64 2.2.40-1.1 [651 kB]
Get: 191 http://deb.debian.org/debian bookworm/main arm64 gnupg all 2.2.40-1.1 [846 kB]
Get: 192 http://deb.debian.org/debian bookworm/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 193 http://deb.debian.org/debian bookworm/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 194 http://deb.debian.org/debian bookworm/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 195 http://deb.debian.org/debian bookworm/main arm64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 196 http://deb.debian.org/debian bookworm/main arm64 libio-pty-perl arm64 1:1.17-1 [34.5 kB]
Get: 197 http://deb.debian.org/debian bookworm/main arm64 libipc-run-perl all 20220807.0-1 [104 kB]
Get: 198 http://deb.debian.org/debian bookworm/main arm64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB]
Get: 199 http://deb.debian.org/debian bookworm/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b1 [35.3 kB]
Get: 200 http://deb.debian.org/debian bookworm/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b1 [10.4 kB]
Get: 201 http://deb.debian.org/debian bookworm/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get: 202 http://deb.debian.org/debian bookworm/main arm64 libdevel-callchecker-perl arm64 0.008-2 [15.9 kB]
Get: 203 http://deb.debian.org/debian bookworm/main arm64 libparams-classify-perl arm64 0.015-2+b1 [22.9 kB]
Get: 204 http://deb.debian.org/debian bookworm/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 205 http://deb.debian.org/debian bookworm/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 206 http://deb.debian.org/debian bookworm/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 207 http://deb.debian.org/debian bookworm/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 208 http://deb.debian.org/debian bookworm/main arm64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 209 http://deb.debian.org/debian bookworm/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 210 http://deb.debian.org/debian bookworm/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 211 http://deb.debian.org/debian bookworm/main arm64 libhttp-date-perl all 6.05-2 [10.5 kB]
Get: 212 http://deb.debian.org/debian bookworm/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB]
Get: 213 http://deb.debian.org/debian bookworm/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get: 214 http://deb.debian.org/debian bookworm/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get: 215 http://deb.debian.org/debian bookworm/main arm64 liburi-perl all 5.17-1 [90.4 kB]
Get: 216 http://deb.debian.org/debian bookworm/main arm64 libhtml-parser-perl arm64 3.81-1 [98.6 kB]
Get: 217 http://deb.debian.org/debian bookworm/main arm64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 218 http://deb.debian.org/debian bookworm/main arm64 libclone-perl arm64 0.46-1 [13.5 kB]
Get: 219 http://deb.debian.org/debian bookworm/main arm64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 220 http://deb.debian.org/debian bookworm/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 221 http://deb.debian.org/debian bookworm/main arm64 libhttp-message-perl all 6.44-1 [81.7 kB]
Get: 222 http://deb.debian.org/debian bookworm/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB]
Get: 223 http://deb.debian.org/debian bookworm/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 224 http://deb.debian.org/debian bookworm/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B]
Get: 225 http://deb.debian.org/debian bookworm/main arm64 libnet-ssleay-perl arm64 1.92-2+b1 [308 kB]
Get: 226 http://deb.debian.org/debian bookworm/main arm64 libio-socket-ssl-perl all 2.081-2 [219 kB]
Get: 227 http://deb.debian.org/debian bookworm/main arm64 libnet-http-perl all 6.22-1 [25.3 kB]
Get: 228 http://deb.debian.org/debian bookworm/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB]
Get: 229 http://deb.debian.org/debian bookworm/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 230 http://deb.debian.org/debian bookworm/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 231 http://deb.debian.org/debian bookworm/main arm64 libwww-perl all 6.68-1 [186 kB]
Get: 232 http://deb.debian.org/debian bookworm/main arm64 patchutils arm64 0.4.2-1 [73.5 kB]
Get: 233 http://deb.debian.org/debian bookworm/main arm64 wdiff arm64 1.2.2-5 [119 kB]
Get: 234 http://deb.debian.org/debian bookworm/main arm64 devscripts arm64 2.23.3 [1073 kB]
Get: 235 http://deb.debian.org/debian bookworm/main arm64 ivy all 2.5.1-2 [1288 kB]
Get: 236 http://deb.debian.org/debian bookworm/main arm64 libasm-java all 9.4-1 [389 kB]
Get: 237 http://deb.debian.org/debian bookworm/main arm64 libbsf-java all 1:2.4.0-8 [76.3 kB]
Get: 238 http://deb.debian.org/debian bookworm/main arm64 libcommons-cli-java all 1.5.0-1 [60.0 kB]
Get: 239 http://deb.debian.org/debian bookworm/main arm64 libapache-pom-java all 29-2 [5276 B]
Get: 240 http://deb.debian.org/debian bookworm/main arm64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 241 http://deb.debian.org/debian bookworm/main arm64 libcommons-logging-java all 1.2-3 [62.4 kB]
Get: 242 http://deb.debian.org/debian bookworm/main arm64 libjansi-java all 2.4.0-2 [105 kB]
Get: 243 http://deb.debian.org/debian bookworm/main arm64 libqdox-java all 1.12.1-3 [172 kB]
Get: 244 http://deb.debian.org/debian bookworm/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 245 http://deb.debian.org/debian bookworm/main arm64 libxpp3-java all 1.1.4c-3 [292 kB]
Get: 246 http://deb.debian.org/debian bookworm/main arm64 libxstream-java all 1.4.20-1 [565 kB]
Get: 247 http://deb.debian.org/debian bookworm/main arm64 groovy all 2.4.21-7 [12.9 MB]
Get: 248 http://deb.debian.org/debian bookworm/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get: 249 http://deb.debian.org/debian bookworm/main arm64 libcommons-collections3-java all 3.2.2-2 [526 kB]
Get: 250 http://deb.debian.org/debian bookworm/main arm64 libcommons-compress-java all 1.22-1 [615 kB]
Get: 251 http://deb.debian.org/debian bookworm/main arm64 libcommons-io-java all 2.11.0-2 [319 kB]
Get: 252 http://deb.debian.org/debian bookworm/main arm64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 253 http://deb.debian.org/debian bookworm/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 254 http://deb.debian.org/debian bookworm/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get: 255 http://deb.debian.org/debian bookworm/main arm64 libguava-java all 31.1-1 [2613 kB]
Get: 256 http://deb.debian.org/debian bookworm/main arm64 libcommons-codec-java all 1.15-1 [292 kB]
Get: 257 http://deb.debian.org/debian bookworm/main arm64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 258 http://deb.debian.org/debian bookworm/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 259 http://deb.debian.org/debian bookworm/main arm64 libjarjar-java all 1.4+svn142-12 [205 kB]
Get: 260 http://deb.debian.org/debian bookworm/main arm64 libjcip-annotations-java all 20060626-6 [11.8 kB]
Get: 261 http://deb.debian.org/debian bookworm/main arm64 libjna-jni arm64 5.13.0-2 [60.9 kB]
Get: 262 http://deb.debian.org/debian bookworm/main arm64 libjna-java all 5.13.0-2 [236 kB]
Get: 263 http://deb.debian.org/debian bookworm/main arm64 libjzlib-java all 1.1.3-2 [80.0 kB]
Get: 264 http://deb.debian.org/debian bookworm/main arm64 libjsch-java all 0.1.55-1 [298 kB]
Get: 265 http://deb.debian.org/debian bookworm/main arm64 libminlog-java all 1.3.0-1.1 [7928 B]
Get: 266 http://deb.debian.org/debian bookworm/main arm64 libobjenesis-java all 3.3-3 [41.3 kB]
Get: 267 http://deb.debian.org/debian bookworm/main arm64 libreflectasm-java all 1.11.9+dfsg-4 [25.0 kB]
Get: 268 http://deb.debian.org/debian bookworm/main arm64 libkryo-java all 2.20-7 [158 kB]
Get: 269 http://deb.debian.org/debian bookworm/main arm64 liblogback-java all 1:1.2.11-2 [700 kB]
Get: 270 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB]
Get: 271 http://deb.debian.org/debian bookworm/main arm64 libnative-platform-jni arm64 0.14-5 [13.0 kB]
Get: 272 http://deb.debian.org/debian bookworm/main arm64 libnative-platform-java all 0.14-5 [71.0 kB]
Get: 273 http://deb.debian.org/debian bookworm/main arm64 libxml-commons-external-java all 1.4.01-5 [240 kB]
Get: 274 http://deb.debian.org/debian bookworm/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 275 http://deb.debian.org/debian bookworm/main arm64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 276 http://deb.debian.org/debian bookworm/main arm64 libnekohtml-java all 1.9.22.noko2-0.1 [125 kB]
Get: 277 http://deb.debian.org/debian bookworm/main arm64 libxbean-reflect-java all 4.5-8 [133 kB]
Get: 278 http://deb.debian.org/debian bookworm/main arm64 libgradle-core-java all 4.4.1-18 [4286 kB]
Get: 279 http://deb.debian.org/debian bookworm/main arm64 libbcprov-java all 1.72-2 [8225 kB]
Get: 280 http://deb.debian.org/debian bookworm/main arm64 libbcpg-java all 1.72-2 [383 kB]
Get: 281 http://deb.debian.org/debian bookworm/main arm64 libbsh-java all 2.0b4-20 [291 kB]
Get: 282 http://deb.debian.org/debian bookworm/main arm64 libdd-plist-java all 1.20-1.1 [72.6 kB]
Get: 283 http://deb.debian.org/debian bookworm/main arm64 libjaxen-java all 1.1.6-4 [214 kB]
Get: 284 http://deb.debian.org/debian bookworm/main arm64 libdom4j-java all 2.1.3-2 [310 kB]
Get: 285 http://deb.debian.org/debian bookworm/main arm64 libbcel-java all 6.5.0-2 [634 kB]
Get: 286 http://deb.debian.org/debian bookworm/main arm64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB]
Get: 287 http://deb.debian.org/debian bookworm/main arm64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB]
Get: 288 http://deb.debian.org/debian bookworm/main arm64 libgoogle-gson-java all 2.10-1 [261 kB]
Get: 289 http://deb.debian.org/debian bookworm/main arm64 libaopalliance-java all 20070526-7 [8572 B]
Get: 290 http://deb.debian.org/debian bookworm/main arm64 libguice-java all 4.2.3-2 [1435 kB]
Get: 291 http://deb.debian.org/debian bookworm/main arm64 libjatl-java all 0.2.3-1.1 [29.0 kB]
Get: 292 http://deb.debian.org/debian bookworm/main arm64 libjcifs-java all 1.3.19-2 [394 kB]
Get: 293 http://deb.debian.org/debian bookworm/main arm64 libeclipse-jdt-annotation-java all 2.2.700+eclipse4.26-2 [25.3 kB]
Get: 294 http://deb.debian.org/debian bookworm/main arm64 libjavaewah-java all 1.1.7-1 [156 kB]
Get: 295 http://deb.debian.org/debian bookworm/main arm64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 296 http://deb.debian.org/debian bookworm/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 297 http://deb.debian.org/debian bookworm/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 298 http://deb.debian.org/debian bookworm/main arm64 libjetty9-java all 9.4.50-3 [2962 kB]
Get: 299 http://deb.debian.org/debian bookworm/main arm64 libjgit-java all 4.11.9-2 [2534 kB]
Get: 300 http://deb.debian.org/debian bookworm/main arm64 libcommons-lang3-java all 3.12.0-2 [561 kB]
Get: 301 http://deb.debian.org/debian bookworm/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 302 http://deb.debian.org/debian bookworm/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 303 http://deb.debian.org/debian bookworm/main arm64 libmaven-resolver-java all 1.6.3-1 [548 kB]
Get: 304 http://deb.debian.org/debian bookworm/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 305 http://deb.debian.org/debian bookworm/main arm64 libmaven-parent-java all 35-1 [6140 B]
Get: 306 http://deb.debian.org/debian bookworm/main arm64 libmaven-shared-utils-java all 3.3.4-1 [138 kB]
Get: 307 http://deb.debian.org/debian bookworm/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 308 http://deb.debian.org/debian bookworm/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 309 http://deb.debian.org/debian bookworm/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 310 http://deb.debian.org/debian bookworm/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB]
Get: 311 http://deb.debian.org/debian bookworm/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 312 http://deb.debian.org/debian bookworm/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B]
Get: 313 http://deb.debian.org/debian bookworm/main arm64 libcdi-api-java all 1.2-3 [54.3 kB]
Get: 314 http://deb.debian.org/debian bookworm/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get: 315 http://deb.debian.org/debian bookworm/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get: 316 http://deb.debian.org/debian bookworm/main arm64 libmaven3-core-java all 3.8.7-1 [1572 kB]
Get: 317 http://deb.debian.org/debian bookworm/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 318 http://deb.debian.org/debian bookworm/main arm64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB]
Get: 319 http://deb.debian.org/debian bookworm/main arm64 librhino-java all 1.7.7.2-3 [1200 kB]
Get: 320 http://deb.debian.org/debian bookworm/main arm64 libsimple-http-java all 4.1.21-1.1 [211 kB]
Get: 321 http://deb.debian.org/debian bookworm/main arm64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 322 http://deb.debian.org/debian bookworm/main arm64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 323 http://deb.debian.org/debian bookworm/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB]
Get: 324 http://deb.debian.org/debian bookworm/main arm64 libjcommander-java all 1.71-4 [73.0 kB]
Get: 325 http://deb.debian.org/debian bookworm/main arm64 testng all 6.9.12-4 [795 kB]
Get: 326 http://deb.debian.org/debian bookworm/main arm64 libgradle-plugins-java all 4.4.1-18 [5212 kB]
Get: 327 http://deb.debian.org/debian bookworm/main arm64 gradle all 4.4.1-18 [398 kB]
Get: 328 http://deb.debian.org/debian bookworm/main arm64 maven-repo-helper all 1.11 [142 kB]
Get: 329 http://deb.debian.org/debian bookworm/main arm64 gradle-debian-helper all 2.4 [24.5 kB]
Get: 330 http://deb.debian.org/debian bookworm/main arm64 javahelper all 0.78 [97.2 kB]
Get: 331 http://deb.debian.org/debian bookworm/main arm64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 332 http://deb.debian.org/debian bookworm/main arm64 libargs4j-java all 2.33-2 [138 kB]
Get: 333 http://deb.debian.org/debian bookworm/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 334 http://deb.debian.org/debian bookworm/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get: 335 http://deb.debian.org/debian bookworm/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 336 http://deb.debian.org/debian bookworm/main arm64 libsnappy1v5 arm64 1.1.9-3 [25.4 kB]
Get: 337 http://deb.debian.org/debian bookworm/main arm64 libsnappy-jni arm64 1.1.8.3-1 [7056 B]
Get: 338 http://deb.debian.org/debian bookworm/main arm64 libsnappy-java all 1.1.8.3-1 [98.9 kB]
Get: 339 http://deb.debian.org/debian bookworm/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 340 http://deb.debian.org/debian bookworm/main arm64 libistack-commons-java all 3.0.6-5 [145 kB]
Get: 341 http://deb.debian.org/debian bookworm/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-10.1 [164 kB]
Get: 342 http://deb.debian.org/debian bookworm/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 343 http://deb.debian.org/debian bookworm/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB]
Get: 344 http://deb.debian.org/debian bookworm/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 345 http://deb.debian.org/debian bookworm/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB]
Get: 346 http://deb.debian.org/debian bookworm/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB]
Get: 347 http://deb.debian.org/debian bookworm/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB]
Get: 348 http://deb.debian.org/debian bookworm/main arm64 libxsom-java all 2.3.0.1-10.1 [400 kB]
Get: 349 http://deb.debian.org/debian bookworm/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB]
Get: 350 http://deb.debian.org/debian bookworm/main arm64 librngom-java all 2.3.0.1-10.1 [290 kB]
Get: 351 http://deb.debian.org/debian bookworm/main arm64 libtxw2-java all 2.3.0.1-10.1 [134 kB]
Get: 352 http://deb.debian.org/debian bookworm/main arm64 libjaxb-java all 2.3.0.1-10.1 [1973 kB]
Get: 353 http://deb.debian.org/debian bookworm/main arm64 libjimfs-java all 1.1-6 [191 kB]
Get: 354 http://deb.debian.org/debian bookworm/main arm64 libmbedcrypto7 arm64 2.28.3-1 [263 kB]
Get: 355 http://deb.debian.org/debian bookworm/main arm64 libmbedx509-1 arm64 2.28.3-1 [127 kB]
Get: 356 http://deb.debian.org/debian bookworm/main arm64 libmbedtls14 arm64 2.28.3-1 [156 kB]
Get: 357 http://deb.debian.org/debian bookworm/main arm64 libmjson-java all 1.4.0-3 [60.4 kB]
Get: 358 http://deb.debian.org/debian bookworm/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB]
Get: 359 http://deb.debian.org/debian bookworm/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [977 kB]
Get: 360 http://deb.debian.org/debian bookworm/main arm64 libncbi-ngs3 arm64 3.0.3+dfsg-5 [141 kB]
Get: 361 http://deb.debian.org/debian bookworm/main arm64 libngs-jni arm64 3.0.3+dfsg-5 [23.4 kB]
Get: 362 http://deb.debian.org/debian bookworm/main arm64 libngs-java arm64 3.0.3+dfsg-5 [110 kB]
Get: 363 http://deb.debian.org/debian bookworm/main arm64 scala-library all 2.11.12-5 [9588 kB]
Fetched 473 MB in 38s (12.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:arm64.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ...
Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:arm64.
Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ...
Unpacking libexpat1:arm64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:arm64 (3.11.2-6) ...
Setting up libexpat1:arm64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19932 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:arm64.
Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ...
Unpacking libreadline8:arm64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:arm64.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ...
Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ...
Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:arm64.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ...
Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20366 files and directories currently installed.)
Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package netbase.
Preparing to unpack .../001-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package openssl.
Preparing to unpack .../003-openssl_3.0.8-1_arm64.deb ...
Unpacking openssl (3.0.8-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../004-ca-certificates_20230311_all.deb ...
Unpacking ca-certificates (20230311) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:arm64.
Preparing to unpack .../006-libmagic1_1%3a5.44-3_arm64.deb ...
Unpacking libmagic1:arm64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../007-file_1%3a5.44-3_arm64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../008-gettext-base_0.21-12_arm64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../009-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../010-groff-base_1.22.4-10_arm64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_arm64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../012-libpipeline1_1.5.7-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../013-man-db_2.11.2-2_arm64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../014-hicolor-icon-theme_0.17-2_all.deb ...
Unpacking hicolor-icon-theme (0.17-2) ...
Selecting previously unselected package libgdk-pixbuf2.0-common.
Preparing to unpack .../015-libgdk-pixbuf2.0-common_2.42.10+dfsg-1_all.deb ...
Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ...
Selecting previously unselected package libglib2.0-0:arm64.
Preparing to unpack .../016-libglib2.0-0_2.74.6-1_arm64.deb ...
Unpacking libglib2.0-0:arm64 (2.74.6-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../017-libicu72_72.1-3_arm64.deb ...
Unpacking libicu72:arm64 (72.1-3) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../018-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ...
Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package shared-mime-info.
Preparing to unpack .../019-shared-mime-info_2.2-1_arm64.deb ...
Unpacking shared-mime-info (2.2-1) ...
Selecting previously unselected package libjpeg62-turbo:arm64.
Preparing to unpack .../020-libjpeg62-turbo_1%3a2.1.5-2_arm64.deb ...
Unpacking libjpeg62-turbo:arm64 (1:2.1.5-2) ...
Selecting previously unselected package libpng16-16:arm64.
Preparing to unpack .../021-libpng16-16_1.6.39-2_arm64.deb ...
Unpacking libpng16-16:arm64 (1.6.39-2) ...
Selecting previously unselected package libdeflate0:arm64.
Preparing to unpack .../022-libdeflate0_1.14-1_arm64.deb ...
Unpacking libdeflate0:arm64 (1.14-1) ...
Selecting previously unselected package libjbig0:arm64.
Preparing to unpack .../023-libjbig0_2.1-6.1_arm64.deb ...
Unpacking libjbig0:arm64 (2.1-6.1) ...
Selecting previously unselected package liblerc4:arm64.
Preparing to unpack .../024-liblerc4_4.0.0+ds-2_arm64.deb ...
Unpacking liblerc4:arm64 (4.0.0+ds-2) ...
Selecting previously unselected package libwebp7:arm64.
Preparing to unpack .../025-libwebp7_1.2.4-0.1_arm64.deb ...
Unpacking libwebp7:arm64 (1.2.4-0.1) ...
Selecting previously unselected package libtiff6:arm64.
Preparing to unpack .../026-libtiff6_4.5.0-5_arm64.deb ...
Unpacking libtiff6:arm64 (4.5.0-5) ...
Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64.
Preparing to unpack .../027-libgdk-pixbuf-2.0-0_2.42.10+dfsg-1+b1_arm64.deb ...
Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-1+b1) ...
Selecting previously unselected package gtk-update-icon-cache.
Preparing to unpack .../028-gtk-update-icon-cache_3.24.37-2_arm64.deb ...
Unpacking gtk-update-icon-cache (3.24.37-2) ...
Selecting previously unselected package adwaita-icon-theme.
Preparing to unpack .../029-adwaita-icon-theme_43-1_all.deb ...
Unpacking adwaita-icon-theme (43-1) ...
Selecting previously unselected package ca-certificates-java.
Preparing to unpack .../030-ca-certificates-java_20230103_all.deb ...
Unpacking ca-certificates-java (20230103) ...
Selecting previously unselected package java-common.
Preparing to unpack .../031-java-common_0.74_all.deb ...
Unpacking java-common (0.74) ...
Selecting previously unselected package libavahi-common-data:arm64.
Preparing to unpack .../032-libavahi-common-data_0.8-9_arm64.deb ...
Unpacking libavahi-common-data:arm64 (0.8-9) ...
Selecting previously unselected package libavahi-common3:arm64.
Preparing to unpack .../033-libavahi-common3_0.8-9_arm64.deb ...
Unpacking libavahi-common3:arm64 (0.8-9) ...
Selecting previously unselected package libdbus-1-3:arm64.
Preparing to unpack .../034-libdbus-1-3_1.14.6-1_arm64.deb ...
Unpacking libdbus-1-3:arm64 (1.14.6-1) ...
Selecting previously unselected package libavahi-client3:arm64.
Preparing to unpack .../035-libavahi-client3_0.8-9_arm64.deb ...
Unpacking libavahi-client3:arm64 (0.8-9) ...
Selecting previously unselected package libcups2:arm64.
Preparing to unpack .../036-libcups2_2.4.2-3_arm64.deb ...
Unpacking libcups2:arm64 (2.4.2-3) ...
Selecting previously unselected package liblcms2-2:arm64.
Preparing to unpack .../037-liblcms2-2_2.14-2_arm64.deb ...
Unpacking liblcms2-2:arm64 (2.14-2) ...
Selecting previously unselected package libbrotli1:arm64.
Preparing to unpack .../038-libbrotli1_1.0.9-2+b6_arm64.deb ...
Unpacking libbrotli1:arm64 (1.0.9-2+b6) ...
Selecting previously unselected package libfreetype6:arm64.
Preparing to unpack .../039-libfreetype6_2.12.1+dfsg-4_arm64.deb ...
Unpacking libfreetype6:arm64 (2.12.1+dfsg-4) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../040-fonts-dejavu-core_2.37-6_all.deb ...
Unpacking fonts-dejavu-core (2.37-6) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../041-fontconfig-config_2.14.1-4_arm64.deb ...
Unpacking fontconfig-config (2.14.1-4) ...
Selecting previously unselected package libfontconfig1:arm64.
Preparing to unpack .../042-libfontconfig1_2.14.1-4_arm64.deb ...
Unpacking libfontconfig1:arm64 (2.14.1-4) ...
Selecting previously unselected package libnspr4:arm64.
Preparing to unpack .../043-libnspr4_2%3a4.35-1_arm64.deb ...
Unpacking libnspr4:arm64 (2:4.35-1) ...
Selecting previously unselected package libnss3:arm64.
Preparing to unpack .../044-libnss3_2%3a3.87.1-1_arm64.deb ...
Unpacking libnss3:arm64 (2:3.87.1-1) ...
Selecting previously unselected package libasound2-data.
Preparing to unpack .../045-libasound2-data_1.2.8-1_all.deb ...
Unpacking libasound2-data (1.2.8-1) ...
Selecting previously unselected package libasound2:arm64.
Preparing to unpack .../046-libasound2_1.2.8-1+b1_arm64.deb ...
Unpacking libasound2:arm64 (1.2.8-1+b1) ...
Selecting previously unselected package libgraphite2-3:arm64.
Preparing to unpack .../047-libgraphite2-3_1.3.14-1_arm64.deb ...
Unpacking libgraphite2-3:arm64 (1.3.14-1) ...
Selecting previously unselected package libharfbuzz0b:arm64.
Preparing to unpack .../048-libharfbuzz0b_6.0.0+dfsg-3_arm64.deb ...
Unpacking libharfbuzz0b:arm64 (6.0.0+dfsg-3) ...
Selecting previously unselected package libpcsclite1:arm64.
Preparing to unpack .../049-libpcsclite1_1.9.9-1_arm64.deb ...
Unpacking libpcsclite1:arm64 (1.9.9-1) ...
Selecting previously unselected package openjdk-17-jre-headless:arm64.
Preparing to unpack .../050-openjdk-17-jre-headless_17.0.6+10-1_arm64.deb ...
Unpacking openjdk-17-jre-headless:arm64 (17.0.6+10-1) ...
Selecting previously unselected package default-jre-headless.
Preparing to unpack .../051-default-jre-headless_2%3a1.17-74_arm64.deb ...
Unpacking default-jre-headless (2:1.17-74) ...
Selecting previously unselected package ant.
Preparing to unpack .../052-ant_1.10.13-1_all.deb ...
Unpacking ant (1.10.13-1) ...
Selecting previously unselected package ant-optional.
Preparing to unpack .../053-ant-optional_1.10.13-1_all.deb ...
Unpacking ant-optional (1.10.13-1) ...
Selecting previously unselected package libantlr-java.
Preparing to unpack .../054-libantlr-java_2.7.7+dfsg-12_all.deb ...
Unpacking libantlr-java (2.7.7+dfsg-12) ...
Selecting previously unselected package antlr.
Preparing to unpack .../055-antlr_2.7.7+dfsg-12_all.deb ...
Unpacking antlr (2.7.7+dfsg-12) ...
Selecting previously unselected package at-spi2-common.
Preparing to unpack .../056-at-spi2-common_2.46.0-5_all.deb ...
Unpacking at-spi2-common (2.46.0-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../057-m4_1.4.19-3_arm64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../058-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../059-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../060-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../061-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package unzip.
Preparing to unpack .../062-unzip_6.0-28_arm64.deb ...
Unpacking unzip (6.0-28) ...
Selecting previously unselected package java-wrappers.
Preparing to unpack .../063-java-wrappers_0.4_all.deb ...
Unpacking java-wrappers (0.4) ...
Selecting previously unselected package libhamcrest-java.
Preparing to unpack .../064-libhamcrest-java_2.2-1_all.deb ...
Unpacking libhamcrest-java (2.2-1) ...
Selecting previously unselected package junit4.
Preparing to unpack .../065-junit4_4.13.2-3_all.deb ...
Unpacking junit4 (4.13.2-3) ...
Selecting previously unselected package libfelix-framework-java.
Preparing to unpack .../066-libfelix-framework-java_4.6.1-2.1_all.deb ...
Unpacking libfelix-framework-java (4.6.1-2.1) ...
Selecting previously unselected package libfelix-gogo-runtime-java.
Preparing to unpack .../067-libfelix-gogo-runtime-java_0.16.2-1.1_all.deb ...
Unpacking libfelix-gogo-runtime-java (0.16.2-1.1) ...
Selecting previously unselected package libosgi-annotation-java.
Preparing to unpack .../068-libosgi-annotation-java_8.1.0-1_all.deb ...
Unpacking libosgi-annotation-java (8.1.0-1) ...
Selecting previously unselected package libosgi-core-java.
Preparing to unpack .../069-libosgi-core-java_8.0.0-2_all.deb ...
Unpacking libosgi-core-java (8.0.0-2) ...
Selecting previously unselected package libfelix-resolver-java.
Preparing to unpack .../070-libfelix-resolver-java_1.16.0-1_all.deb ...
Unpacking libfelix-resolver-java (1.16.0-1) ...
Selecting previously unselected package libhawtjni-runtime-java.
Preparing to unpack .../071-libhawtjni-runtime-java_1.18-1_all.deb ...
Unpacking libhawtjni-runtime-java (1.18-1) ...
Selecting previously unselected package libjansi-native-java.
Preparing to unpack .../072-libjansi-native-java_1.8-1_all.deb ...
Unpacking libjansi-native-java (1.8-1) ...
Selecting previously unselected package libjansi1-java.
Preparing to unpack .../073-libjansi1-java_1.18-3_all.deb ...
Unpacking libjansi1-java (1.18-3) ...
Selecting previously unselected package libjline2-java.
Preparing to unpack .../074-libjline2-java_2.14.6-5_all.deb ...
Unpacking libjline2-java (2.14.6-5) ...
Selecting previously unselected package libosgi-compendium-java.
Preparing to unpack .../075-libosgi-compendium-java_7.0.0-1_all.deb ...
Unpacking libosgi-compendium-java (7.0.0-1) ...
Selecting previously unselected package libslf4j-java.
Preparing to unpack .../076-libslf4j-java_1.7.32-1_all.deb ...
Unpacking libslf4j-java (1.7.32-1) ...
Selecting previously unselected package libxz-java.
Preparing to unpack .../077-libxz-java_1.9-1_all.deb ...
Unpacking libxz-java (1.9-1) ...
Selecting previously unselected package libyaml-snake-java.
Preparing to unpack .../078-libyaml-snake-java_1.33-2_all.deb ...
Unpacking libyaml-snake-java (1.33-2) ...
Selecting previously unselected package bnd.
Preparing to unpack .../079-bnd_5.0.1-3_all.deb ...
Unpacking bnd (5.0.1-3) ...
Selecting previously unselected package dctrl-tools.
Preparing to unpack .../080-dctrl-tools_2.24-3_arm64.deb ...
Unpacking dctrl-tools (2.24-3) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../081-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../082-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../083-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../084-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../085-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../086-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../087-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:arm64.
Preparing to unpack .../088-libelf1_0.188-2.1_arm64.deb ...
Unpacking libelf1:arm64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../089-dwz_0.15-1_arm64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../090-gettext_0.21-12_arm64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../091-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../092-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../093-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package libgtk2.0-common.
Preparing to unpack .../094-libgtk2.0-common_2.24.33-2_all.deb ...
Unpacking libgtk2.0-common (2.24.33-2) ...
Selecting previously unselected package libatk1.0-0:arm64.
Preparing to unpack .../095-libatk1.0-0_2.46.0-5_arm64.deb ...
Unpacking libatk1.0-0:arm64 (2.46.0-5) ...
Selecting previously unselected package libpixman-1-0:arm64.
Preparing to unpack .../096-libpixman-1-0_0.42.2-1_arm64.deb ...
Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
Selecting previously unselected package libxau6:arm64.
Preparing to unpack .../097-libxau6_1%3a1.0.9-1_arm64.deb ...
Unpacking libxau6:arm64 (1:1.0.9-1) ...
Selecting previously unselected package libbsd0:arm64.
Preparing to unpack .../098-libbsd0_0.11.7-2_arm64.deb ...
Unpacking libbsd0:arm64 (0.11.7-2) ...
Selecting previously unselected package libxdmcp6:arm64.
Preparing to unpack .../099-libxdmcp6_1%3a1.1.2-3_arm64.deb ...
Unpacking libxdmcp6:arm64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:arm64.
Preparing to unpack .../100-libxcb1_1.15-1_arm64.deb ...
Unpacking libxcb1:arm64 (1.15-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../101-libx11-data_2%3a1.8.4-2_all.deb ...
Unpacking libx11-data (2:1.8.4-2) ...
Selecting previously unselected package libx11-6:arm64.
Preparing to unpack .../102-libx11-6_2%3a1.8.4-2_arm64.deb ...
Unpacking libx11-6:arm64 (2:1.8.4-2) ...
Selecting previously unselected package libxcb-render0:arm64.
Preparing to unpack .../103-libxcb-render0_1.15-1_arm64.deb ...
Unpacking libxcb-render0:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-shm0:arm64.
Preparing to unpack .../104-libxcb-shm0_1.15-1_arm64.deb ...
Unpacking libxcb-shm0:arm64 (1.15-1) ...
Selecting previously unselected package libxext6:arm64.
Preparing to unpack .../105-libxext6_2%3a1.3.4-1+b1_arm64.deb ...
Unpacking libxext6:arm64 (2:1.3.4-1+b1) ...
Selecting previously unselected package libxrender1:arm64.
Preparing to unpack .../106-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
Selecting previously unselected package libcairo2:arm64.
Preparing to unpack .../107-libcairo2_1.16.0-7_arm64.deb ...
Unpacking libcairo2:arm64 (1.16.0-7) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../108-fontconfig_2.14.1-4_arm64.deb ...
Unpacking fontconfig (2.14.1-4) ...
Selecting previously unselected package libfribidi0:arm64.
Preparing to unpack .../109-libfribidi0_1.0.8-2.1_arm64.deb ...
Unpacking libfribidi0:arm64 (1.0.8-2.1) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../110-libthai-data_0.1.29-1_all.deb ...
Unpacking libthai-data (0.1.29-1) ...
Selecting previously unselected package libdatrie1:arm64.
Preparing to unpack .../111-libdatrie1_0.2.13-2+b1_arm64.deb ...
Unpacking libdatrie1:arm64 (0.2.13-2+b1) ...
Selecting previously unselected package libthai0:arm64.
Preparing to unpack .../112-libthai0_0.1.29-1_arm64.deb ...
Unpacking libthai0:arm64 (0.1.29-1) ...
Selecting previously unselected package libpango-1.0-0:arm64.
Preparing to unpack .../113-libpango-1.0-0_1.50.12+ds-1_arm64.deb ...
Unpacking libpango-1.0-0:arm64 (1.50.12+ds-1) ...
Selecting previously unselected package libpangoft2-1.0-0:arm64.
Preparing to unpack .../114-libpangoft2-1.0-0_1.50.12+ds-1_arm64.deb ...
Unpacking libpangoft2-1.0-0:arm64 (1.50.12+ds-1) ...
Selecting previously unselected package libpangocairo-1.0-0:arm64.
Preparing to unpack .../115-libpangocairo-1.0-0_1.50.12+ds-1_arm64.deb ...
Unpacking libpangocairo-1.0-0:arm64 (1.50.12+ds-1) ...
Selecting previously unselected package libxcomposite1:arm64.
Preparing to unpack .../116-libxcomposite1_1%3a0.4.5-1_arm64.deb ...
Unpacking libxcomposite1:arm64 (1:0.4.5-1) ...
Selecting previously unselected package libxfixes3:arm64.
Preparing to unpack .../117-libxfixes3_1%3a6.0.0-2_arm64.deb ...
Unpacking libxfixes3:arm64 (1:6.0.0-2) ...
Selecting previously unselected package libxcursor1:arm64.
Preparing to unpack .../118-libxcursor1_1%3a1.2.1-1_arm64.deb ...
Unpacking libxcursor1:arm64 (1:1.2.1-1) ...
Selecting previously unselected package libxdamage1:arm64.
Preparing to unpack .../119-libxdamage1_1%3a1.1.6-1_arm64.deb ...
Unpacking libxdamage1:arm64 (1:1.1.6-1) ...
Selecting previously unselected package libxi6:arm64.
Preparing to unpack .../120-libxi6_2%3a1.8-1+b1_arm64.deb ...
Unpacking libxi6:arm64 (2:1.8-1+b1) ...
Selecting previously unselected package libxinerama1:arm64.
Preparing to unpack .../121-libxinerama1_2%3a1.1.4-3_arm64.deb ...
Unpacking libxinerama1:arm64 (2:1.1.4-3) ...
Selecting previously unselected package libxrandr2:arm64.
Preparing to unpack .../122-libxrandr2_2%3a1.5.2-2+b1_arm64.deb ...
Unpacking libxrandr2:arm64 (2:1.5.2-2+b1) ...
Selecting previously unselected package libgtk2.0-0:arm64.
Preparing to unpack .../123-libgtk2.0-0_2.24.33-2_arm64.deb ...
Unpacking libgtk2.0-0:arm64 (2.24.33-2) ...
Selecting previously unselected package libglvnd0:arm64.
Preparing to unpack .../124-libglvnd0_1.6.0-1_arm64.deb ...
Unpacking libglvnd0:arm64 (1.6.0-1) ...
Selecting previously unselected package libdrm-common.
Preparing to unpack .../125-libdrm-common_2.4.114-1_all.deb ...
Unpacking libdrm-common (2.4.114-1) ...
Selecting previously unselected package libdrm2:arm64.
Preparing to unpack .../126-libdrm2_2.4.114-1+b1_arm64.deb ...
Unpacking libdrm2:arm64 (2.4.114-1+b1) ...
Selecting previously unselected package libglapi-mesa:arm64.
Preparing to unpack .../127-libglapi-mesa_22.3.6-1+deb12u1_arm64.deb ...
Unpacking libglapi-mesa:arm64 (22.3.6-1+deb12u1) ...
Selecting previously unselected package libx11-xcb1:arm64.
Preparing to unpack .../128-libx11-xcb1_2%3a1.8.4-2_arm64.deb ...
Unpacking libx11-xcb1:arm64 (2:1.8.4-2) ...
Selecting previously unselected package libxcb-dri2-0:arm64.
Preparing to unpack .../129-libxcb-dri2-0_1.15-1_arm64.deb ...
Unpacking libxcb-dri2-0:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-dri3-0:arm64.
Preparing to unpack .../130-libxcb-dri3-0_1.15-1_arm64.deb ...
Unpacking libxcb-dri3-0:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-glx0:arm64.
Preparing to unpack .../131-libxcb-glx0_1.15-1_arm64.deb ...
Unpacking libxcb-glx0:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-present0:arm64.
Preparing to unpack .../132-libxcb-present0_1.15-1_arm64.deb ...
Unpacking libxcb-present0:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-randr0:arm64.
Preparing to unpack .../133-libxcb-randr0_1.15-1_arm64.deb ...
Unpacking libxcb-randr0:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-sync1:arm64.
Preparing to unpack .../134-libxcb-sync1_1.15-1_arm64.deb ...
Unpacking libxcb-sync1:arm64 (1.15-1) ...
Selecting previously unselected package libxcb-xfixes0:arm64.
Preparing to unpack .../135-libxcb-xfixes0_1.15-1_arm64.deb ...
Unpacking libxcb-xfixes0:arm64 (1.15-1) ...
Selecting previously unselected package libxshmfence1:arm64.
Preparing to unpack .../136-libxshmfence1_1.3-1_arm64.deb ...
Unpacking libxshmfence1:arm64 (1.3-1) ...
Selecting previously unselected package libxxf86vm1:arm64.
Preparing to unpack .../137-libxxf86vm1_1%3a1.1.4-1+b2_arm64.deb ...
Unpacking libxxf86vm1:arm64 (1:1.1.4-1+b2) ...
Selecting previously unselected package libdrm-amdgpu1:arm64.
Preparing to unpack .../138-libdrm-amdgpu1_2.4.114-1+b1_arm64.deb ...
Unpacking libdrm-amdgpu1:arm64 (2.4.114-1+b1) ...
Selecting previously unselected package libdrm-nouveau2:arm64.
Preparing to unpack .../139-libdrm-nouveau2_2.4.114-1+b1_arm64.deb ...
Unpacking libdrm-nouveau2:arm64 (2.4.114-1+b1) ...
Selecting previously unselected package libdrm-radeon1:arm64.
Preparing to unpack .../140-libdrm-radeon1_2.4.114-1+b1_arm64.deb ...
Unpacking libdrm-radeon1:arm64 (2.4.114-1+b1) ...
Selecting previously unselected package libedit2:arm64.
Preparing to unpack .../141-libedit2_3.1-20221030-2_arm64.deb ...
Unpacking libedit2:arm64 (3.1-20221030-2) ...
Selecting previously unselected package libz3-4:arm64.
Preparing to unpack .../142-libz3-4_4.8.12-3.1_arm64.deb ...
Unpacking libz3-4:arm64 (4.8.12-3.1) ...
Selecting previously unselected package libllvm15:arm64.
Preparing to unpack .../143-libllvm15_1%3a15.0.6-4+b1_arm64.deb ...
Unpacking libllvm15:arm64 (1:15.0.6-4+b1) ...
Selecting previously unselected package libsensors-config.
Preparing to unpack .../144-libsensors-config_1%3a3.6.0-7.1_all.deb ...
Unpacking libsensors-config (1:3.6.0-7.1) ...
Selecting previously unselected package libsensors5:arm64.
Preparing to unpack .../145-libsensors5_1%3a3.6.0-7.1_arm64.deb ...
Unpacking libsensors5:arm64 (1:3.6.0-7.1) ...
Selecting previously unselected package libgl1-mesa-dri:arm64.
Preparing to unpack .../146-libgl1-mesa-dri_22.3.6-1+deb12u1_arm64.deb ...
Unpacking libgl1-mesa-dri:arm64 (22.3.6-1+deb12u1) ...
Selecting previously unselected package libglx-mesa0:arm64.
Preparing to unpack .../147-libglx-mesa0_22.3.6-1+deb12u1_arm64.deb ...
Unpacking libglx-mesa0:arm64 (22.3.6-1+deb12u1) ...
Selecting previously unselected package libglx0:arm64.
Preparing to unpack .../148-libglx0_1.6.0-1_arm64.deb ...
Unpacking libglx0:arm64 (1.6.0-1) ...
Selecting previously unselected package libgl1:arm64.
Preparing to unpack .../149-libgl1_1.6.0-1_arm64.deb ...
Unpacking libgl1:arm64 (1.6.0-1) ...
Selecting previously unselected package libgif7:arm64.
Preparing to unpack .../150-libgif7_5.2.1-2.5_arm64.deb ...
Unpacking libgif7:arm64 (5.2.1-2.5) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../151-x11-common_1%3a7.7+23_all.deb ...
Unpacking x11-common (1:7.7+23) ...
Selecting previously unselected package libxtst6:arm64.
Preparing to unpack .../152-libxtst6_2%3a1.2.3-1.1_arm64.deb ...
Unpacking libxtst6:arm64 (2:1.2.3-1.1) ...
Selecting previously unselected package openjdk-17-jre:arm64.
Preparing to unpack .../153-openjdk-17-jre_17.0.6+10-1_arm64.deb ...
Unpacking openjdk-17-jre:arm64 (17.0.6+10-1) ...
Selecting previously unselected package default-jre.
Preparing to unpack .../154-default-jre_2%3a1.17-74_arm64.deb ...
Unpacking default-jre (2:1.17-74) ...
Selecting previously unselected package openjdk-17-jdk-headless:arm64.
Preparing to unpack .../155-openjdk-17-jdk-headless_17.0.6+10-1_arm64.deb ...
Unpacking openjdk-17-jdk-headless:arm64 (17.0.6+10-1) ...
Selecting previously unselected package default-jdk-headless.
Preparing to unpack .../156-default-jdk-headless_2%3a1.17-74_arm64.deb ...
Unpacking default-jdk-headless (2:1.17-74) ...
Selecting previously unselected package openjdk-17-jdk:arm64.
Preparing to unpack .../157-openjdk-17-jdk_17.0.6+10-1_arm64.deb ...
Unpacking openjdk-17-jdk:arm64 (17.0.6+10-1) ...
Selecting previously unselected package default-jdk.
Preparing to unpack .../158-default-jdk_2%3a1.17-74_arm64.deb ...
Unpacking default-jdk (2:1.17-74) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../159-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../160-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
Selecting previously unselected package libjs-jquery-ui-theme-base.
Preparing to unpack .../161-libjs-jquery-ui-theme-base_1.12.1+dfsg-1.1_all.deb ...
Unpacking libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ...
Selecting previously unselected package openjdk-17-doc.
Preparing to unpack .../162-openjdk-17-doc_17.0.6+10-1_all.deb ...
Unpacking openjdk-17-doc (17.0.6+10-1) ...
Selecting previously unselected package default-jdk-doc.
Preparing to unpack .../163-default-jdk-doc_2%3a1.17-74_arm64.deb ...
Unpacking default-jdk-doc (2:1.17-74) ...
Selecting previously unselected package libassuan0:arm64.
Preparing to unpack .../164-libassuan0_2.5.5-5_arm64.deb ...
Unpacking libassuan0:arm64 (2.5.5-5) ...
Selecting previously unselected package gpgconf.
Preparing to unpack .../165-gpgconf_2.2.40-1.1_arm64.deb ...
Unpacking gpgconf (2.2.40-1.1) ...
Selecting previously unselected package libksba8:arm64.
Preparing to unpack .../166-libksba8_1.6.3-2_arm64.deb ...
Unpacking libksba8:arm64 (1.6.3-2) ...
Selecting previously unselected package libsasl2-modules-db:arm64.
Preparing to unpack .../167-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ...
Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ...
Selecting previously unselected package libsasl2-2:arm64.
Preparing to unpack .../168-libsasl2-2_2.1.28+dfsg-10_arm64.deb ...
Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ...
Selecting previously unselected package libldap-2.5-0:arm64.
Preparing to unpack .../169-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ...
Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ...
Selecting previously unselected package libnpth0:arm64.
Preparing to unpack .../170-libnpth0_1.6-3_arm64.deb ...
Unpacking libnpth0:arm64 (1.6-3) ...
Selecting previously unselected package dirmngr.
Preparing to unpack .../171-dirmngr_2.2.40-1.1_arm64.deb ...
Unpacking dirmngr (2.2.40-1.1) ...
Selecting previously unselected package gnupg-l10n.
Preparing to unpack .../172-gnupg-l10n_2.2.40-1.1_all.deb ...
Unpacking gnupg-l10n (2.2.40-1.1) ...
Selecting previously unselected package gnupg-utils.
Preparing to unpack .../173-gnupg-utils_2.2.40-1.1_arm64.deb ...
Unpacking gnupg-utils (2.2.40-1.1) ...
Selecting previously unselected package gpg.
Preparing to unpack .../174-gpg_2.2.40-1.1_arm64.deb ...
Unpacking gpg (2.2.40-1.1) ...
Selecting previously unselected package pinentry-curses.
Preparing to unpack .../175-pinentry-curses_1.2.1-1_arm64.deb ...
Unpacking pinentry-curses (1.2.1-1) ...
Selecting previously unselected package gpg-agent.
Preparing to unpack .../176-gpg-agent_2.2.40-1.1_arm64.deb ...
Unpacking gpg-agent (2.2.40-1.1) ...
Selecting previously unselected package gpg-wks-client.
Preparing to unpack .../177-gpg-wks-client_2.2.40-1.1_arm64.deb ...
Unpacking gpg-wks-client (2.2.40-1.1) ...
Selecting previously unselected package gpg-wks-server.
Preparing to unpack .../178-gpg-wks-server_2.2.40-1.1_arm64.deb ...
Unpacking gpg-wks-server (2.2.40-1.1) ...
Selecting previously unselected package gpgsm.
Preparing to unpack .../179-gpgsm_2.2.40-1.1_arm64.deb ...
Unpacking gpgsm (2.2.40-1.1) ...
Selecting previously unselected package gnupg.
Preparing to unpack .../180-gnupg_2.2.40-1.1_all.deb ...
Unpacking gnupg (2.2.40-1.1) ...
Selecting previously unselected package libfile-dirlist-perl.
Preparing to unpack .../181-libfile-dirlist-perl_0.05-3_all.deb ...
Unpacking libfile-dirlist-perl (0.05-3) ...
Selecting previously unselected package libfile-which-perl.
Preparing to unpack .../182-libfile-which-perl_1.27-2_all.deb ...
Unpacking libfile-which-perl (1.27-2) ...
Selecting previously unselected package libfile-homedir-perl.
Preparing to unpack .../183-libfile-homedir-perl_1.006-2_all.deb ...
Unpacking libfile-homedir-perl (1.006-2) ...
Selecting previously unselected package libfile-touch-perl.
Preparing to unpack .../184-libfile-touch-perl_0.12-2_all.deb ...
Unpacking libfile-touch-perl (0.12-2) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../185-libio-pty-perl_1%3a1.17-1_arm64.deb ...
Unpacking libio-pty-perl (1:1.17-1) ...
Selecting previously unselected package libipc-run-perl.
Preparing to unpack .../186-libipc-run-perl_20220807.0-1_all.deb ...
Unpacking libipc-run-perl (20220807.0-1) ...
Selecting previously unselected package libclass-method-modifiers-perl.
Preparing to unpack .../187-libclass-method-modifiers-perl_2.14-1_all.deb ...
Unpacking libclass-method-modifiers-perl (2.14-1) ...
Selecting previously unselected package libclass-xsaccessor-perl.
Preparing to unpack .../188-libclass-xsaccessor-perl_1.19-4+b1_arm64.deb ...
Unpacking libclass-xsaccessor-perl (1.19-4+b1) ...
Selecting previously unselected package libb-hooks-op-check-perl:arm64.
Preparing to unpack .../189-libb-hooks-op-check-perl_0.22-2+b1_arm64.deb ...
Unpacking libb-hooks-op-check-perl:arm64 (0.22-2+b1) ...
Selecting previously unselected package libdynaloader-functions-perl.
Preparing to unpack .../190-libdynaloader-functions-perl_0.003-3_all.deb ...
Unpacking libdynaloader-functions-perl (0.003-3) ...
Selecting previously unselected package libdevel-callchecker-perl:arm64.
Preparing to unpack .../191-libdevel-callchecker-perl_0.008-2_arm64.deb ...
Unpacking libdevel-callchecker-perl:arm64 (0.008-2) ...
Selecting previously unselected package libparams-classify-perl:arm64.
Preparing to unpack .../192-libparams-classify-perl_0.015-2+b1_arm64.deb ...
Unpacking libparams-classify-perl:arm64 (0.015-2+b1) ...
Selecting previously unselected package libmodule-runtime-perl.
Preparing to unpack .../193-libmodule-runtime-perl_0.016-2_all.deb ...
Unpacking libmodule-runtime-perl (0.016-2) ...
Selecting previously unselected package libimport-into-perl.
Preparing to unpack .../194-libimport-into-perl_1.002005-2_all.deb ...
Unpacking libimport-into-perl (1.002005-2) ...
Selecting previously unselected package librole-tiny-perl.
Preparing to unpack .../195-librole-tiny-perl_2.002004-1_all.deb ...
Unpacking librole-tiny-perl (2.002004-1) ...
Selecting previously unselected package libsub-quote-perl.
Preparing to unpack .../196-libsub-quote-perl_2.006008-1_all.deb ...
Unpacking libsub-quote-perl (2.006008-1) ...
Selecting previously unselected package libmoo-perl.
Preparing to unpack .../197-libmoo-perl_2.005005-1_all.deb ...
Unpacking libmoo-perl (2.005005-1) ...
Selecting previously unselected package libencode-locale-perl.
Preparing to unpack .../198-libencode-locale-perl_1.05-3_all.deb ...
Unpacking libencode-locale-perl (1.05-3) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../199-libtimedate-perl_2.3300-2_all.deb ...
Unpacking libtimedate-perl (2.3300-2) ...
Selecting previously unselected package libhttp-date-perl.
Preparing to unpack .../200-libhttp-date-perl_6.05-2_all.deb ...
Unpacking libhttp-date-perl (6.05-2) ...
Selecting previously unselected package libfile-listing-perl.
Preparing to unpack .../201-libfile-listing-perl_6.15-1_all.deb ...
Unpacking libfile-listing-perl (6.15-1) ...
Selecting previously unselected package libhtml-tagset-perl.
Preparing to unpack .../202-libhtml-tagset-perl_3.20-6_all.deb ...
Unpacking libhtml-tagset-perl (3.20-6) ...
Selecting previously unselected package libregexp-ipv6-perl.
Preparing to unpack .../203-libregexp-ipv6-perl_0.03-3_all.deb ...
Unpacking libregexp-ipv6-perl (0.03-3) ...
Selecting previously unselected package liburi-perl.
Preparing to unpack .../204-liburi-perl_5.17-1_all.deb ...
Unpacking liburi-perl (5.17-1) ...
Selecting previously unselected package libhtml-parser-perl:arm64.
Preparing to unpack .../205-libhtml-parser-perl_3.81-1_arm64.deb ...
Unpacking libhtml-parser-perl:arm64 (3.81-1) ...
Selecting previously unselected package libhtml-tree-perl.
Preparing to unpack .../206-libhtml-tree-perl_5.07-3_all.deb ...
Unpacking libhtml-tree-perl (5.07-3) ...
Selecting previously unselected package libclone-perl:arm64.
Preparing to unpack .../207-libclone-perl_0.46-1_arm64.deb ...
Unpacking libclone-perl:arm64 (0.46-1) ...
Selecting previously unselected package libio-html-perl.
Preparing to unpack .../208-libio-html-perl_1.004-3_all.deb ...
Unpacking libio-html-perl (1.004-3) ...
Selecting previously unselected package liblwp-mediatypes-perl.
Preparing to unpack .../209-liblwp-mediatypes-perl_6.04-2_all.deb ...
Unpacking liblwp-mediatypes-perl (6.04-2) ...
Selecting previously unselected package libhttp-message-perl.
Preparing to unpack .../210-libhttp-message-perl_6.44-1_all.deb ...
Unpacking libhttp-message-perl (6.44-1) ...
Selecting previously unselected package libhttp-cookies-perl.
Preparing to unpack .../211-libhttp-cookies-perl_6.10-1_all.deb ...
Unpacking libhttp-cookies-perl (6.10-1) ...
Selecting previously unselected package libhttp-negotiate-perl.
Preparing to unpack .../212-libhttp-negotiate-perl_6.01-2_all.deb ...
Unpacking libhttp-negotiate-perl (6.01-2) ...
Selecting previously unselected package perl-openssl-defaults:arm64.
Preparing to unpack .../213-perl-openssl-defaults_7+b1_arm64.deb ...
Unpacking perl-openssl-defaults:arm64 (7+b1) ...
Selecting previously unselected package libnet-ssleay-perl:arm64.
Preparing to unpack .../214-libnet-ssleay-perl_1.92-2+b1_arm64.deb ...
Unpacking libnet-ssleay-perl:arm64 (1.92-2+b1) ...
Selecting previously unselected package libio-socket-ssl-perl.
Preparing to unpack .../215-libio-socket-ssl-perl_2.081-2_all.deb ...
Unpacking libio-socket-ssl-perl (2.081-2) ...
Selecting previously unselected package libnet-http-perl.
Preparing to unpack .../216-libnet-http-perl_6.22-1_all.deb ...
Unpacking libnet-http-perl (6.22-1) ...
Selecting previously unselected package liblwp-protocol-https-perl.
Preparing to unpack .../217-liblwp-protocol-https-perl_6.10-1_all.deb ...
Unpacking liblwp-protocol-https-perl (6.10-1) ...
Selecting previously unselected package libtry-tiny-perl.
Preparing to unpack .../218-libtry-tiny-perl_0.31-2_all.deb ...
Unpacking libtry-tiny-perl (0.31-2) ...
Selecting previously unselected package libwww-robotrules-perl.
Preparing to unpack .../219-libwww-robotrules-perl_6.02-1_all.deb ...
Unpacking libwww-robotrules-perl (6.02-1) ...
Selecting previously unselected package libwww-perl.
Preparing to unpack .../220-libwww-perl_6.68-1_all.deb ...
Unpacking libwww-perl (6.68-1) ...
Selecting previously unselected package patchutils.
Preparing to unpack .../221-patchutils_0.4.2-1_arm64.deb ...
Unpacking patchutils (0.4.2-1) ...
Selecting previously unselected package wdiff.
Preparing to unpack .../222-wdiff_1.2.2-5_arm64.deb ...
Unpacking wdiff (1.2.2-5) ...
Selecting previously unselected package devscripts.
Preparing to unpack .../223-devscripts_2.23.3_arm64.deb ...
Unpacking devscripts (2.23.3) ...
Selecting previously unselected package ivy.
Preparing to unpack .../224-ivy_2.5.1-2_all.deb ...
Unpacking ivy (2.5.1-2) ...
Selecting previously unselected package libasm-java.
Preparing to unpack .../225-libasm-java_9.4-1_all.deb ...
Unpacking libasm-java (9.4-1) ...
Selecting previously unselected package libbsf-java.
Preparing to unpack .../226-libbsf-java_1%3a2.4.0-8_all.deb ...
Unpacking libbsf-java (1:2.4.0-8) ...
Selecting previously unselected package libcommons-cli-java.
Preparing to unpack .../227-libcommons-cli-java_1.5.0-1_all.deb ...
Unpacking libcommons-cli-java (1.5.0-1) ...
Selecting previously unselected package libapache-pom-java.
Preparing to unpack .../228-libapache-pom-java_29-2_all.deb ...
Unpacking libapache-pom-java (29-2) ...
Selecting previously unselected package libcommons-parent-java.
Preparing to unpack .../229-libcommons-parent-java_56-1_all.deb ...
Unpacking libcommons-parent-java (56-1) ...
Selecting previously unselected package libcommons-logging-java.
Preparing to unpack .../230-libcommons-logging-java_1.2-3_all.deb ...
Unpacking libcommons-logging-java (1.2-3) ...
Selecting previously unselected package libjansi-java.
Preparing to unpack .../231-libjansi-java_2.4.0-2_all.deb ...
Unpacking libjansi-java (2.4.0-2) ...
Selecting previously unselected package libqdox-java.
Preparing to unpack .../232-libqdox-java_1.12.1-3_all.deb ...
Unpacking libqdox-java (1.12.1-3) ...
Selecting previously unselected package libservlet-api-java.
Preparing to unpack .../233-libservlet-api-java_4.0.1-2_all.deb ...
Unpacking libservlet-api-java (4.0.1-2) ...
Selecting previously unselected package libxpp3-java.
Preparing to unpack .../234-libxpp3-java_1.1.4c-3_all.deb ...
Unpacking libxpp3-java (1.1.4c-3) ...
Selecting previously unselected package libxstream-java.
Preparing to unpack .../235-libxstream-java_1.4.20-1_all.deb ...
Unpacking libxstream-java (1.4.20-1) ...
Selecting previously unselected package groovy.
Preparing to unpack .../236-groovy_2.4.21-7_all.deb ...
Unpacking groovy (2.4.21-7) ...
Selecting previously unselected package libatinject-jsr330-api-java.
Preparing to unpack .../237-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ...
Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ...
Selecting previously unselected package libcommons-collections3-java.
Preparing to unpack .../238-libcommons-collections3-java_3.2.2-2_all.deb ...
Unpacking libcommons-collections3-java (3.2.2-2) ...
Selecting previously unselected package libcommons-compress-java.
Preparing to unpack .../239-libcommons-compress-java_1.22-1_all.deb ...
Unpacking libcommons-compress-java (1.22-1) ...
Selecting previously unselected package libcommons-io-java.
Preparing to unpack .../240-libcommons-io-java_2.11.0-2_all.deb ...
Unpacking libcommons-io-java (2.11.0-2) ...
Selecting previously unselected package libcommons-lang-java.
Preparing to unpack .../241-libcommons-lang-java_2.6-10_all.deb ...
Unpacking libcommons-lang-java (2.6-10) ...
Selecting previously unselected package liberror-prone-java.
Preparing to unpack .../242-liberror-prone-java_2.18.0-1_all.deb ...
Unpacking liberror-prone-java (2.18.0-1) ...
Selecting previously unselected package libjsr305-java.
Preparing to unpack .../243-libjsr305-java_0.1~+svn49-11_all.deb ...
Unpacking libjsr305-java (0.1~+svn49-11) ...
Selecting previously unselected package libguava-java.
Preparing to unpack .../244-libguava-java_31.1-1_all.deb ...
Unpacking libguava-java (31.1-1) ...
Selecting previously unselected package libcommons-codec-java.
Preparing to unpack .../245-libcommons-codec-java_1.15-1_all.deb ...
Unpacking libcommons-codec-java (1.15-1) ...
Selecting previously unselected package libhttpcore-java.
Preparing to unpack .../246-libhttpcore-java_4.4.16-1_all.deb ...
Unpacking libhttpcore-java (4.4.16-1) ...
Selecting previously unselected package libhttpclient-java.
Preparing to unpack .../247-libhttpclient-java_4.5.14-1_all.deb ...
Unpacking libhttpclient-java (4.5.14-1) ...
Selecting previously unselected package libjarjar-java.
Preparing to unpack .../248-libjarjar-java_1.4+svn142-12_all.deb ...
Unpacking libjarjar-java (1.4+svn142-12) ...
Selecting previously unselected package libjcip-annotations-java.
Preparing to unpack .../249-libjcip-annotations-java_20060626-6_all.deb ...
Unpacking libjcip-annotations-java (20060626-6) ...
Selecting previously unselected package libjna-jni.
Preparing to unpack .../250-libjna-jni_5.13.0-2_arm64.deb ...
Unpacking libjna-jni (5.13.0-2) ...
Selecting previously unselected package libjna-java.
Preparing to unpack .../251-libjna-java_5.13.0-2_all.deb ...
Unpacking libjna-java (5.13.0-2) ...
Selecting previously unselected package libjzlib-java.
Preparing to unpack .../252-libjzlib-java_1.1.3-2_all.deb ...
Unpacking libjzlib-java (1.1.3-2) ...
Selecting previously unselected package libjsch-java.
Preparing to unpack .../253-libjsch-java_0.1.55-1_all.deb ...
Unpacking libjsch-java (0.1.55-1) ...
Selecting previously unselected package libminlog-java.
Preparing to unpack .../254-libminlog-java_1.3.0-1.1_all.deb ...
Unpacking libminlog-java (1.3.0-1.1) ...
Selecting previously unselected package libobjenesis-java.
Preparing to unpack .../255-libobjenesis-java_3.3-3_all.deb ...
Unpacking libobjenesis-java (3.3-3) ...
Selecting previously unselected package libreflectasm-java.
Preparing to unpack .../256-libreflectasm-java_1.11.9+dfsg-4_all.deb ...
Unpacking libreflectasm-java (1.11.9+dfsg-4) ...
Selecting previously unselected package libkryo-java.
Preparing to unpack .../257-libkryo-java_2.20-7_all.deb ...
Unpacking libkryo-java (2.20-7) ...
Selecting previously unselected package liblogback-java.
Preparing to unpack .../258-liblogback-java_1%3a1.2.11-2_all.deb ...
Unpacking liblogback-java (1:1.2.11-2) ...
Selecting previously unselected package libncurses6:arm64.
Preparing to unpack .../259-libncurses6_6.4-2_arm64.deb ...
Unpacking libncurses6:arm64 (6.4-2) ...
Selecting previously unselected package libnative-platform-jni.
Preparing to unpack .../260-libnative-platform-jni_0.14-5_arm64.deb ...
Unpacking libnative-platform-jni (0.14-5) ...
Selecting previously unselected package libnative-platform-java.
Preparing to unpack .../261-libnative-platform-java_0.14-5_all.deb ...
Unpacking libnative-platform-java (0.14-5) ...
Selecting previously unselected package libxml-commons-external-java.
Preparing to unpack .../262-libxml-commons-external-java_1.4.01-5_all.deb ...
Unpacking libxml-commons-external-java (1.4.01-5) ...
Selecting previously unselected package libxml-commons-resolver1.1-java.
Preparing to unpack .../263-libxml-commons-resolver1.1-java_1.2-11_all.deb ...
Unpacking libxml-commons-resolver1.1-java (1.2-11) ...
Selecting previously unselected package libxerces2-java.
Preparing to unpack .../264-libxerces2-java_2.12.2-1_all.deb ...
Unpacking libxerces2-java (2.12.2-1) ...
Selecting previously unselected package libnekohtml-java.
Preparing to unpack .../265-libnekohtml-java_1.9.22.noko2-0.1_all.deb ...
Unpacking libnekohtml-java (1.9.22.noko2-0.1) ...
Selecting previously unselected package libxbean-reflect-java.
Preparing to unpack .../266-libxbean-reflect-java_4.5-8_all.deb ...
Unpacking libxbean-reflect-java (4.5-8) ...
Selecting previously unselected package libgradle-core-java.
Preparing to unpack .../267-libgradle-core-java_4.4.1-18_all.deb ...
Unpacking libgradle-core-java (4.4.1-18) ...
Selecting previously unselected package libbcprov-java.
Preparing to unpack .../268-libbcprov-java_1.72-2_all.deb ...
Unpacking libbcprov-java (1.72-2) ...
Selecting previously unselected package libbcpg-java.
Preparing to unpack .../269-libbcpg-java_1.72-2_all.deb ...
Unpacking libbcpg-java (1.72-2) ...
Selecting previously unselected package libbsh-java.
Preparing to unpack .../270-libbsh-java_2.0b4-20_all.deb ...
Unpacking libbsh-java (2.0b4-20) ...
Selecting previously unselected package libdd-plist-java.
Preparing to unpack .../271-libdd-plist-java_1.20-1.1_all.deb ...
Unpacking libdd-plist-java (1.20-1.1) ...
Selecting previously unselected package libjaxen-java.
Preparing to unpack .../272-libjaxen-java_1.1.6-4_all.deb ...
Unpacking libjaxen-java (1.1.6-4) ...
Selecting previously unselected package libdom4j-java.
Preparing to unpack .../273-libdom4j-java_2.1.3-2_all.deb ...
Unpacking libdom4j-java (2.1.3-2) ...
Selecting previously unselected package libbcel-java.
Preparing to unpack .../274-libbcel-java_6.5.0-2_all.deb ...
Unpacking libbcel-java (6.5.0-2) ...
Selecting previously unselected package libjformatstring-java.
Preparing to unpack .../275-libjformatstring-java_0.10~20131207-2.1_all.deb ...
Unpacking libjformatstring-java (0.10~20131207-2.1) ...
Selecting previously unselected package libfindbugs-java.
Preparing to unpack .../276-libfindbugs-java_3.1.0~preview2-3_all.deb ...
Unpacking libfindbugs-java (3.1.0~preview2-3) ...
Selecting previously unselected package libgoogle-gson-java.
Preparing to unpack .../277-libgoogle-gson-java_2.10-1_all.deb ...
Unpacking libgoogle-gson-java (2.10-1) ...
Selecting previously unselected package libaopalliance-java.
Preparing to unpack .../278-libaopalliance-java_20070526-7_all.deb ...
Unpacking libaopalliance-java (20070526-7) ...
Selecting previously unselected package libguice-java.
Preparing to unpack .../279-libguice-java_4.2.3-2_all.deb ...
Unpacking libguice-java (4.2.3-2) ...
Selecting previously unselected package libjatl-java.
Preparing to unpack .../280-libjatl-java_0.2.3-1.1_all.deb ...
Unpacking libjatl-java (0.2.3-1.1) ...
Selecting previously unselected package libjcifs-java.
Preparing to unpack .../281-libjcifs-java_1.3.19-2_all.deb ...
Unpacking libjcifs-java (1.3.19-2) ...
Selecting previously unselected package libeclipse-jdt-annotation-java.
Preparing to unpack .../282-libeclipse-jdt-annotation-java_2.2.700+eclipse4.26-2_all.deb ...
Unpacking libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ...
Selecting previously unselected package libjavaewah-java.
Preparing to unpack .../283-libjavaewah-java_1.1.7-1_all.deb ...
Unpacking libjavaewah-java (1.1.7-1) ...
Selecting previously unselected package libel-api-java.
Preparing to unpack .../284-libel-api-java_3.0.0-3_all.deb ...
Unpacking libel-api-java (3.0.0-3) ...
Selecting previously unselected package libjsp-api-java.
Preparing to unpack .../285-libjsp-api-java_2.3.4-3_all.deb ...
Unpacking libjsp-api-java (2.3.4-3) ...
Selecting previously unselected package libwebsocket-api-java.
Preparing to unpack .../286-libwebsocket-api-java_1.1-2_all.deb ...
Unpacking libwebsocket-api-java (1.1-2) ...
Selecting previously unselected package libjetty9-java.
Preparing to unpack .../287-libjetty9-java_9.4.50-3_all.deb ...
Unpacking libjetty9-java (9.4.50-3) ...
Selecting previously unselected package libjgit-java.
Preparing to unpack .../288-libjgit-java_4.11.9-2_all.deb ...
Unpacking libjgit-java (4.11.9-2) ...
Selecting previously unselected package libcommons-lang3-java.
Preparing to unpack .../289-libcommons-lang3-java_3.12.0-2_all.deb ...
Unpacking libcommons-lang3-java (3.12.0-2) ...
Selecting previously unselected package libplexus-utils2-java.
Preparing to unpack .../290-libplexus-utils2-java_3.4.2-1_all.deb ...
Unpacking libplexus-utils2-java (3.4.2-1) ...
Selecting previously unselected package libwagon-provider-api-java.
Preparing to unpack .../291-libwagon-provider-api-java_3.5.3-1_all.deb ...
Unpacking libwagon-provider-api-java (3.5.3-1) ...
Selecting previously unselected package libmaven-resolver-java.
Preparing to unpack .../292-libmaven-resolver-java_1.6.3-1_all.deb ...
Unpacking libmaven-resolver-java (1.6.3-1) ...
Selecting previously unselected package libgeronimo-annotation-1.3-spec-java.
Preparing to unpack .../293-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ...
Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Selecting previously unselected package libmaven-parent-java.
Preparing to unpack .../294-libmaven-parent-java_35-1_all.deb ...
Unpacking libmaven-parent-java (35-1) ...
Selecting previously unselected package libmaven-shared-utils-java.
Preparing to unpack .../295-libmaven-shared-utils-java_3.3.4-1_all.deb ...
Unpacking libmaven-shared-utils-java (3.3.4-1) ...
Selecting previously unselected package libplexus-cipher-java.
Preparing to unpack .../296-libplexus-cipher-java_2.0-1_all.deb ...
Unpacking libplexus-cipher-java (2.0-1) ...
Selecting previously unselected package libplexus-classworlds-java.
Preparing to unpack .../297-libplexus-classworlds-java_2.7.0-1_all.deb ...
Unpacking libplexus-classworlds-java (2.7.0-1) ...
Selecting previously unselected package libplexus-component-annotations-java.
Preparing to unpack .../298-libplexus-component-annotations-java_2.1.1-1_all.deb ...
Unpacking libplexus-component-annotations-java (2.1.1-1) ...
Selecting previously unselected package libplexus-interpolation-java.
Preparing to unpack .../299-libplexus-interpolation-java_1.26-1_all.deb ...
Unpacking libplexus-interpolation-java (1.26-1) ...
Selecting previously unselected package libplexus-sec-dispatcher-java.
Preparing to unpack .../300-libplexus-sec-dispatcher-java_2.0-3_all.deb ...
Unpacking libplexus-sec-dispatcher-java (2.0-3) ...
Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java.
Preparing to unpack .../301-libgeronimo-interceptor-3.0-spec-java_1.0.1-4_all.deb ...
Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ...
Selecting previously unselected package libcdi-api-java.
Preparing to unpack .../302-libcdi-api-java_1.2-3_all.deb ...
Unpacking libcdi-api-java (1.2-3) ...
Selecting previously unselected package libsisu-inject-java.
Preparing to unpack .../303-libsisu-inject-java_0.3.4-2_all.deb ...
Unpacking libsisu-inject-java (0.3.4-2) ...
Selecting previously unselected package libsisu-plexus-java.
Preparing to unpack .../304-libsisu-plexus-java_0.3.4-3_all.deb ...
Unpacking libsisu-plexus-java (0.3.4-3) ...
Selecting previously unselected package libmaven3-core-java.
Preparing to unpack .../305-libmaven3-core-java_3.8.7-1_all.deb ...
Unpacking libmaven3-core-java (3.8.7-1) ...
Selecting previously unselected package libplexus-container-default-java.
Preparing to unpack .../306-libplexus-container-default-java_2.1.1-1_all.deb ...
Unpacking libplexus-container-default-java (2.1.1-1) ...
Selecting previously unselected package libpolyglot-maven-java.
Preparing to unpack .../307-libpolyglot-maven-java_0.8~tobrien+git20120905-10_all.deb ...
Unpacking libpolyglot-maven-java (0.8~tobrien+git20120905-10) ...
Selecting previously unselected package librhino-java.
Preparing to unpack .../308-librhino-java_1.7.7.2-3_all.deb ...
Unpacking librhino-java (1.7.7.2-3) ...
Selecting previously unselected package libsimple-http-java.
Preparing to unpack .../309-libsimple-http-java_4.1.21-1.1_all.deb ...
Unpacking libsimple-http-java (4.1.21-1.1) ...
Selecting previously unselected package libwagon-file-java.
Preparing to unpack .../310-libwagon-file-java_3.5.3-1_all.deb ...
Unpacking libwagon-file-java (3.5.3-1) ...
Selecting previously unselected package libjsoup-java.
Preparing to unpack .../311-libjsoup-java_1.15.3-1_all.deb ...
Unpacking libjsoup-java (1.15.3-1) ...
Selecting previously unselected package libwagon-http-java.
Preparing to unpack .../312-libwagon-http-java_3.5.3-1_all.deb ...
Unpacking libwagon-http-java (3.5.3-1) ...
Selecting previously unselected package libjcommander-java.
Preparing to unpack .../313-libjcommander-java_1.71-4_all.deb ...
Unpacking libjcommander-java (1.71-4) ...
Selecting previously unselected package testng.
Preparing to unpack .../314-testng_6.9.12-4_all.deb ...
Unpacking testng (6.9.12-4) ...
Selecting previously unselected package libgradle-plugins-java.
Preparing to unpack .../315-libgradle-plugins-java_4.4.1-18_all.deb ...
Unpacking libgradle-plugins-java (4.4.1-18) ...
Selecting previously unselected package gradle.
Preparing to unpack .../316-gradle_4.4.1-18_all.deb ...
Unpacking gradle (4.4.1-18) ...
Selecting previously unselected package maven-repo-helper.
Preparing to unpack .../317-maven-repo-helper_1.11_all.deb ...
Unpacking maven-repo-helper (1.11) ...
Selecting previously unselected package gradle-debian-helper.
Preparing to unpack .../318-gradle-debian-helper_2.4_all.deb ...
Unpacking gradle-debian-helper (2.4) ...
Selecting previously unselected package javahelper.
Preparing to unpack .../319-javahelper_0.78_all.deb ...
Unpacking javahelper (0.78) ...
Selecting previously unselected package libactivation-java.
Preparing to unpack .../320-libactivation-java_1.2.0-2_all.deb ...
Unpacking libactivation-java (1.2.0-2) ...
Selecting previously unselected package libargs4j-java.
Preparing to unpack .../321-libargs4j-java_2.33-2_all.deb ...
Unpacking libargs4j-java (2.33-2) ...
Selecting previously unselected package libmaven-shared-io-java.
Preparing to unpack .../322-libmaven-shared-io-java_3.0.0-4_all.deb ...
Unpacking libmaven-shared-io-java (3.0.0-4) ...
Selecting previously unselected package libmaven-file-management-java.
Preparing to unpack .../323-libmaven-file-management-java_3.0.0-1_all.deb ...
Unpacking libmaven-file-management-java (3.0.0-1) ...
Selecting previously unselected package libplexus-io-java.
Preparing to unpack .../324-libplexus-io-java_3.3.1-2_all.deb ...
Unpacking libplexus-io-java (3.3.1-2) ...
Selecting previously unselected package libsnappy1v5:arm64.
Preparing to unpack .../325-libsnappy1v5_1.1.9-3_arm64.deb ...
Unpacking libsnappy1v5:arm64 (1.1.9-3) ...
Selecting previously unselected package libsnappy-jni.
Preparing to unpack .../326-libsnappy-jni_1.1.8.3-1_arm64.deb ...
Unpacking libsnappy-jni (1.1.8.3-1) ...
Selecting previously unselected package libsnappy-java.
Preparing to unpack .../327-libsnappy-java_1.1.8.3-1_all.deb ...
Unpacking libsnappy-java (1.1.8.3-1) ...
Selecting previously unselected package libplexus-archiver-java.
Preparing to unpack .../328-libplexus-archiver-java_4.6.1-1_all.deb ...
Unpacking libplexus-archiver-java (4.6.1-1) ...
Selecting previously unselected package libistack-commons-java.
Preparing to unpack .../329-libistack-commons-java_3.0.6-5_all.deb ...
Unpacking libistack-commons-java (3.0.6-5) ...
Selecting previously unselected package libcodemodel-java.
Preparing to unpack .../330-libcodemodel-java_2.6+jaxb2.3.0.1-10.1_all.deb ...
Unpacking libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ...
Selecting previously unselected package libcommons-jexl2-java.
Preparing to unpack .../331-libcommons-jexl2-java_2.1.1-6_all.deb ...
Unpacking libcommons-jexl2-java (2.1.1-6) ...
Selecting previously unselected package libdtd-parser-java.
Preparing to unpack .../332-libdtd-parser-java_1.2-1_all.deb ...
Unpacking libdtd-parser-java (1.2-1) ...
Selecting previously unselected package libjaxb-api-java.
Preparing to unpack .../333-libjaxb-api-java_2.3.1-1_all.deb ...
Unpacking libjaxb-api-java (2.3.1-1) ...
Selecting previously unselected package libstax-ex-java.
Preparing to unpack .../334-libstax-ex-java_1.7.8-3_all.deb ...
Unpacking libstax-ex-java (1.7.8-3) ...
Selecting previously unselected package libstreambuffer-java.
Preparing to unpack .../335-libstreambuffer-java_1.5.4-1.1_all.deb ...
Unpacking libstreambuffer-java (1.5.4-1.1) ...
Selecting previously unselected package librelaxng-datatype-java.
Preparing to unpack .../336-librelaxng-datatype-java_1.0+ds1-3.1_all.deb ...
Unpacking librelaxng-datatype-java (1.0+ds1-3.1) ...
Selecting previously unselected package libxsom-java.
Preparing to unpack .../337-libxsom-java_2.3.0.1-10.1_all.deb ...
Unpacking libxsom-java (2.3.0.1-10.1) ...
Selecting previously unselected package libfastinfoset-java.
Preparing to unpack .../338-libfastinfoset-java_1.2.12-3_all.deb ...
Unpacking libfastinfoset-java (1.2.12-3) ...
Selecting previously unselected package librngom-java.
Preparing to unpack .../339-librngom-java_2.3.0.1-10.1_all.deb ...
Unpacking librngom-java (2.3.0.1-10.1) ...
Selecting previously unselected package libtxw2-java.
Preparing to unpack .../340-libtxw2-java_2.3.0.1-10.1_all.deb ...
Unpacking libtxw2-java (2.3.0.1-10.1) ...
Selecting previously unselected package libjaxb-java.
Preparing to unpack .../341-libjaxb-java_2.3.0.1-10.1_all.deb ...
Unpacking libjaxb-java (2.3.0.1-10.1) ...
Selecting previously unselected package libjimfs-java.
Preparing to unpack .../342-libjimfs-java_1.1-6_all.deb ...
Unpacking libjimfs-java (1.1-6) ...
Selecting previously unselected package libmbedcrypto7:arm64.
Preparing to unpack .../343-libmbedcrypto7_2.28.3-1_arm64.deb ...
Unpacking libmbedcrypto7:arm64 (2.28.3-1) ...
Selecting previously unselected package libmbedx509-1:arm64.
Preparing to unpack .../344-libmbedx509-1_2.28.3-1_arm64.deb ...
Unpacking libmbedx509-1:arm64 (2.28.3-1) ...
Selecting previously unselected package libmbedtls14:arm64.
Preparing to unpack .../345-libmbedtls14_2.28.3-1_arm64.deb ...
Unpacking libmbedtls14:arm64 (2.28.3-1) ...
Selecting previously unselected package libmjson-java.
Preparing to unpack .../346-libmjson-java_1.4.0-3_all.deb ...
Unpacking libmjson-java (1.4.0-3) ...
Selecting previously unselected package ncbi-vdb-data.
Preparing to unpack .../347-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ...
Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ...
Selecting previously unselected package libncbi-vdb3:arm64.
Preparing to unpack .../348-libncbi-vdb3_3.0.2+dfsg-2_arm64.deb ...
Unpacking libncbi-vdb3:arm64 (3.0.2+dfsg-2) ...
Selecting previously unselected package libncbi-ngs3:arm64.
Preparing to unpack .../349-libncbi-ngs3_3.0.3+dfsg-5_arm64.deb ...
Unpacking libncbi-ngs3:arm64 (3.0.3+dfsg-5) ...
Selecting previously unselected package libngs-jni:arm64.
Preparing to unpack .../350-libngs-jni_3.0.3+dfsg-5_arm64.deb ...
Unpacking libngs-jni:arm64 (3.0.3+dfsg-5) ...
Selecting previously unselected package libngs-java:arm64.
Preparing to unpack .../351-libngs-java_3.0.3+dfsg-5_arm64.deb ...
Unpacking libngs-java:arm64 (3.0.3+dfsg-5) ...
Selecting previously unselected package scala-library.
Preparing to unpack .../352-scala-library_2.11.12-5_all.deb ...
Unpacking scala-library (2.11.12-5) ...
Setting up libjcifs-java (1.3.19-2) ...
Setting up libbcprov-java (1.72-2) ...
Setting up libksba8:arm64 (1.6.3-2) ...
Setting up media-types (10.0.0) ...
Setting up libpipeline1:arm64 (1.5.7-1) ...
Setting up libgraphite2-3:arm64 (1.3.14-1) ...
Setting up liblcms2-2:arm64 (2.14-2) ...
Setting up libpixman-1-0:arm64 (0.42.2-1) ...
Setting up libjcommander-java (1.71-4) ...
Setting up libdtd-parser-java (1.2-1) ...
Setting up wdiff (1.2.2-5) ...
Setting up libslf4j-java (1.7.32-1) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libxau6:arm64 (1:1.0.9-1) ...
Setting up libplexus-utils2-java (3.4.2-1) ...
Setting up libplexus-classworlds-java (2.7.0-1) ...
Setting up libqdox-java (1.12.1-3) ...
Setting up libicu72:arm64 (72.1-3) ...
Setting up liblerc4:arm64 (4.0.0+ds-2) ...
Setting up libjsr305-java (0.1~+svn49-11) ...
Setting up libsimple-http-java (4.1.21-1.1) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up hicolor-icon-theme (0.17-2) ...
Setting up java-common (0.74) ...
Setting up libdynaloader-functions-perl (0.003-3) ...
Setting up libdatrie1:arm64 (0.2.13-2+b1) ...
Setting up libjcip-annotations-java (20060626-6) ...
Setting up libobjenesis-java (3.3-3) ...
Setting up libclass-method-modifiers-perl (2.14-1) ...
Setting up libaopalliance-java (20070526-7) ...
Setting up libcommons-cli-java (1.5.0-1) ...
Setting up libio-pty-perl (1:1.17-1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up liblogback-java (1:1.2.11-2) ...
Setting up libclone-perl:arm64 (0.46-1) ...
Setting up libminlog-java (1.3.0-1.1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:arm64 (2.74.6-1) ...
No schema files found: doing nothing.
Setting up libglvnd0:arm64 (1.6.0-1) ...
Setting up libgoogle-gson-java (2.10-1) ...
Setting up libmjson-java (1.4.0-3) ...
Setting up libhtml-tagset-perl (3.20-6) ...
Setting up unzip (6.0-28) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libbrotli1:arm64 (1.0.9-2+b6) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ...
Setting up libasm-java (9.4-1) ...
Setting up libjs-jquery-ui-theme-base (1.12.1+dfsg-1.1) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libtry-tiny-perl (0.31-2) ...
Setting up libsensors-config (1:3.6.0-7.1) ...
Setting up libmagic1:arm64 (1:5.44-3) ...
Setting up libdeflate0:arm64 (1.14-1) ...
Setting up perl-openssl-defaults:arm64 (7+b1) ...
Setting up libdd-plist-java (1.20-1.1) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up libel-api-java (3.0.0-3) ...
Setting up scala-library (2.11.12-5) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libplexus-component-annotations-java (2.1.1-1) ...
Setting up libnpth0:arm64 (1.6-3) ...
Setting up file (1:5.44-3) ...
Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ...
Setting up libfelix-gogo-runtime-java (0.16.2-1.1) ...
Setting up libassuan0:arm64 (2.5.5-5) ...
Setting up libjzlib-java (1.1.3-2) ...
Setting up libjbig0:arm64 (2.1-6.1) ...
Setting up libsnappy1v5:arm64 (1.1.9-3) ...
Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ...
Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ...
Setting up libcommons-collections3-java (3.2.2-2) ...
Setting up libasound2-data (1.2.8-1) ...
Setting up libjsch-java (0.1.55-1) ...
Setting up libreflectasm-java (1.11.9+dfsg-4) ...
Setting up librhino-java (1.7.7.2-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:arm64 (4.8.12-3.1) ...
Setting up libbsf-java (1:2.4.0-8) ...
Setting up libosgi-annotation-java (8.1.0-1) ...
Setting up libjformatstring-java (0.10~20131207-2.1) ...
Setting up libjavaewah-java (1.1.7-1) ...
Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ...
Setting up libjaxen-java (1.1.6-4) ...
Setting up libmbedcrypto7:arm64 (2.28.3-1) ...
Setting up libx11-data (2:1.8.4-2) ...
Setting up libnspr4:arm64 (2:4.35-1) ...
Setting up gnupg-l10n (2.2.40-1.1) ...
Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ...
Setting up libjansi-java (2.4.0-2) ...
Setting up libapache-pom-java (29-2) ...
Setting up libavahi-common-data:arm64 (0.8-9) ...
Setting up libxpp3-java (1.1.4c-3) ...
Setting up libncurses6:arm64 (6.4-2) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
Setting up libdbus-1-3:arm64 (1.14.6-1) ...
Setting up libwebsocket-api-java (1.1-2) ...
Setting up libfribidi0:arm64 (1.0.8-2.1) ...
Setting up libplexus-interpolation-java (1.26-1) ...
Setting up libpng16-16:arm64 (1.6.39-2) ...
Setting up libxml-commons-resolver1.1-java (1.2-11) ...
Setting up libkryo-java (2.20-7) ...
Setting up libxz-java (1.9-1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libjna-jni (5.13.0-2) ...
Setting up autopoint (0.21-12) ...
Setting up libb-hooks-op-check-perl:arm64 (0.22-2+b1) ...
Setting up fonts-dejavu-core (2.37-6) ...
Setting up libfelix-framework-java (4.6.1-2.1) ...
Setting up libipc-run-perl (20220807.0-1) ...
Setting up libpcsclite1:arm64 (1.9.9-1) ...
Setting up libsensors5:arm64 (1:3.6.0-7.1) ...
Setting up libjimfs-java (1.1-6) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-1) ...
Setting up libglapi-mesa:arm64 (22.3.6-1+deb12u1) ...
Setting up libbsh-java (2.0b4-20) ...
Setting up libjsp-api-java (2.3.4-3) ...
Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:arm64 (1.2.4-0.1) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libregexp-ipv6-perl (0.03-3) ...
Setting up libgif7:arm64 (5.2.1-2.5) ...
Setting up libjarjar-java (1.4+svn142-12) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libxshmfence1:arm64 (1.3-1) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.46.0-5) ...
Setting up libtiff6:arm64 (4.5.0-5) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up libxml-commons-external-java (1.4.01-5) ...
Setting up libjna-java (5.13.0-2) ...
Setting up libxbean-reflect-java (4.5-8) ...
Setting up libasound2:arm64 (1.2.8-1+b1) ...
Setting up libservlet-api-java (4.0.1-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up ncbi-vdb-data (3.0.2+dfsg-2) ...
Setting up libthai-data (0.1.29-1) ...
Setting up netbase (6.4) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libnative-platform-jni (0.14-5) ...
Setting up libclass-xsaccessor-perl (1.19-4+b1) ...
Setting up libgtk2.0-common (2.24.33-2) ...
Setting up libatk1.0-0:arm64 (2.46.0-5) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libbcpg-java (1.72-2) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up libfile-dirlist-perl (0.05-3) ...
Setting up libfile-homedir-perl (1.006-2) ...
Setting up librelaxng-datatype-java (1.0+ds1-3.1) ...
Setting up libantlr-java (2.7.7+dfsg-12) ...
Setting up libyaml-snake-java (1.33-2) ...
Setting up openssl (3.0.8-1) ...
Setting up libbsd0:arm64 (0.11.7-2) ...
Setting up libdrm-common (2.4.114-1) ...
Setting up libcdi-api-java (1.2-3) ...
Setting up libelf1:arm64 (0.188-2.1) ...
Setting up libsnappy-jni (1.1.8.3-1) ...
Setting up readline-common (8.2-1.3) ...
Setting up libhawtjni-runtime-java (1.18-1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ...
Setting up liburi-perl (5.17-1) ...
Setting up libargs4j-java (2.33-2) ...
Setting up libfile-touch-perl (0.12-2) ...
Setting up dctrl-tools (2.24-3) ...
Setting up libjatl-java (0.2.3-1.1) ...
Setting up libnet-ssleay-perl:arm64 (1.92-2+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up pinentry-curses (1.2.1-1) ...
Setting up libdom4j-java (2.1.3-2) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libnative-platform-java (0.14-5) ...
Setting up libosgi-core-java (8.0.0-2) ...
Setting up libhttp-date-perl (6.05-2) ...
Setting up libxstream-java (1.4.20-1) ...
Setting up libnekohtml-java (1.9.22.noko2-0.1) ...
Setting up libxdmcp6:arm64 (1:1.1.2-3) ...
Setting up libxcb1:arm64 (1.15-1) ...
Setting up gettext (0.21-12) ...
Setting up libjetty9-java (9.4.50-3) ...
Setting up libxcb-xfixes0:arm64 (1.15-1) ...
Setting up java-wrappers (0.4) ...
Setting up libfile-listing-perl (6.15-1) ...
Setting up libosgi-compendium-java (7.0.0-1) ...
Setting up libmbedx509-1:arm64 (2.28.3-1) ...
Setting up libmbedtls14:arm64 (2.28.3-1) ...
Setting up libtool (2.4.7-5) ...
Setting up libxcb-render0:arm64 (1.15-1) ...
Setting up fontconfig-config (2.14.1-4) ...
Setting up libstax-ex-java (1.7.8-3) ...
Setting up libxcb-glx0:arm64 (1.15-1) ...
Setting up libmaven-parent-java (35-1) ...
Setting up libedit2:arm64 (3.1-20221030-2) ...
Setting up libreadline8:arm64 (8.2-1.3) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:arm64 (0.8-9) ...
Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ...
Setting up libcommons-logging-java (1.2-3) ...
Setting up libnet-http-perl (6.22-1) ...
Setting up libsisu-inject-java (0.3.4-2) ...
Setting up libnss3:arm64 (2:3.87.1-1) ...
Setting up libxcb-shm0:arm64 (1.15-1) ...
Setting up libdevel-callchecker-perl:arm64 (0.008-2) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libxcb-present0:arm64 (1.15-1) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:arm64 (0.1.29-1) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.4-3) ...
Setting up libbcel-java (6.5.0-2) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ...
Setting up libxcb-sync1:arm64 (1.15-1) ...
Setting up testng (6.9.12-4) ...
Setting up shared-mime-info (2.2-1) ...
Setting up libstreambuffer-java (1.5.4-1.1) ...
Setting up libcommons-lang3-java (3.12.0-2) ...
Setting up libxcb-dri2-0:arm64 (1.15-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libfelix-resolver-java (1.16.0-1) ...
Setting up librngom-java (2.3.0.1-10.1) ...
Setting up libdrm2:arm64 (2.4.114-1+b1) ...
Setting up dwz (0.15-1) ...
Setting up libjansi-native-java (1.8-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up libxcb-randr0:arm64 (1.15-1) ...
Setting up libhtml-parser-perl:arm64 (3.81-1) ...
Setting up libllvm15:arm64 (1:15.0.6-4+b1) ...
Setting up gpgconf (2.2.40-1.1) ...
Setting up openjdk-17-doc (17.0.6+10-1) ...
Setting up libjansi1-java (1.18-3) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libx11-6:arm64 (2:1.8.4-2) ...
Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ...
Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-1+b1) ...
Setting up libsnappy-java (1.1.8.3-1) ...
Setting up libfontconfig1:arm64 (2.14.1-4) ...
Setting up libxsom-java (2.3.0.1-10.1) ...
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libcommons-codec-java (1.15-1) ...
Setting up libjline2-java (2.14.6-5) ...
Setting up libxcomposite1:arm64 (1:0.4.5-1) ...
Setting up libavahi-client3:arm64 (0.8-9) ...
Setting up libio-socket-ssl-perl (2.081-2) ...
Setting up gpg (2.2.40-1.1) ...
Setting up gnupg-utils (2.2.40-1.1) ...
Setting up libhttp-message-perl (6.44-1) ...
Setting up libdrm-amdgpu1:arm64 (2.4.114-1+b1) ...
Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-5) ...
Setting up libxcb-dri3-0:arm64 (1.15-1) ...
Setting up gtk-update-icon-cache (3.24.37-2) ...
Setting up libx11-xcb1:arm64 (2:1.8.4-2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up fontconfig (2.14.1-4) ...
Regenerating fonts cache... done.
Setting up libngs-jni:arm64 (3.0.3+dfsg-5) ...
Setting up libdrm-nouveau2:arm64 (2.4.114-1+b1) ...
Setting up libfindbugs-java (3.1.0~preview2-3) ...
Setting up libxdamage1:arm64 (1:1.1.6-1) ...
Setting up gpg-agent (2.2.40-1.1) ...
Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
Setting up libcommons-compress-java (1.22-1) ...
Setting up libhttp-cookies-perl (6.10-1) ...
Setting up libcommons-io-java (2.11.0-2) ...
Setting up libdrm-radeon1:arm64 (2.4.114-1+b1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ...
Setting up libparams-classify-perl:arm64 (0.015-2+b1) ...
Setting up gpgsm (2.2.40-1.1) ...
Setting up libpango-1.0-0:arm64 (1.50.12+ds-1) ...
Setting up libgl1-mesa-dri:arm64 (22.3.6-1+deb12u1) ...
Setting up libxext6:arm64 (2:1.3.4-1+b1) ...
Setting up default-jdk-doc (2:1.17-74) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:arm64 (1.16.0-7) ...
Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ...
Setting up dirmngr (2.2.40-1.1) ...
Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up adwaita-icon-theme (43-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libxfixes3:arm64 (1:6.0.0-2) ...
Setting up libxinerama1:arm64 (2:1.1.4-3) ...
Setting up libxrandr2:arm64 (2:1.5.2-2+b1) ...
Setting up gpg-wks-server (2.2.40-1.1) ...
Setting up libcups2:arm64 (2.4.2-3) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libwagon-http-java (3.5.3-1) ...
Setting up libmaven-shared-utils-java (3.3.4-1) ...
Setting up libfastinfoset-java (1.2.12-3) ...
Setting up libngs-java:arm64 (3.0.3+dfsg-5) ...
Setting up libpangoft2-1.0-0:arm64 (1.50.12+ds-1) ...
Setting up libpangocairo-1.0-0:arm64 (1.50.12+ds-1) ...
Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up libjgit-java (4.11.9-2) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libglx-mesa0:arm64 (22.3.6-1+deb12u1) ...
Setting up libxi6:arm64 (2:1.8-1+b1) ...
Setting up gpg-wks-client (2.2.40-1.1) ...
Setting up libglx0:arm64 (1.6.0-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libxtst6:arm64 (2:1.2.3-1.1) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up libxcursor1:arm64 (1:1.2.1-1) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up libgl1:arm64 (1.6.0-1) ...
Setting up gnupg (2.2.40-1.1) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libgtk2.0-0:arm64 (2.24.33-2) ...
Setting up openjdk-17-jre-headless:arm64 (17.0.6+10-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up ca-certificates-java (20230103) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem
Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up junit4 (4.13.2-3) ...
Setting up liblwp-protocol-https-perl (6.10-1) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up default-jre-headless (2:1.17-74) ...
Setting up libwww-perl (6.68-1) ...
Setting up openjdk-17-jre:arm64 (17.0.6+10-1) ...
Setting up maven-repo-helper (1.11) ...
Setting up default-jre (2:1.17-74) ...
Setting up antlr (2.7.7+dfsg-12) ...
Setting up bnd (5.0.1-3) ...
Setting up devscripts (2.23.3) ...
Setting up libguava-java (31.1-1) ...
Setting up openjdk-17-jdk-headless:arm64 (17.0.6+10-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up ivy (2.5.1-2) ...
Setting up ant (1.10.13-1) ...
Setting up javahelper (0.78) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up groovy (2.4.21-7) ...
update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode
update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode
update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode
update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode
update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode
Setting up openjdk-17-jdk:arm64 (17.0.6+10-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up libguice-java (4.2.3-2) ...
Setting up ant-optional (1.10.13-1) ...
Setting up default-jdk-headless (2:1.17-74) ...
Setting up libgradle-core-java (4.4.1-18) ...
Setting up libmaven3-core-java (3.8.7-1) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up default-jdk (2:1.17-74) ...
Setting up libgradle-plugins-java (4.4.1-18) ...
Setting up libmaven-file-management-java (3.0.0-1) ...
Setting up gradle (4.4.1-18) ...
Setting up libistack-commons-java (3.0.6-5) ...
Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10.1) ...
Setting up gradle-debian-helper (2.4) ...
Setting up libtxw2-java (2.3.0.1-10.1) ...
Setting up libjaxb-java (2.3.0.1-10.1) ...
Processing triggers for libc-bin (2.36-8) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20230103) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/A99_set_merged_usr finished
hostname: Temporary failure in name resolution
I: Running cd /build/htsjdk-3.0.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../htsjdk_3.0.4+dfsg-2_source.changes
dpkg-buildpackage: info: source package htsjdk
dpkg-buildpackage: info: source version 3.0.4+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Aaron M. Ucko <ucko@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh  clean  --buildsystem=gradle --with javahelper,jh_maven_repo_helper
   dh_auto_clean -O--buildsystem=gradle
	sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf"
	sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf"
	rm -Rf /build/htsjdk-3.0.4\+dfsg/.gradle /build/htsjdk-3.0.4\+dfsg/buildSrc/.gradle .m2
   dh_autoreconf_clean -O--buildsystem=gradle
   jh_clean -O--buildsystem=gradle
	rm -fr debian/_jh_manifest* debian/_jh_build*
	rm -fr debian/.eclipse-build
	rm -f debian/orbitdeps.debhelper
   dh_clean -O--buildsystem=gradle
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/libhtsjdk-java.substvars debian/libhtsjdk-java-doc.substvars debian/files
	rm -fr -- debian/libhtsjdk-java/ debian/tmp/ debian/libhtsjdk-java-doc/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh  binary  --buildsystem=gradle --with javahelper,jh_maven_repo_helper
   dh_update_autotools_config -O--buildsystem=gradle
   dh_autoreconf -O--buildsystem=gradle
   dh_auto_configure -O--buildsystem=gradle
   jh_linkjars -O--buildsystem=gradle
   debian/rules override_dh_auto_build
make[1]: Map '/build/htsjdk-3.0.4+dfsg' wordt binnengegaan
dh_auto_build -- jar javadoc
	mkdir -p .gradle/init.d
	cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
	gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=8 jar javadoc
openjdk version "17.0.6" 2023-01-17
OpenJDK Runtime Environment (build 17.0.6+10-Debian-1)
OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing)
Initialized native services in: /build/htsjdk-3.0.4+dfsg/.gradle/native
To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html.
Starting process 'Gradle build daemon'. Working directory: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 2.118 secs.
The client will now receive all logging from the daemon (pid: 23214). The daemon log file: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1/daemon-23214.out.log
Daemon will be stopped at the end of the build stopping after processing
Closing daemon's stdin at end of input.
The daemon will no longer process any standard input.
Using 8 worker leases.
Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@190a0d6d
Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@190a0d6d
Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6f64bb45
Starting Build
Compiling initialization script '/build/htsjdk-3.0.4+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer.
Creating new cache for metadata-1.1/results, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@4c73bc43
Compiling initialization script '/build/htsjdk-3.0.4+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer.
Compiling settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle' using SubsetScriptTransformer.
Compiling settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle' using BuildScriptTransformer.
Settings evaluated using settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle'.
Projects loaded. Root project using build file '/build/htsjdk-3.0.4+dfsg/build.gradle'.
Included projects: [root project 'htsjdk']
	Keep-alive timer started
	Adding Debian repository to project 'htsjdk'
Parallel execution is an incubating feature.
Evaluating root project 'htsjdk' using build file '/build/htsjdk-3.0.4+dfsg/build.gradle'.
Compiling build file '/build/htsjdk-3.0.4+dfsg/build.gradle' using SubsetScriptTransformer.
Compiling build file '/build/htsjdk-3.0.4+dfsg/build.gradle' using BuildScriptTransformer.
Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/htsjdk-3.0.4+dfsg Command: dpkg-parsechangelog -S Version
Successfully started process 'command 'dpkg-parsechangelog''
build for version:3.0.4
	Adding Maven pom generation to project 'htsjdk'
	Linking the generated javadoc to the system JDK API documentation
All projects evaluated.
Selected primary task 'jar' from project :
Creating new cache for annotation-processors, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@1101fcab
Selected primary task 'javadoc' from project :
Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc']
Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6f64bb45
Creating new cache for taskHistory, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@5281621
Creating new cache for outputFiles, path /build/htsjdk-3.0.4+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@2607c28b
:compileJava (Thread[Task worker for ':',5,main]) started.
:compileJava
executing task ':compileJava' ...
Putting task artifact state for task ':compileJava' into context took 0.022 secs.
Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5e764a0d
	Loading the Maven rules...
	Replacing org.apache.commons:commons-jexl:jar:2.1.1  ->  org.apache.commons:commons-jexl:jar:debian
	Passing through org.apache.commons:commons-parent:jar:debian
	Passing through org.apache:apache:jar:debian
	Replacing commons-logging:commons-logging:jar:1.1.1  ->  commons-logging:commons-logging:jar:debian
	Replacing org.xerial.snappy:snappy-java:jar:1.1.8.4  ->  org.xerial.snappy:snappy-java:jar:debian
	Replacing org.apache.commons:commons-compress:jar:1.19  ->  org.apache.commons:commons-compress:jar:debian
	Replacing org.tukaani:xz:jar:1.8  ->  org.tukaani:xz:jar:debian
	Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0  ->  gov.nih.nlm.ncbi:ngs-java:jar:debian
	Passing through javax.xml.bind:jaxb-api:jar:debian
	Passing through javax.xml.bind:jaxb-api-parent:jar:debian
	Passing through org.mozilla:rhino:jar:debian
	Replacing org.sharegov:mjson:jar:1.4.1  ->  org.sharegov:mjson:jar:debian
	Passing through javax.activation:javax.activation-api:jar:debian
javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies.
	Passing through com.sun.activation:javax.activation:jar:debian
	Passing through com.sun.activation:all:jar:debian
Up-to-date check for task ':compileJava' took 2.911 secs. It is not up-to-date because:
  No history is available.
All input files are considered out-of-date for incremental task ':compileJava'.
Compiling with JDK Java compiler API.
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/TextTagCodec.java:207: warning: [removal] Float(String) in Float has been deprecated and marked for removal
                return new Float(stringVal);
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/Defaults.java:169: warning: [removal] AccessControlException in java.security has been deprecated and marked for removal
        } catch (final java.security.AccessControlException error) {
                                    ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/Defaults.java:181: warning: [removal] AccessControlException in java.security has been deprecated and marked for removal
        } catch (final java.security.AccessControlException error) {
                                    ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
3 warnings
:compileJava (Thread[Task worker for ':',5,main]) completed. Took 31.909 secs.
:processResources (Thread[Task worker for ':' Thread 7,5,main]) started.
:processResources
executing task ':processResources' ...
Putting task artifact state for task ':processResources' into context took 0.0 secs.
Up-to-date check for task ':processResources' took 0.013 secs. It is not up-to-date because:
  No history is available.
:processResources (Thread[Task worker for ':' Thread 7,5,main]) completed. Took 0.063 secs.
:classes (Thread[Task worker for ':' Thread 7,5,main]) started.
:classes
executing task ':classes' ...
Skipping task ':classes' as it has no actions.
:classes (Thread[Task worker for ':' Thread 7,5,main]) completed. Took 0.003 secs.
:debianMavenPom (Thread[Task worker for ':' Thread 7,5,main]) started.
:debianMavenPom
executing task ':debianMavenPom' ...
Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs.
Up-to-date check for task ':debianMavenPom' took 0.003 secs. It is not up-to-date because:
  No history is available.
	Generating pom file /build/htsjdk-3.0.4+dfsg/build/debian/htsjdk.pom
:debianMavenPom (Thread[Task worker for ':' Thread 7,5,main]) completed. Took 0.215 secs.
:jar (Thread[Task worker for ':' Thread 7,5,main]) started.
:jar
executing task ':jar' ...
Putting task artifact state for task ':jar' into context took 0.0 secs.
Up-to-date check for task ':jar' took 0.121 secs. It is not up-to-date because:
  No history is available.
:jar (Thread[Task worker for ':' Thread 7,5,main]) completed. Took 1.009 secs.
:javadoc (Thread[Task worker for ':' Thread 7,5,main]) started.
:javadoc
executing task ':javadoc' ...
Putting task artifact state for task ':javadoc' into context took 0.0 secs.
Up-to-date check for task ':javadoc' took 0.41 secs. It is not up-to-date because:
  No history is available.
Starting process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc''. Working directory: /build/htsjdk-3.0.4+dfsg Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc @/build/htsjdk-3.0.4+dfsg/build/tmp/javadoc/javadoc.options
Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc''
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<'
     * Closes inner <code>SamIterator</>.
                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<'
     * Closes inner <code>SamIterator</>.
                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:123: warning: invalid input: '<'
     * @return the compression level for these options, 1 <= compressionLevel <= 9
                                                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:123: warning: invalid input: '<'
     * @return the compression level for these options, 1 <= compressionLevel <= 9
                                                                              ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:133: warning: invalid input: '<'
     * @param compressionLevel the compression level for these options, 1 <= compressionLevel <= 9
                                                                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java:133: warning: invalid input: '<'
     * @param compressionLevel the compression level for these options, 1 <= compressionLevel <= 9
                                                                                              ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/Bin.java:108: warning: invalid input: '<'
     * @return -1 if this < other, 0 if this == other, 1 if this > other.
                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:140: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:140: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:148: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:148: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:158: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:158: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:167: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:167: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning: invalid input: '<'
     * @param compressionLevel 1 <= compressionLevel <= 9
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/BlockGunzipper.java:104: warning: Parameter "compressedBlock" is documented more than once.
     * @param compressedBlock  the offset into the compressed data.
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/CloserUtil.java:57: warning: invalid input: '<'
     * NOTE: This method must take a List<? extends Object>, not List<Object>, otherwise the overload above will be selected
                                         ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/cram/structure/CompressionHeader.java:87: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method, inline text.
     * @return a new CompressionHeader
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/cram/structure/ContainerHeader.java:131: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method, inline text.
     * @return a new {@link ContainerHeader} object with container header values filled out but empty body (no slices and blocks).
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java:194: warning: invalid input: '<'
     * @return number of elements stored in RAM.  Always <= size()
                                                         ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java:90: warning: invalid input: '<'
    * This number must be < the value for {@link #getReadsPerSlice}
                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:125: warning: invalid input: '<'
     * We allow different scoring strategies. We return <0 if rec1 has a better strategy than rec2.
                                                        ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:150: warning: invalid input: '<'
     * We allow different scoring strategies. We return <0 if rec1 has a better strategy than rec2.
                                                        ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java:56: warning: invalid input: '<'
 *      for (int i = 0; i < seqNames.length; i++) {
                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&'
    /** Formats date & time */
                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&'
    /** Formats date & time */
                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:106: warning: invalid input: '&'
     * Described in "The Human Genome Browser at UCSC. Kent & al. doi: 10.1101/gr.229102 "
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:124: warning: invalid input: '&'
     * Described in "The Human Genome Browser at UCSC. Kent & al. doi: 10.1101/gr.229102 "
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:443: warning: invalid input: '&lt'
     * @throws IllegalArgumentException if altAlleles or ploidy &lt= 0
                                                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:456: warning: invalid input: '<'
     * @throws IllegalStateException if PLindex < 0 or ploidy < 0
                                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/variant/variantcontext/GenotypeLikelihoods.java:456: warning: invalid input: '<'
     * @throws IllegalStateException if PLindex < 0 or ploidy < 0
                                                              ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning: invalid input: '<'
     * Returns the cumulative probability of observing a value <= v when sampling the
                                                               ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning: invalid input: '<'
     * Trims the histogram so that only bins <= width are kept.
                                             ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning: invalid input: '<'
     * Returns the cumulative probability of observing a value <= v when sampling the
                                                               ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning: invalid input: '<'
     * Trims the histogram so that only bins <= width are kept.
                                             ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/plugin/HtsCodec.java:79: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
 *     <li> For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package </li>
                                                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:18: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
 *     <li> For {@link HtsContentType#FEATURES} codecs, see the {@link htsjdk.beta.plugin.features} package </li>
                                                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
     * Features content type (see {@link htsjdk.beta.plugin.features} for related formats)
                                  ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
     * Features content type (see {@link htsjdk.beta.plugin.features} for related formats)
                                  ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/io/HtsPath.java:55: warning: invalid input: '<'
 *     <scheme>:<scheme-specific-part>
                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/io/HtsPath.java:68: warning: invalid input: '&'
 *         uric_no_slash = unreserved | escaped | ";" | "?" | ":" | "@" | "&" | "=" | "+" | "$" | ","
                                                                           ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/io/IOPath.java:48: warning: invalid input: '{@code java.nio File System
     * There are cases where a valid URI with a valid scheme backed by an installed {@code java.nio File System
                                                                                    ^
   still can't be turned into a {@code java.nio.file.Path}, i.e., the following specifies an invalid
   authority "namenode":
  
    hdfs://namenode/to/file
  
   The current implementation returns false for these cases (toPath will fail, getInvalidPathReason
   returns the reason code).'
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/filter/IntervalFilter.java:53: warning: invalid input: '&'
     * @param intervals -- must be locus-ordered & non-overlapping
                                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning: invalid usage of tag {@link #uniqued()#getIntervals()
     * @deprecated use {@link #uniqued()#getIntervals()} instead.
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning: invalid usage of tag {@link #uniqued(boolean)#getIntervals()
     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning: invalid usage of tag {@link #uniqued()#getIntervals()
     * @deprecated use {@link #uniqued()#getIntervals()} instead.
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning: invalid usage of tag {@link #uniqued(boolean)#getIntervals()
     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/io/IOPath.java:48: warning: invalid input: '{@code java.nio File System
     * There are cases where a valid URI with a valid scheme backed by an installed {@code java.nio File System
                                                                                    ^
   still can't be turned into a {@code java.nio.file.Path}, i.e., the following specifies an invalid
   authority "namenode":
  
    hdfs://namenode/to/file
  
   The current implementation returns false for these cases (toPath will fail, getInvalidPathReason
   returns the reason code).'
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:167: warning: invalid input: '<'
     * @param compressionLevel 0 <= compressionLevel <= 9
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IOUtil.java:167: warning: invalid input: '<'
     * @param compressionLevel 0 <= compressionLevel <= 9
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:17: warning: invalid input: '<'
 * If highest bit < 8:
                  ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:166: warning: invalid input: '<'
     * <= ((i + 1) * binWidth))
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:75: warning: invalid input: '<'
     * @throws IllegalArgumentException If sz is <= 0
                                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:453: warning: invalid input: '<'
     * @throws IllegalArgumentException If readAheadLimit is < 0
                                                             ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/QueryInterval.java:18: warning: invalid input: '<'
    /** 1-based, inclusive.  If <= 0, implies that the interval goes to the end of the reference sequence */
                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMFileWriterImpl.java:35: warning: invalid input: '&'
 * Mostly this manages accumulation & sorting of SAMRecords when appropriate,
                                    ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMLineParser.java:221: warning: invalid input: '<'
     *                   can be <=0.
                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:60: warning: invalid input: '&'
 * Note also that there are a number of getters & setters that are linked, i.e. they present different representations
                                                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:166: warning: invalid input: '<'
     * abs(insertSize) must be <= this
                               ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:1644: warning: invalid input: ''
     * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:166: warning: invalid input: '<'
     * abs(insertSize) must be <= this
                               ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:778: warning: invalid input: '&'
     * @return insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0.
                                                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:1644: warning: invalid input: ''
     * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordComparator.java:37: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning: invalid input: '<'
 * if A < B, then B > A
        ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<'
 * if A < B && B < C, then A < C
        ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '&'
 * if A < B && B < C, then A < C
            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '&'
 * if A < B && B < C, then A < C
             ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<'
 * if A < B && B < C, then A < C
                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning: invalid input: '<'
 * if A < B && B < C, then A < C
                             ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:85: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordComparator.java:37: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java:77: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java:77: warning: invalid input: '<'
     * @return negative if samRecord1 < samRecord2,  0 if equal, else positive
                                      ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMSortOrderChecker.java:42: warning: invalid input: '<'
     * @return True if sort order is unsorted, if this is the first record, or if previous <= rec.
                                                                                           ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:644: warning: invalid input: '<'
     * @return negative if mapq1 < mapq2, etc.
                                 ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:645: warning: invalid input: '<'
     * Note that MAPQ(0) < MAPQ(255) < MAPQ(1)
                         ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:645: warning: invalid input: '<'
     * Note that MAPQ(0) < MAPQ(255) < MAPQ(1)
                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:1128: warning: invalid input: '<'
     * @return true if value is >= 0 and <= {@link BinaryCodec#MAX_UINT}, and false otherwise
                                         ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/cram/structure/Slice.java:171: warning: Tag @return cannot be used in constructor documentation.  It can only be used in the following types of documentation: method, inline text.
     * @return a Slice corresponding to the given records
       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:778: warning: invalid input: '&'
     * @return insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0.
                                                          ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/StringUtil.java:201: warning: invalid input: '<'
     * have length <= maxLineLength.  if a word is too long, it is simply broken
                   ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/StringUtil.java:201: warning: invalid input: '<'
     * have length <= maxLineLength.  if a word is too long, it is simply broken
                   ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java:381: warning: @return tag cannot be used in method with void return type.
    public static void unsetDefaultOption(final Options option) {
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/variant/vcf/VCFEncoder.java:103: warning: @return tag cannot be used in method with void return type.
    public void write(final Appendable vcfOutput, final VariantContext context) throws IOException {
                ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:52: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMFileHeader.java:291: warning: invalid input: 'instead'
     * @deprecated Use {@link #setAttribute(String, String) instead
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning: invalid usage of tag {@link #uniqued()#getIntervals()
     * @deprecated use {@link #uniqued()#getIntervals()} instead.
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning: invalid usage of tag {@link #uniqued(boolean)#getIntervals()
     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
                       ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:211: warning: invalid input: '<'
     * Closes inner <code>SamIterator</>.
                                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/beta/plugin/HtsContentType.java:46: warning: Tag @link: reference not found: htsjdk.beta.plugin.features
     * Features content type (see {@link htsjdk.beta.plugin.features} for related formats)
                                  ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning: invalid input: '&'
    /** Formats date & time */
                     ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning: invalid input: '<'
     * Returns the cumulative probability of observing a value <= v when sampling the
                                                               ^
/build/htsjdk-3.0.4+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:1644: warning: invalid input: ''
     * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position.
       ^
100 warnings
:javadoc (Thread[Task worker for ':' Thread 7,5,main]) completed. Took 34.257 secs.

BUILD SUCCESSFUL in 1m 21s
5 actionable tasks: 5 executed
make[1]: Map '/build/htsjdk-3.0.4+dfsg' wordt verlaten
   jh_build -O--buildsystem=gradle
	rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Map '/build/htsjdk-3.0.4+dfsg' wordt binnengegaan
# testng bug 895886: testng: jcommander classes not found
dh_auto_build -- test
	mkdir -p .gradle/init.d
	cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/
	gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=8 test
openjdk version "17.0.6" 2023-01-17
OpenJDK Runtime Environment (build 17.0.6+10-Debian-1)
OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing)
Initialized native services in: /build/htsjdk-3.0.4+dfsg/.gradle/native
To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html.
Starting process 'Gradle build daemon'. Working directory: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 2.145 secs.
The client will now receive all logging from the daemon (pid: 25649). The daemon log file: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1/daemon-25649.out.log
Daemon will be stopped at the end of the build stopping after processing
Closing daemon's stdin at end of input.
The daemon will no longer process any standard input.
Using 8 worker leases.
Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6b52f679
Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6b52f679
Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a172207
Starting Build
Creating new cache for metadata-1.1/results, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@2175a6be
Settings evaluated using settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle'.
Projects loaded. Root project using build file '/build/htsjdk-3.0.4+dfsg/build.gradle'.
Included projects: [root project 'htsjdk']
	Keep-alive timer started
	Adding Debian repository to project 'htsjdk'
Parallel execution is an incubating feature.
Evaluating root project 'htsjdk' using build file '/build/htsjdk-3.0.4+dfsg/build.gradle'.
Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/htsjdk-3.0.4+dfsg Command: dpkg-parsechangelog -S Version
Successfully started process 'command 'dpkg-parsechangelog''
build for version:3.0.4
	Adding Maven pom generation to project 'htsjdk'
	Linking the generated javadoc to the system JDK API documentation
All projects evaluated.
Selected primary task 'test' from project :
Creating new cache for annotation-processors, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@44e3834f
Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':findScalaAndJavaTypes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':testWithDefaultReference', task ':test']
Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a172207
Creating new cache for taskHistory, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@191cda08
Creating new cache for outputFiles, path /build/htsjdk-3.0.4+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@486ead34
:compileJava (Thread[Task worker for ':',5,main]) started.
:compileJava
executing task ':compileJava' ...
Putting task artifact state for task ':compileJava' into context took 0.012 secs.
Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@296e3a14
	Loading the Maven rules...
	Replacing org.apache.commons:commons-jexl:jar:2.1.1  ->  org.apache.commons:commons-jexl:jar:debian
	Passing through org.apache.commons:commons-parent:jar:debian
	Passing through org.apache:apache:jar:debian
	Replacing commons-logging:commons-logging:jar:1.1.1  ->  commons-logging:commons-logging:jar:debian
	Replacing org.xerial.snappy:snappy-java:jar:1.1.8.4  ->  org.xerial.snappy:snappy-java:jar:debian
	Replacing org.apache.commons:commons-compress:jar:1.19  ->  org.apache.commons:commons-compress:jar:debian
	Replacing org.tukaani:xz:jar:1.8  ->  org.tukaani:xz:jar:debian
	Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0  ->  gov.nih.nlm.ncbi:ngs-java:jar:debian
	Passing through javax.xml.bind:jaxb-api:jar:debian
	Passing through javax.xml.bind:jaxb-api-parent:jar:debian
	Passing through org.mozilla:rhino:jar:debian
	Replacing org.sharegov:mjson:jar:1.4.1  ->  org.sharegov:mjson:jar:debian
	Passing through javax.activation:javax.activation-api:jar:debian
javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies.
	Passing through com.sun.activation:javax.activation:jar:debian
	Passing through com.sun.activation:all:jar:debian
Skipping task ':compileJava' as it is up-to-date (took 1.839 secs).
:compileJava UP-TO-DATE
:compileJava (Thread[Task worker for ':',5,main]) completed. Took 1.981 secs.
:processResources (Thread[Task worker for ':',5,main]) started.
:processResources
executing task ':processResources' ...
Putting task artifact state for task ':processResources' into context took 0.0 secs.
Skipping task ':processResources' as it is up-to-date (took 0.009 secs).
:processResources UP-TO-DATE
:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.023 secs.
:classes (Thread[Task worker for ':',5,main]) started.
:classes
executing task ':classes' ...
Skipping task ':classes' as it has no actions.
:classes UP-TO-DATE
:classes (Thread[Task worker for ':',5,main]) completed. Took 0.004 secs.
:findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) started.
:findScalaAndJavaTypes
executing task ':findScalaAndJavaTypes' ...
Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.003 secs.
Up-to-date check for task ':findScalaAndJavaTypes' took 0.0 secs. It is not up-to-date because:
  Task has not declared any outputs.
Starting process 'command './scripts/checkScalaAndJavaFiles.sh''. Working directory: /build/htsjdk-3.0.4+dfsg Command: ./scripts/checkScalaAndJavaFiles.sh 
Successfully started process 'command './scripts/checkScalaAndJavaFiles.sh''
:findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) completed. Took 0.05 secs.
:compileTestJava (Thread[Task worker for ':',5,main]) started.
:compileTestJava
executing task ':compileTestJava' ...
Putting task artifact state for task ':compileTestJava' into context took 0.0 secs.
	Passing through org.scala-lang:scala-library:jar:2.11.x
	Passing through org.testng:testng:jar:debian
	Passing through com.google.jimfs:jimfs:jar:debian
	Passing through com.google.jimfs:jimfs-parent:jar:debian
	Passing through com.google.guava:guava:jar:debian
	Passing through com.google.guava:guava-parent:jar:debian
	Passing through org.apache.commons:commons-lang3:jar:debian
	Passing through org.beanshell:bsh:jar:debian
	Passing through com.beust:jcommander:jar:debian
	Passing through org.jsr-305:jsr305:jar:0.x
	Passing through com.google.errorprone:error_prone_annotations:jar:debian
	Passing through com.google.errorprone:error_prone_parent:jar:debian
Up-to-date check for task ':compileTestJava' took 5.489 secs. It is not up-to-date because:
  No history is available.
All input files are considered out-of-date for incremental task ':compileTestJava'.
Compiling with JDK Java compiler API.
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java:154: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
            this(new Integer(value), type);
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java:158: warning: [removal] Double(double) in Double has been deprecated and marked for removal
            this(new Double(value), type);
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal
        tagMap.put("XC", new Character('q'));
                         ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:345: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(0L), record.getUnsignedIntegerAttribute(stringTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:346: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(0L), record.getUnsignedIntegerAttribute(binaryTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:349: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(BinaryCodec.MAX_UINT), record.getUnsignedIntegerAttribute(stringTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:350: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(BinaryCodec.MAX_UINT), record.getUnsignedIntegerAttribute(binaryTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:358: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(0L), record.getUnsignedIntegerAttribute(stringTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:359: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(0L), record.getUnsignedIntegerAttribute(binaryTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:367: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(BinaryCodec.MAX_UINT), record.getUnsignedIntegerAttribute(stringTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:368: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(BinaryCodec.MAX_UINT), record.getUnsignedIntegerAttribute(binaryTag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:383: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(0L), record.getUnsignedIntegerAttribute(tag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:387: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(BinaryCodec.MAX_UINT), record.getUnsignedIntegerAttribute("UI"));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:409: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Byte((byte) 0)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:410: warning: [removal] Short(short) in Short has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Short((short) 0)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:411: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Integer(0)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:413: warning: [removal] Character(char) in Character has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Character('C')));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:414: warning: [removal] Float(float) in Float has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Float(0.1F)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:421: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Long(0)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:422: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Long(BinaryCodec.MAX_UINT)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:423: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertTrue(SAMRecord.isAllowedAttributeValue(new Long(-1L)));
                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:424: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertFalse(SAMRecord.isAllowedAttributeValue(new Long(BinaryCodec.MAX_UINT + 1L)));
                                                             ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:425: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertFalse(SAMRecord.isAllowedAttributeValue(new Long(Integer.MIN_VALUE - 1L)));
                                                             ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:466: warning: [removal] Long(long) in Long has been deprecated and marked for removal
        Assert.assertEquals(new Long(BinaryCodec.MAX_UINT), record.getUnsignedIntegerAttribute(tag));
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:880: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
        Assert.assertEquals(sam.getReferenceIndex(), new Integer(0));
                                                     ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:889: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
        Assert.assertEquals(new Integer(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX), sam.getReferenceIndex());
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
        Assert.assertEquals(new Integer(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX), sam.getMateReferenceIndex());
                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:923: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
        Assert.assertEquals(SAMRecord.resolveIndexFromName(contigName, samHeader, true), new Integer(samHeader.getSequenceIndex(contigName)));
                                                                                         ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, samHeader, true), new Integer(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX));
                                                                         ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:15: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new Byte((byte) 7)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:16: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new Short((short) 8)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:17: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new Integer(0)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:18: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new Character('C')},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:19: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new Float(0.1F)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:21: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(0)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:22: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(BinaryCodec.MAX_UINT)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:24: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(-1L)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:25: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(Integer.MAX_VALUE)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:26: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(Integer.MIN_VALUE)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:48: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(BinaryCodec.MAX_UINT + 1L)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new Long(Integer.MIN_VALUE - 1L)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:50: warning: [removal] Double(double) in Double has been deprecated and marked for removal
                {new Double(0.3F)},
                 ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:103: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), true, true},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:103: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), true, true},
                                                                                                  ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:104: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 1)), false, false},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:104: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Byte((byte) 0)), new SAMBinaryTagAndValue(tag, new Byte((byte) 1)), false, false},
                                                                                                  ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:106: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 0)), true, true},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:106: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 0)), true, true},
                                                                                                    ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:107: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 1)), false, false},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:107: warning: [removal] Short(short) in Short has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Short((short) 0)), new SAMBinaryTagAndValue(tag, new Short((short) 1)), false, false},
                                                                                                    ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:109: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:109: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                                                                              ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:110: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:110: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Integer(0)), new SAMBinaryTagAndValue(tag, new Integer(0)), true, true},
                                                                                              ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:112: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('C')), true, true},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:112: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('C')), true, true},
                                                                                                  ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:113: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('D')), false, false},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:113: warning: [removal] Character(char) in Character has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Character('C')), new SAMBinaryTagAndValue(tag, new Character('D')), false, false},
                                                                                                  ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:115: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.1F)), true, true},
                                              ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:115: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.1F)), true, true},
                                                                                              ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:116: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.2F)), false, false},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:116: warning: [removal] Float(float) in Float has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Float(0.1F)), new SAMBinaryTagAndValue(tag, new Float(0.2F)), false, false},
                                                                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:118: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(37L)), true, true},
                                              ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:118: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(37L)), true, true},
                                                                                            ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:119: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(38L)), false, false},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:119: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(37L)), new SAMBinaryTagAndValue(tag, new Long(38L)), false, false},
                                                                                             ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:121: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), true, true},
                                              ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:121: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag,new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), true, true},
                                                                                                             ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:122: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false},
                                               ^
/build/htsjdk-3.0.4+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:122: warning: [removal] Long(long) in Long has been deprecated and marked for removal
                {new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false},
                                                                                                              ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
70 warnings
:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 33.544 secs.
:processTestResources (Thread[Task worker for ':' Thread 2,5,main]) started.
:processTestResources
executing task ':processTestResources' ...
Putting task artifact state for task ':processTestResources' into context took 0.0 secs.
Up-to-date check for task ':processTestResources' took 0.667 secs. It is not up-to-date because:
  No history is available.
:processTestResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.695 secs.
:testClasses (Thread[Task worker for ':' Thread 2,5,main]) started.
:testClasses
executing task ':testClasses' ...
Skipping task ':testClasses' as it has no actions.
:testClasses (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.002 secs.
:testWithDefaultReference (Thread[Task worker for ':' Thread 2,5,main]) started.
:testWithDefaultReference
executing task ':testWithDefaultReference' ...
Putting task artifact state for task ':testWithDefaultReference' into context took 0.001 secs.
Up-to-date check for task ':testWithDefaultReference' took 0.754 secs. It is not up-to-date because:
  Task.upToDateWhen is false.
Finished generating test XML results (0.004 secs) into: /build/htsjdk-3.0.4+dfsg/build/test-results/testWithDefaultReference
Generating HTML test report...
Finished generating test html results (0.039 secs) into: /build/htsjdk-3.0.4+dfsg/build/reports/tests/testWithDefaultReference
:testWithDefaultReference (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.06 secs.
:test (Thread[Task worker for ':' Thread 2,5,main]) started.
:test
executing task ':test' ...
Putting task artifact state for task ':test' into context took 0.0 secs.
Up-to-date check for task ':test' took 0.136 secs. It is not up-to-date because:
  Task.upToDateWhen is false.
Starting process 'Gradle Test Executor 1'. Working directory: /build/htsjdk-3.0.4+dfsg Command: /usr/lib/jvm/java-17-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath9066990022704644597txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1'
Successfully started process 'Gradle Test Executor 1'
Gradle Test Executor 1 started executing tests.

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[71](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[72](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[73](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[74](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[75](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[76](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[77](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[78](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[79](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[80](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[81](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:30:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[156](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[157](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[158](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[159](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[160](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[161](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[162](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[163](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[164](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[165](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[166](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:32:43	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[370](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 20:32:49	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR
    WARNING	2023-04-15 20:32:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR
    WARNING	2023-04-15 20:32:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR
    WARNING	2023-04-15 20:32:50	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR
    java.lang.RuntimeException: oops
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_1$0(VariantContextWriterBuilderUnitTest.java:497)
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:522)
    	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    	at java.base/java.lang.Thread.run(Thread.java:833)

Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR
    java.lang.RuntimeException: oops
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_2$1(VariantContextWriterBuilderUnitTest.java:503)
    	at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$testWriteToPipe$2(VariantContextWriterBuilderUnitTest.java:522)
    	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    	at java.base/java.lang.Thread.run(Thread.java:833)

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstCompleteContigRead runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstElementOfIterator runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequence runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequence runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstSequence runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstSequenceExtended runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 17ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 11ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 17ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 23ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testLastCompleteContigRead runtime: 16ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 6ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testLastCompleteContigRead runtime: 19ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testFirstOfChr1 runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testFirstOfChr1 runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 16ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 14ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testNextElementOfIterator runtime: 13ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 4ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testNextElementOfIterator runtime: 4ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testOpenFile runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadPastEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadStartingInCenterOfFirstLine runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadStartingInCenterOfMiddleLine runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 1ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReadThroughEndOfContig runtime: 0ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 2ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 3ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 16ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 16ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    testReset runtime: 16ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 6ms

Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR
    testReset runtime: 6ms

Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR
    WARNING	2023-04-15 20:35:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@520ee8b7, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR
    WARNING	2023-04-15 20:35:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR
    WARNING	2023-04-15 20:35:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR
    WARNING	2023-04-15 20:35:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR
    WARNING	2023-04-15 20:35:20	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT
    Found start of unmapped reads.  Num mapped reads: 9721
    Time so far: 0
    Linear scan total time: 0
    queryUnmapped time: 0
    Number of unmapped reads:279

Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testRandomQueries STANDARD_OUT
    Testing query chr11_random:7211102-7392752 ...
    Testing query chrX_random:2969904-3087323 ...
    Testing query chr5:9255377-9796767 ...
    Testing query chr16_random:9067406-9976989 ...
    Testing query chr6:2164417-9572211 ...
    Testing query chr8_random:5688357-6576007 ...
    Testing query chr4_random:4241203-6327831 ...
    Testing query chr2_random:411082-4462819 ...
    Testing query chr13_random:145947-4307287 ...
    Testing query chr15_random:3298214-6356603 ...
    Testing query chr21:472385-8291032 ...
    Testing query chr2:4177649-9835176 ...
    Testing query chr22_random:1490587-8781106 ...
    Testing query chr14:2167927-6299701 ...
    Testing query chr7:4700515-5593851 ...
    Testing query chr22:5016764-7470151 ...
    Testing query chr22_random:7524398-8627117 ...
    Testing query chr8:3764754-6977071 ...
    Testing query chr1_random:1725504-3204042 ...
    Testing query chr21:2025794-4625889 ...
    Testing query chr14:1426554-6327490 ...
    Testing query chrX_random:1992622-9650667 ...
    Testing query chr4:2669418-7183639 ...
    Testing query chr10:2967472-3641376 ...
    Testing query chr10_random:3273594-3427480 ...
    Testing query chr19_random:4582311-5090524 ...
    Testing query chr9_random:7218100-8812477 ...
    Testing query chrX:257134-4337775 ...
    Testing query chr9_random:713930-3536575 ...
    Testing query chrX:2523687-4774316 ...
    Testing query chr21:513221-829881 ...
    Testing query chr14:6924617-9048044 ...
    Testing query chr6:4945372-7173211 ...
    Testing query chr6_random:7501139-9077397 ...
    Testing query chr19:2934833-5141776 ...
    Testing query chr9:863231-7545153 ...
    Testing query chr2:4308042-6742767 ...
    Testing query chr12:293858-324418 ...
    Testing query chr6_random:3308674-4557713 ...
    Testing query chr2_random:6755655-7330097 ...
    Testing query chr9_random:1234763-6135261 ...
    Testing query chr17:7042296-7582149 ...
    Testing query chr18:6749235-8476299 ...
    Testing query chr22:1198031-6226173 ...
    Testing query chr22:9446557-9458998 ...
    Testing query chr15:473293-1136600 ...
    Testing query chr13:8001267-8034858 ...
    Testing query chr7_random:12779-8349897 ...
    Testing query chrX:6476995-9046675 ...
    Testing query chr22:455684-9901546 ...
    Testing query chr20:2540726-9004820 ...
    Testing query chr1:5290124-7772462 ...
    Testing query chr2_random:4562177-7629291 ...
    Testing query chr4:5992612-7734912 ...
    Testing query chr5:1027938-6017856 ...
    Testing query chr5:3945452-4558863 ...
    Testing query chr7_random:1434224-8766265 ...
    Testing query chr13_random:2806926-8471270 ...
    Testing query chr21:5896937-6230120 ...
    Testing query chr10_random:2325170-6773979 ...
    Testing query chr4:768115-9242973 ...
    Testing query chr9:204376-1523700 ...
    Testing query chr15:6918456-9920136 ...
    Testing query chr8:195836-2912231 ...
    Testing query chr4_random:8569316-9601747 ...
    Testing query chr14:7539676-8479802 ...
    Testing query chr17_random:6016149-9676582 ...
    Testing query chr3:2401075-5926977 ...
    Testing query chr7:6825835-8610049 ...
    Testing query chr4:8589977-9226779 ...
    Testing query chr22_random:881883-9900377 ...
    Testing query chr19:2282185-2974234 ...
    Testing query chr2_random:530137-7997036 ...
    Testing query chr11_random:1524078-8571487 ...
    Testing query chrX:3561537-3812547 ...
    Testing query chr7_random:5345040-8399303 ...
    Testing query chr22:1586323-6546266 ...
    Testing query chr13:356087-8263221 ...
    Testing query chr9:6308509-8761532 ...
    Testing query chr8:3702301-5705153 ...
    Testing query chr13_random:1656308-4034137 ...
    Testing query chr3:4684965-7862719 ...
    Testing query chr19_random:5585589-7312648 ...
    Testing query chr18:8395777-9280098 ...
    Testing query chr6_random:738052-6252176 ...
    Testing query chr5_random:6874632-8838246 ...
    Testing query chr7_random:4576401-9601286 ...
    Testing query chr6_random:1277796-9240909 ...
    Testing query chr22:2128956-7451924 ...
    Testing query chr9:5866041-7641214 ...
    Testing query chr6_random:2900603-6324004 ...
    Testing query chr5:3340073-3878152 ...
    Testing query chr7_random:6065731-8117472 ...
    Testing query chr22:6980282-9420307 ...
    Testing query chr3_random:7896234-9902729 ...
    Testing query chr4:5226514-9465698 ...
    Testing query chr11_random:2710966-7297413 ...
    Testing query chr4:5814391-6477874 ...
    Testing query chr17:3411447-7945931 ...
    Testing query chr19_random:1563833-8954930 ...
    Testing query chr4:2666458-5577064 ...
    Testing query chrM:2495375-2785830 ...
    Testing query chr22_random:2741863-7160257 ...
    Testing query chr20:3030962-4839827 ...
    Testing query chrX_random:1999206-3290596 ...
    Testing query chr1_random:7581574-9491516 ...
    Testing query chr5:8544911-9905206 ...
    Testing query chr17_random:5247411-8818598 ...
    Testing query chr18:2206748-2542618 ...
    Testing query chr6:5560095-6841213 ...
    Testing query chrX:5584638-8069137 ...
    Testing query chr2_random:893746-4019636 ...
    Testing query chr4_random:7220619-8625179 ...
    Testing query chr17_random:7487783-7745825 ...
    Testing query chr13_random:140415-4339843 ...
    Testing query chr22:3465880-9918684 ...
    Testing query chr16_random:2228554-5218116 ...
    Testing query chr6:3812651-9020894 ...
    Testing query chr19:4897072-8152584 ...
    Testing query chr15_random:2493596-3303830 ...
    Testing query chr17:7330256-9331563 ...
    Testing query chr7_random:2372609-7660988 ...
    Testing query chr21:16468-1408282 ...
    Testing query chrM:946718-7866529 ...
    Testing query chr6:636772-5261193 ...
    Testing query chr4:4081985-5160778 ...
    Testing query chr4_random:3992937-8001782 ...
    Testing query chr3_random:4269902-7314671 ...
    Testing query chr8_random:5398008-9100867 ...
    Testing query chr11_random:4717946-5886722 ...
    Testing query chr14:3324888-9762784 ...
    Testing query chr3_random:447076-2904415 ...
    Testing query chr18_random:4656587-8830031 ...
    Testing query chr15_random:2677992-8013872 ...
    Testing query chr8:8741342-9773821 ...
    Testing query chrM:638643-3884353 ...
    Testing query chr6:1102480-2996219 ...
    Testing query chr13:27071-9001996 ...
    Testing query chr8_random:133575-8239847 ...
    Testing query chr4:5119076-7497751 ...
    Testing query chr6_random:8932876-9157638 ...
    Testing query chr2:8039126-9556281 ...
    Testing query chr18:2759483-4424919 ...
    Testing query chr7_random:2162721-7693312 ...
    Testing query chr17_random:3212242-7079443 ...
    Testing query chrX_random:9441944-9675063 ...
    Testing query chrX:1483850-9503277 ...
    Testing query chrY:708618-2939362 ...
    Testing query chr1:1457571-8460228 ...
    Testing query chrM:5153488-6390263 ...
    Testing query chr8:2469944-5489240 ...
    Testing query chr4:2270560-9937550 ...
    Testing query chr10:1924284-4282155 ...
    Testing query chrY:5044757-9726553 ...
    Testing query chr21_random:8138434-8862076 ...
    Testing query chr17_random:8064209-8585636 ...
    Testing query chr22:7325448-9656485 ...
    Testing query chr11:6475178-6915306 ...
    Testing query chrM:1569370-6357214 ...
    Testing query chr8_random:1676954-7528262 ...
    Testing query chr8:3436473-9972209 ...
    Testing query chr19_random:8309162-8766514 ...
    Testing query chr7_random:6416981-6735864 ...
    Testing query chr19:3484685-3801122 ...
    Testing query chr1:1868925-6151268 ...
    Testing query chr1:536419-4044558 ...
    Testing query chr1:2522877-4924643 ...
    Testing query chr11_random:676633-9128847 ...
    Testing query chr6_random:3598124-6981657 ...
    Testing query chr5_random:7166103-8219161 ...
    Testing query chr19:1684800-5872548 ...
    Testing query chr1_random:3315026-8441262 ...
    Testing query chr18_random:2290355-8594736 ...
    Testing query chr20:3121858-8750525 ...
    Testing query chr5:1854779-7785465 ...
    Testing query chr3:2844488-8229201 ...
    Testing query chr9:98994-6937193 ...
    Testing query chr7_random:566405-4329525 ...
    Testing query chrM:3349123-8858299 ...
    Testing query chr18_random:2476805-3333909 ...
    Testing query chr5_random:2947230-5023103 ...
    Testing query chrY:858711-3764404 ...
    Testing query chrM:3202756-4087290 ...
    Testing query chr3:2241212-3744434 ...
    Testing query chr2:294299-2791063 ...
    Testing query chr16:5636813-7725712 ...
    Testing query chrY:190457-4183568 ...
    Testing query chr15_random:1757556-6243468 ...
    Testing query chr21_random:2404640-9698959 ...
    Testing query chrY:2899895-8525822 ...
    Testing query chr14:5316023-9325638 ...
    Testing query chr5_random:3836137-6496666 ...
    Testing query chr10_random:1992029-2390509 ...
    Testing query chr15:2008393-5397033 ...
    Testing query chr6:3033491-5689013 ...
    Testing query chr13:4802709-6651494 ...
    Testing query chr11_random:1126435-2590416 ...
    Testing query chr14:674415-1741256 ...
    Testing query chr2:5945864-7917088 ...
    Testing query chr4:2984861-4376484 ...
    Testing query chr1_random:5661261-9348854 ...
    Testing query chr18:2892586-9538492 ...
    Testing query chr19_random:2666788-6214501 ...
    Testing query chr5_random:2892340-8892790 ...
    Testing query chr3:8321138-9156829 ...
    Testing query chr20:1010051-2675065 ...
    Testing query chr12:2016127-9734230 ...
    Testing query chr17:6565364-9842724 ...
    Testing query chr2_random:1534009-9935421 ...
    Testing query chr22_random:1798866-3566302 ...
    Testing query chr9_random:2863862-4098636 ...
    Testing query chr7_random:6695702-7166373 ...
    Testing query chr19_random:7774915-8904502 ...
    Testing query chr4_random:1354793-3060860 ...
    Testing query chr16_random:680783-7967813 ...
    Testing query chr22_random:1679274-1962853 ...
    Testing query chr5:1405068-3861785 ...
    Testing query chr8_random:6642950-9011653 ...
    Testing query chr16:1873173-7921837 ...
    Testing query chr7_random:2750681-9520458 ...
    Testing query chr16_random:885218-3713066 ...
    Testing query chr10_random:4952036-9328892 ...
    Testing query chr1_random:1556041-9207413 ...
    Testing query chrX:3509058-4668683 ...
    Testing query chr22_random:5775297-9086853 ...
    Testing query chr1:1171026-6903635 ...
    Testing query chr17_random:706069-7256916 ...
    Testing query chr1:7825983-8559769 ...
    Testing query chr7_random:7709758-9250068 ...
    Testing query chr6:4475592-7218806 ...
    Testing query chr5_random:7263397-7305993 ...
    Testing query chr16_random:5376132-9863064 ...
    Testing query chr5:4383593-4921390 ...
    Testing query chr12:5541381-6329888 ...
    Testing query chr7_random:297473-6191920 ...
    Testing query chr7_random:5797186-6007720 ...
    Testing query chr14:6288978-7147625 ...
    Testing query chrY:3280527-6071425 ...
    Testing query chr2_random:341241-9849655 ...
    Testing query chr18_random:2756400-5124352 ...
    Testing query chr18_random:3245587-6421468 ...
    Testing query chr7_random:1108885-7011416 ...
    Testing query chr19:55506-8032351 ...
    Testing query chr9_random:507759-1925801 ...
    Testing query chr21_random:5641470-6291456 ...
    Testing query chr16_random:2647045-6473932 ...
    Testing query chr3:8883638-9872842 ...
    Testing query chr17:2328196-3652679 ...
    Testing query chr22_random:2297511-5498425 ...
    Testing query chrX_random:3773240-4693054 ...
    Testing query chr13:1575245-9070298 ...
    Testing query chr8_random:5301468-7005527 ...
    Testing query chr4:6535020-9656212 ...
    Testing query chr18:5782944-8199590 ...
    Testing query chr5_random:1102579-7463246 ...
    Testing query chr5:2779653-6802521 ...
    Testing query chr10:99615-2172940 ...
    Testing query chr7:2762506-2870870 ...
    Testing query chr15_random:981768-8907527 ...
    Testing query chr16:436530-5189740 ...
    Testing query chr15:9551545-9569163 ...
    Testing query chr17_random:432471-8074112 ...
    Testing query chr8:4845184-5039976 ...
    Testing query chr7:3531770-6086719 ...
    Testing query chr17:2693356-7185572 ...
    Testing query chr6:6650063-9646384 ...
    Testing query chrY:121317-4718433 ...
    Testing query chr1_random:1003027-1831870 ...
    Testing query chr21:8788645-9420609 ...
    Testing query chr13_random:987064-4341370 ...
    Testing query chr13_random:842466-5111480 ...
    Testing query chrM:7654248-8310027 ...
    Testing query chr2:1532378-3980671 ...
    Testing query chr16_random:2308350-8259941 ...
    Testing query chr18_random:7619793-8200073 ...
    Testing query chr16:908998-6962421 ...
    Testing query chr1_random:4760134-7897692 ...
    Testing query chr4_random:351969-2613223 ...
    Testing query chr16:3482498-9633584 ...
    Testing query chr22:7907949-9933800 ...
    Testing query chr15:5854248-7275283 ...
    Testing query chr14:3664791-8748133 ...
    Testing query chrX:896137-9572469 ...
    Testing query chrX:1865390-3062428 ...
    Testing query chr6:595893-8247348 ...
    Testing query chr9_random:1425130-4402172 ...
    Testing query chr7_random:463001-1378501 ...
    Testing query chr10:5465621-8140677 ...
    Testing query chr22:4007755-6030817 ...
    Testing query chr19:2152758-4285738 ...
    Testing query chrX_random:6197638-7278734 ...
    Testing query chr8_random:2506286-3132074 ...
    Testing query chr3:5088917-6346018 ...
    Testing query chr21_random:709245-2447062 ...
    Testing query chr7_random:2297450-2733491 ...
    Testing query chrX_random:75616-6715390 ...
    Testing query chr14:1451557-9217186 ...
    Testing query chr22:4216648-4273083 ...
    Testing query chr22_random:2900019-9495009 ...
    Testing query chr4:6062237-9450155 ...
    Testing query chr3_random:2205998-8038523 ...
    Testing query chr19:4006735-8497976 ...
    Testing query chrM:4367909-8743630 ...
    Testing query chr1:3235237-5886681 ...
    Testing query chr18:2455071-8918070 ...
    Testing query chr3:715763-7415212 ...
    Testing query chr2_random:3698070-6718252 ...
    Testing query chr10:4035923-8780337 ...
    Testing query chr1_random:4369783-9221375 ...
    Testing query chr11:3488452-9565235 ...
    Testing query chrX:3524615-7110878 ...
    Testing query chr19_random:7779323-8424172 ...
    Testing query chr15_random:910898-4876910 ...
    Testing query chr15_random:1015024-3678499 ...
    Testing query chr9:3393986-9417756 ...
    Testing query chr18_random:857279-9200045 ...
    Testing query chr18:1396324-2772435 ...
    Testing query chr12:5614369-9031405 ...
    Testing query chr5:3780359-4070909 ...
    Testing query chr17:4508678-5389778 ...
    Testing query chr21_random:6972726-7854603 ...
    Testing query chr12:3182535-8039198 ...
    Testing query chr10:3951103-7166395 ...
    Testing query chr5_random:6532707-9837900 ...
    Testing query chr13_random:7985015-9743703 ...
    Testing query chr20:6134113-9969678 ...
    Testing query chrY:1542908-4899134 ...
    Testing query chr19_random:324180-7673324 ...
    Testing query chr22_random:4465119-8807791 ...
    Testing query chr14:4342424-6275354 ...
    Testing query chr21:3393386-7099240 ...
    Testing query chr3_random:2130566-2642809 ...
    Testing query chr1_random:2534189-6047752 ...
    Testing query chrM:3319509-8627744 ...
    Testing query chr4_random:7027413-8546790 ...
    Testing query chr18:5213087-7307044 ...
    Testing query chrX_random:5138706-7179617 ...
    Testing query chr21:1746459-3369825 ...
    Testing query chr17_random:4364489-9952653 ...
    Testing query chr21_random:2852383-6343308 ...
    Testing query chr16:1718072-7027200 ...
    Testing query chr7:2836942-5941970 ...
    Testing query chr21_random:6013526-6739121 ...
    Testing query chr6:2041720-8080188 ...
    Testing query chr20:5614189-8320637 ...
    Testing query chr18:7510033-9259036 ...
    Testing query chr7_random:5464431-5858425 ...
    Testing query chrX_random:2642097-9170108 ...
    Testing query chr21_random:2372613-7228145 ...
    Testing query chr7:7643929-8629915 ...
    Testing query chrM:1496669-3662785 ...
    Testing query chrM:5816559-7988640 ...
    Testing query chr4_random:3216837-5344216 ...
    Testing query chr8_random:7939352-9193364 ...
    Testing query chr11_random:4477474-7119222 ...
    Testing query chr22:1795085-7018163 ...
    Testing query chr2:489045-5507534 ...
    Testing query chr20:228222-2645827 ...
    Testing query chr2_random:6696262-7193942 ...
    Testing query chrX:624678-2022130 ...
    Testing query chr11_random:7420609-7476969 ...
    Testing query chr7_random:35741-8947140 ...
    Testing query chr9:2887670-8574309 ...
    Testing query chr9_random:5022666-8213630 ...
    Testing query chr16_random:2811399-8122673 ...
    Testing query chr19:2563169-2938289 ...
    Testing query chr15_random:3165794-8354108 ...
    Testing query chr1_random:4114915-9235471 ...
    Testing query chr10_random:983161-9480146 ...
    Testing query chr2:5984445-9861542 ...
    Testing query chr21:2955353-3709382 ...
    Testing query chr18:4220403-7713605 ...
    Testing query chr9:5837376-6191557 ...
    Testing query chr18:3760903-6211242 ...
    Testing query chr4:2604919-6869284 ...
    Testing query chr14:8243966-8657979 ...
    Testing query chrX:8572226-9566286 ...
    Testing query chr15_random:1776922-9379642 ...
    Testing query chr11:6484864-9835462 ...
    Testing query chr13_random:2265643-8434104 ...
    Testing query chr18_random:2936640-6667223 ...
    Testing query chr21_random:6212251-8673018 ...
    Testing query chr1_random:1062720-2585432 ...
    Testing query chr21_random:5965453-7655829 ...
    Testing query chrX_random:2147524-2773583 ...
    Testing query chr13_random:368974-2821747 ...
    Testing query chr5_random:1943780-5626512 ...
    Testing query chr20:30472-8431478 ...
    Testing query chr10_random:1574710-2300026 ...
    Testing query chr16_random:5290469-9294719 ...
    Testing query chr22:2213818-3185623 ...
    Testing query chr18:2186838-5554932 ...
    Testing query chr1_random:4416515-6829118 ...
    Testing query chr17_random:4168349-9033195 ...
    Testing query chr4_random:7231065-9006087 ...
    Testing query chr3:6627861-7098084 ...
    Testing query chr21:4791386-7462661 ...
    Testing query chr6:5486440-6497547 ...
    Testing query chr7:7583780-8490132 ...
    Testing query chr15:4167629-9516050 ...
    Testing query chr13:412129-3106131 ...
    Testing query chr6:2242528-3392002 ...
    Testing query chr13:4573366-8565166 ...
    Testing query chr14:1012727-4265512 ...
    Testing query chrX:8331093-8914945 ...
    Testing query chr19:3587675-9174187 ...
    Testing query chr7:296443-1800051 ...
    Testing query chr3:5277077-9767087 ...
    Testing query chr21:7692109-7739057 ...
    Testing query chr11:3448455-8411453 ...
    Testing query chr1_random:2275881-3676442 ...
    Testing query chr4_random:6322956-7587151 ...
    Testing query chr22_random:4609088-7067795 ...
    Testing query chr11:1103974-5115622 ...
    Testing query chr17:8733322-9618772 ...
    Testing query chr5_random:1779768-6935553 ...
    Testing query chr8_random:2538535-9879832 ...
    Testing query chr22:768294-3209930 ...
    Testing query chr22:943981-2330158 ...
    Testing query chr12:4987241-7314877 ...
    Testing query chr2:3120747-6311500 ...
    Testing query chrX:1829150-5592634 ...
    Testing query chr7:795351-9692074 ...
    Testing query chr9:5469158-7108447 ...
    Testing query chr18:1967306-6204810 ...
    Testing query chr4_random:8969152-9598463 ...
    Testing query chr4_random:1579186-2839628 ...
    Testing query chr15:5974419-7281533 ...
    Testing query chr8_random:3609626-6631230 ...
    Testing query chr17:3094989-6618173 ...
    Testing query chr15:1799279-6576530 ...
    Testing query chr3:5157964-8423765 ...
    Testing query chr22_random:2813926-5797993 ...
    Testing query chr2:2248206-3931961 ...
    Testing query chr7:3205910-9801772 ...
    Testing query chr21_random:623490-6775587 ...
    Testing query chrM:8166786-8509161 ...
    Testing query chr17:1804940-2950404 ...
    Testing query chr10_random:2511464-6816559 ...
    Testing query chr21_random:153036-5827934 ...
    Testing query chr2_random:8263243-9685626 ...
    Testing query chr21:1111482-5812333 ...
    Testing query chr8:4290604-9166817 ...
    Testing query chr13:3398929-7913910 ...
    Testing query chr10:4553797-9072246 ...
    Testing query chr20:7207944-7471721 ...
    Testing query chrY:1982521-2897985 ...
    Testing query chr10_random:5100074-7818426 ...
    Testing query chr15:4365944-8388476 ...
    Testing query chr13:50044-8373169 ...
    Testing query chr12:5115399-7648840 ...
    Testing query chr4:2962742-8829366 ...
    Testing query chr6_random:1322565-9235978 ...
    Testing query chr12:6057343-7930326 ...
    Testing query chr3:1612029-2982153 ...
    Testing query chr15:6582900-8591795 ...
    Testing query chr21:5009971-6424414 ...
    Testing query chr6:706279-8162934 ...
    Testing query chr16:3267535-9670332 ...
    Testing query chr16:2694606-3346697 ...
    Testing query chrY:9108749-9339860 ...
    Testing query chr18:1265164-5476362 ...
    Testing query chr8_random:1135765-3131623 ...
    Testing query chr1_random:4068577-5850392 ...
    Testing query chr10_random:8086436-9515610 ...
    Testing query chr12:786080-9272524 ...
    Testing query chr2_random:3529918-9107547 ...
    Testing query chrX:33039-720704 ...
    Testing query chrY:7759964-8753893 ...
    Testing query chr18_random:9023306-9399435 ...
    Testing query chr6:5281117-9258674 ...
    Testing query chr2_random:3737881-7335740 ...
    Testing query chr18_random:486302-3415910 ...
    Testing query chr9_random:4036001-4224366 ...
    Testing query chr1_random:676459-981484 ...
    Testing query chr21:213055-9194219 ...
    Testing query chr3:5273397-7935759 ...
    Testing query chr7:5844019-5928029 ...
    Testing query chr22:4400032-4947008 ...
    Testing query chr1_random:6368632-9050986 ...
    Testing query chr6_random:3521181-8577335 ...
    Testing query chr11_random:4864475-5742060 ...
    Testing query chr9:691952-3618418 ...
    Testing query chr16:5899296-6778697 ...
    Testing query chr16:865613-6607475 ...
    Testing query chr17_random:4739682-6923211 ...
    Testing query chrY:2356621-4914419 ...
    Testing query chr3_random:1842297-6259766 ...
    Testing query chr3_random:5126637-7321281 ...
    Testing query chrX:4209013-9761426 ...
    Testing query chr5_random:4596157-5675945 ...
    Testing query chr21_random:3696079-6024271 ...
    Testing query chr3_random:5067064-8876286 ...
    Testing query chr21_random:5565110-6689301 ...
    Testing query chr21_random:15781-4584722 ...
    Testing query chr1:3346110-7059075 ...
    Testing query chrX:5966696-6933232 ...
    Testing query chr17:5021510-8070334 ...
    Testing query chr6:1149206-6788407 ...
    Testing query chr3_random:3744515-8291994 ...
    Testing query chr2:22996-4588290 ...
    Testing query chr17_random:5326761-6699939 ...
    Testing query chr11_random:2696057-3080563 ...
    Testing query chr9:6885746-7594235 ...
    Testing query chr2:4534733-7295296 ...
    Testing query chr13_random:3998213-9469962 ...
    Testing query chr1_random:5426791-6149949 ...
    Testing query chr9_random:530950-725978 ...
    Testing query chr11:4184033-9403368 ...
    Testing query chr15_random:1456012-6938955 ...
    Testing query chr4:527074-2332486 ...
    Testing query chr15:6231961-6744661 ...
    Testing query chr4_random:1429017-4799661 ...
    Testing query chrX_random:1288951-8906564 ...
    Testing query chr5:203973-5396390 ...
    Testing query chr22_random:6924137-9556382 ...
    Testing query chr13:3692768-5792536 ...
    Testing query chr7_random:4736121-7190035 ...
    Testing query chr19_random:1067060-5424230 ...
    Testing query chr5:4645403-9655346 ...
    Testing query chr21:6194788-9692460 ...
    Testing query chr3_random:6249249-8849610 ...
    Testing query chr1_random:116005-4931104 ...
    Testing query chr9_random:2264542-9177908 ...
    Testing query chr5:1920701-3940100 ...
    Testing query chr19:3510626-6120416 ...
    Testing query chr8_random:1385330-9139475 ...
    Testing query chr5_random:4560385-9932819 ...
    Testing query chr10_random:1546770-4255829 ...
    Testing query chrY:1634712-6195051 ...
    Testing query chr21:1934284-3805640 ...
    Testing query chr10:1098075-1222293 ...
    Testing query chrX:3147440-5915627 ...
    Testing query chr12:644340-9578661 ...
    Testing query chr7:3815107-7552297 ...
    Testing query chr7_random:979254-6592345 ...
    Testing query chr15_random:4031375-9529529 ...
    Testing query chr20:809453-6417655 ...
    Testing query chr3_random:1311668-6592135 ...
    Testing query chr16_random:4796848-9917504 ...
    Testing query chr2:2316239-8809758 ...
    Testing query chr22_random:3700813-7193581 ...
    Testing query chr2_random:5629881-8301170 ...
    Testing query chr2:4292815-5793077 ...
    Testing query chr16:4963697-5732378 ...
    Testing query chr20:1818167-2602981 ...
    Testing query chr13_random:857910-3186701 ...
    Testing query chr8:7828099-7863231 ...
    Testing query chr2:3039751-5869790 ...
    Testing query chr7_random:948462-2258714 ...
    Testing query chr12:2176474-8835346 ...
    Testing query chr4_random:4818082-9335116 ...
    Testing query chr9_random:949590-4937462 ...
    Testing query chr3_random:139177-2147902 ...
    Testing query chr15_random:4086655-7110200 ...
    Testing query chr7:1707937-7031178 ...
    Testing query chr15:6704897-7523233 ...
    Testing query chr8_random:3261310-3388805 ...
    Testing query chr11:4627964-9758513 ...
    Testing query chr3_random:1269243-5807226 ...
    Testing query chr9_random:564250-7036410 ...
    Testing query chr8_random:5129373-5437488 ...
    Testing query chr18:2171501-3304941 ...
    Testing query chr17_random:5747642-6505556 ...
    Testing query chrY:3819311-5517038 ...
    Testing query chr11_random:4980823-9419145 ...
    Testing query chrX:3246258-6297440 ...
    Testing query chr1_random:810216-9835846 ...
    Testing query chr9_random:227030-6294798 ...
    Testing query chr1_random:301295-1576363 ...
    Testing query chr21:4560202-9527465 ...
    Testing query chr11:3926303-4702504 ...
    Testing query chr13_random:4053954-7799426 ...
    Testing query chr8_random:1615788-4228091 ...
    Testing query chrX:5354321-7998054 ...
    Testing query chr5:428791-7222158 ...
    Testing query chrY:5600982-5656729 ...
    Testing query chr4_random:3857931-8313241 ...
    Testing query chr15:1925774-5199208 ...
    Testing query chr11_random:1107850-6997032 ...
    Testing query chr14:2769511-5526141 ...
    Testing query chr22:1129798-7717631 ...
    Testing query chr22_random:2940332-5279177 ...
    Testing query chr9:1067427-1150594 ...
    Testing query chr8:5146545-9541542 ...
    Testing query chr15:7089597-8473958 ...
    Testing query chr12:5527737-5802706 ...
    Testing query chr7:1551097-6396733 ...
    Testing query chr2_random:3022570-3558123 ...
    Testing query chr5_random:385945-6563916 ...
    Testing query chr19_random:3546106-9160937 ...
    Testing query chr15_random:3701260-8137083 ...
    Testing query chr5:1805515-5128679 ...
    Testing query chr10_random:748486-5680503 ...
    Testing query chr18:1342370-7881611 ...
    Testing query chr18_random:770908-6308398 ...
    Testing query chr19:7484581-8473209 ...
    Testing query chr7:4518548-7588072 ...
    Testing query chr9_random:7255308-8443827 ...
    Testing query chrX:5799987-8117438 ...
    Testing query chr14:7540848-8413963 ...
    Testing query chr19_random:2328053-2556284 ...
    Testing query chr16_random:7230921-7518347 ...
    Testing query chr19_random:276347-1547597 ...
    Testing query chr13:765679-7048818 ...
    Testing query chrM:2605992-5897739 ...
    Testing query chrX:7913839-8348655 ...
    Testing query chr2_random:7115229-7577760 ...
    Testing query chr21:7618516-8976664 ...
    Testing query chr10_random:5113402-9511617 ...
    Testing query chr3_random:2749825-6235208 ...
    Testing query chr7_random:4542464-5736534 ...
    Testing query chr22:3287391-8684233 ...
    Testing query chr1:6551268-8138439 ...
    Testing query chr18_random:7072081-7642659 ...
    Testing query chr1_random:375703-2560467 ...
    Testing query chr21:5140483-9431223 ...
    Testing query chr19:320517-7295855 ...
    Testing query chr12:585392-5511186 ...
    Testing query chr18_random:8083366-8235379 ...
    Testing query chr10:126713-1547118 ...
    Testing query chr10:5632955-8746379 ...
    Testing query chr10_random:3676138-6848091 ...
    Testing query chr9:4589897-9207905 ...
    Testing query chr6_random:7846883-9764185 ...
    Testing query chr18_random:4290690-8214747 ...
    Testing query chr13_random:2540819-4559633 ...
    Testing query chr11_random:3861379-5778337 ...
    Testing query chr16_random:1701866-3678380 ...
    Testing query chr15:6359944-8126244 ...
    Testing query chr9_random:3748170-8007098 ...
    Testing query chr9:7943740-9455802 ...
    Testing query chr19_random:1042691-5523628 ...
    Testing query chr1_random:1492517-5228447 ...
    Testing query chr6:5705000-6113711 ...
    Testing query chr20:323999-8013692 ...
    Testing query chr10_random:2403788-4666817 ...
    Testing query chr12:809220-4859122 ...
    Testing query chr7:4626441-6767688 ...
    Testing query chr9:1227373-9861818 ...
    Testing query chr9_random:1646320-4830906 ...
    Testing query chr5:1816686-8010796 ...
    Testing query chr18_random:2978620-4099625 ...
    Testing query chr2:2092284-6363784 ...
    Testing query chr11:6697928-8978854 ...
    Testing query chr15:4328362-7736553 ...
    Testing query chr19:2684370-4694361 ...
    Testing query chr8_random:1549783-2052889 ...
    Testing query chr10_random:343773-5114298 ...
    Testing query chr22:239978-7311092 ...
    Testing query chr10:59830-4498628 ...
    Testing query chr6_random:4394006-8726576 ...
    Testing query chr2:2521493-6006376 ...
    Testing query chrY:174190-248602 ...
    Testing query chr5_random:3175374-3810594 ...
    Testing query chr21:458207-4328406 ...
    Testing query chr7:746735-8755260 ...
    Testing query chr1:8376346-9926832 ...
    Testing query chrX:1558302-6671795 ...
    Testing query chr3:90115-6523026 ...
    Testing query chr17_random:1954593-2055586 ...
    Testing query chr9:2137572-9471850 ...
    Testing query chr18_random:7412031-7927783 ...
    Testing query chr7:2153207-4745373 ...
    Testing query chrX:4532293-8914932 ...
    Testing query chr11:2910609-3421044 ...
    Testing query chr9:6096367-7279687 ...
    Testing query chr3:2070513-7395995 ...
    Testing query chr8_random:835918-1827839 ...
    Testing query chr18:248820-4981110 ...
    Testing query chr11_random:4573607-7438971 ...
    Testing query chrX:4061785-7455437 ...
    Testing query chr3:5179852-5811856 ...
    Testing query chr7_random:3320586-3880101 ...
    Testing query chr22:1201575-8615117 ...
    Testing query chr4:6832003-9027563 ...
    Testing query chr5_random:2075108-2231968 ...
    Testing query chrX_random:59800-714902 ...
    Testing query chrX_random:2828941-5491980 ...
    Testing query chr8:1038109-7255118 ...
    Testing query chr19:564478-5162536 ...
    Testing query chr21:6696589-7247970 ...
    Testing query chr6:918960-1474816 ...
    Testing query chrM:5636321-9968137 ...
    Testing query chr7_random:5485027-5682623 ...
    Testing query chrY:4149126-7271874 ...
    Testing query chrX_random:2119447-7981903 ...
    Testing query chr8:392266-4278110 ...
    Testing query chr15:126791-8741531 ...
    Testing query chrY:1970354-3699838 ...
    Testing query chr16:4070891-8181737 ...
    Testing query chr18_random:1308317-5408953 ...
    Testing query chr9:1486842-2579174 ...
    Testing query chr9_random:3614823-8021197 ...
    Testing query chr19_random:4100590-7401362 ...
    Testing query chr13:9198949-9562213 ...
    Testing query chr13_random:3477250-5979150 ...
    Testing query chr8:702816-7724269 ...
    Testing query chrX:1173848-9916277 ...
    Testing query chr19_random:1528939-7213477 ...
    Testing query chrY:4055178-8006125 ...
    Testing query chr21_random:5600720-8897721 ...
    Testing query chr13:5754292-7802376 ...
    Testing query chr6_random:2337681-6172508 ...
    Testing query chr2:5799739-7134812 ...
    Testing query chrX_random:3353632-6262401 ...
    Testing query chr21:945894-5132876 ...
    Testing query chr18_random:2350673-9531784 ...
    Testing query chr22_random:5048930-8474866 ...
    Testing query chr19:6352226-8501858 ...
    Testing query chr20:3392059-9830746 ...
    Testing query chr16_random:4090981-7752074 ...
    Testing query chr11_random:5905570-6251642 ...
    Testing query chr13:360298-9358487 ...
    Testing query chr6_random:882947-4758560 ...
    Testing query chr11:2340078-2932391 ...
    Testing query chr22_random:2213551-2534609 ...
    Testing query chr21:5841676-5846763 ...
    Testing query chr11_random:4038782-7000307 ...
    Testing query chr6_random:25409-5762752 ...
    Testing query chr16:5928354-8501435 ...
    Testing query chrY:694230-6280406 ...
    Testing query chr11:7243231-8376959 ...
    Testing query chr16_random:7306380-8046651 ...
    Testing query chr16:1271045-7843225 ...
    Testing query chr15:3261152-4143715 ...
    Testing query chr16:3643483-7977448 ...
    Testing query chrM:2682115-4251696 ...
    Testing query chrM:8447185-9660353 ...
    Testing query chr17_random:4662108-9040099 ...
    Testing query chr15:2717869-3422290 ...
    Testing query chr9_random:2276674-4258729 ...
    Testing query chrX_random:975097-5521164 ...
    Testing query chr11:2146529-8617542 ...
    Testing query chr10_random:1180053-8007684 ...
    Testing query chr3_random:3693000-4565796 ...
    Testing query chr11:145445-2682401 ...
    Testing query chr8_random:6750591-7945127 ...
    Testing query chr1:8320362-9511438 ...
    Testing query chr8:7013549-9472948 ...
    Testing query chr13_random:3536637-5003209 ...
    Testing query chr9:6558793-7284938 ...
    Testing query chr21_random:2580219-9412760 ...
    Testing query chr10:406321-2977770 ...
    Testing query chr21:492284-7994828 ...
    Testing query chr8:2657319-7983432 ...
    Testing query chrX:4732048-8043746 ...
    Testing query chr20:3307597-9305376 ...
    Testing query chr2_random:755380-8957174 ...
    Testing query chrY:2933069-9880634 ...
    Testing query chr6:774738-5674081 ...
    Testing query chr22_random:715809-9050909 ...
    Testing query chr4:1349527-3344979 ...
    Testing query chr6:8028105-9684178 ...
    Testing query chr5_random:4787471-8881473 ...
    Testing query chr10_random:2634703-3696440 ...
    Testing query chr11_random:829085-1727870 ...
    Testing query chr15_random:592933-9165180 ...
    Testing query chr4_random:4418610-8898086 ...
    Testing query chrX_random:2431444-6884713 ...
    Testing query chr8_random:6475456-8480814 ...
    Testing query chr7:3815530-7026545 ...
    Testing query chr19:7331585-7602899 ...
    Testing query chr1_random:874465-3320587 ...
    Testing query chr13_random:733794-6825035 ...
    Testing query chr15_random:9014536-9668872 ...
    Testing query chr17_random:6591609-9129777 ...
    Testing query chrM:656068-4356620 ...
    Testing query chr8:405654-9125605 ...
    Testing query chrX:2091850-6675177 ...
    Testing query chr17_random:7703315-8296743 ...
    Testing query chr5:6509082-7915180 ...
    Testing query chr22:2553656-7681295 ...
    Testing query chr14:3268086-7514168 ...
    Testing query chr8:4422671-6192314 ...
    Testing query chr1:65591-912831 ...
    Testing query chr3_random:5754696-6365576 ...
    Testing query chr19:3761804-6226235 ...
    Testing query chr15_random:437782-2343429 ...
    Testing query chr21_random:6464723-8352688 ...
    Testing query chr2:2429164-5768260 ...
    Testing query chr4:470318-7002218 ...
    Testing query chr4:3690943-5461445 ...
    Testing query chr22_random:5183905-6703677 ...
    Testing query chr6:956010-4837181 ...
    Testing query chr22_random:4644999-6726863 ...
    Testing query chr3:461910-2847795 ...
    Testing query chrM:1898841-4804510 ...
    Testing query chr17_random:4508018-9521979 ...
    Testing query chr5_random:324986-2917264 ...
    Testing query chr21_random:5399136-5748620 ...
    Testing query chr22:2778077-4812793 ...
    Testing query chr10:4969555-6126688 ...
    Testing query chr18:1713300-5060476 ...
    Testing query chr13_random:3333348-5290509 ...
    Testing query chr11_random:4081564-5917103 ...
    Testing query chr4_random:5054748-8642850 ...
    Testing query chr1:2326146-4227874 ...
    Testing query chr18:1537257-7925976 ...
    Testing query chr22_random:8252153-8805544 ...
    Testing query chr3_random:1198809-9011283 ...
    Testing query chr17_random:6967406-8885184 ...
    Testing query chr13:1386877-2947412 ...
    Testing query chrM:6757870-7928951 ...
    Testing query chr21:4074861-7649457 ...
    Testing query chrX_random:1019101-6500619 ...
    Testing query chrX:1825987-5504513 ...
    Testing query chr21_random:3186073-5713305 ...
    Testing query chr4:6259611-8028235 ...
    Testing query chr4:1743818-8599191 ...
    Testing query chr17:1858282-6524491 ...
    Testing query chr15_random:4438074-7157093 ...
    Testing query chr3_random:397131-735889 ...
    Testing query chr8:6928096-9944821 ...
    Testing query chr4_random:1300717-4919221 ...
    Testing query chr5_random:338852-4544685 ...
    Testing query chr7_random:9056136-9688355 ...
    Testing query chr13:2503131-3346435 ...
    Testing query chr15_random:4163332-8152391 ...
    Testing query chr11_random:3309623-7440495 ...
    Testing query chr5_random:9256148-9879716 ...
    Testing query chr17_random:1285404-9731324 ...
    Testing query chr11:8839451-9081378 ...
    Testing query chr13:8871343-9845159 ...
    Testing query chr22:4961912-7272246 ...
    Testing query chr7_random:1546612-1704922 ...
    Testing query chr4_random:3988885-5892099 ...
    Testing query chr16:3240803-6856154 ...
    Testing query chr16:217614-7256181 ...
    Testing query chr8_random:9247976-9386452 ...
    Testing query chr3_random:6627763-9791298 ...
    Testing query chr2:2529288-4212123 ...
    Testing query chrX_random:2988973-8007994 ...
    Testing query chr15:7917609-9330719 ...
    Testing query chr11_random:3494062-5554433 ...
    Testing query chr10_random:550231-9169795 ...
    Testing query chrM:2348914-4789264 ...
    Testing query chr10_random:1774094-2022615 ...
    Testing query chrY:1233622-1787356 ...
    Testing query chr16:1423379-2759956 ...
    Testing query chr15_random:2179216-5955676 ...
    Testing query chr13_random:4485355-8258869 ...
    Testing query chr16:1540718-7599890 ...
    Testing query chr16:3470124-5210468 ...
    Testing query chr5_random:2480219-3389498 ...
    Testing query chrX_random:2150354-9183393 ...
    Testing query chr4_random:7326066-8687796 ...
    Testing query chr9_random:778644-7335950 ...
    Testing query chr3_random:117405-711777 ...
    Testing query chr3_random:1627027-5946622 ...
    Testing query chr14:1896619-3058485 ...
    Testing query chr4:361451-8469991 ...
    Testing query chr13:8016007-9409673 ...
    Testing query chr15_random:4902505-9345392 ...
    Testing query chr11_random:7321862-9499733 ...
    Testing query chr4:1033220-5712150 ...
    Testing query chr8:3549734-9090035 ...
    Testing query chrM:5081509-5962772 ...
    Testing query chrX_random:97240-6137606 ...
    Testing query chr8_random:4271059-4291635 ...
    Testing query chrX_random:530035-1682825 ...
    Testing query chr15:2788773-5483281 ...
    Testing query chrX_random:4759178-9377757 ...
    Testing query chrM:3245025-4297984 ...
    Testing query chr19_random:3021529-4576251 ...
    Testing query chr4_random:1397040-5761345 ...
    Testing query chrM:561371-7187972 ...
    Testing query chr22:5413646-8736775 ...
    Testing query chr17_random:1425366-7019792 ...
    Testing query chr3_random:572179-7205526 ...
    Testing query chr5:4328737-9239750 ...
    Testing query chr22:5069432-6659616 ...
    Testing query chr13:48249-7303858 ...
    Testing query chr3:305799-6869287 ...
    Testing query chr21:3873459-5093561 ...
    Testing query chr19:5939843-9027189 ...
    Testing query chr2:5873453-6683127 ...
    Testing query chr22_random:3713598-5598641 ...
    Testing query chr20:179927-8450235 ...
    Testing query chr13_random:8308459-9668938 ...
    Testing query chr11:1199780-7649669 ...
    Testing query chr19:4137076-6447341 ...
    Testing query chrM:78280-8559488 ...
    Testing query chr4:623887-7069138 ...
    Testing query chr16:3039657-4345359 ...
    Testing query chr17:3391405-4744719 ...
    Testing query chr20:2910861-7899348 ...
    Testing query chr19_random:913985-2128081 ...
    Testing query chr22:1426695-8605324 ...
    Testing query chr12:1887213-4358077 ...
    Testing query chrX:5563613-8375913 ...
    Testing query chr7_random:136737-595720 ...
    Testing query chr22:3649338-3715557 ...
    Testing query chr22_random:1857324-2876705 ...
    Testing query chr3_random:1299041-9034999 ...
    Testing query chr15:978485-8350193 ...
    Testing query chr19_random:4068601-6523086 ...
    Testing query chr2:201488-4273604 ...
    Testing query chr19_random:5966187-9871009 ...
    Testing query chrM:1330413-9761840 ...
    Testing query chr7:4263424-8956444 ...
    Testing query chr5:710131-1481160 ...
    Testing query chr22_random:3228001-4696776 ...
    Testing query chr3:64585-1673488 ...
    Testing query chr16:8045346-8459636 ...
    Testing query chr13_random:1741393-4393228 ...
    Testing query chr22_random:2624571-7878001 ...
    Testing query chr20:4312366-7263897 ...
    Testing query chr2_random:792986-9926045 ...
    Testing query chr4:876557-8032416 ...
    Testing query chr7_random:9474728-9775529 ...
    Testing query chrY:196281-2297210 ...
    Testing query chr11_random:1815604-1988691 ...
    Testing query chr17:327462-9941596 ...
    Testing query chr4:1225057-5716342 ...
    Testing query chrX_random:5518830-9291836 ...
    Testing query chr19_random:8850582-9837888 ...
    Testing query chr10_random:906079-4133872 ...
    Testing query chrX:1487717-2363048 ...
    Testing query chrX:315413-7567516 ...
    Testing query chr8_random:6478215-9426080 ...
    Testing query chr20:2999407-4776774 ...
    Testing query chr5_random:1309090-5902755 ...
    Testing query chr4_random:4737388-7952008 ...
    Testing query chr21_random:3092337-5111212 ...
    Testing query chr12:4888197-9051400 ...
    Testing query chr13_random:4483564-5744770 ...
    Testing query chr22_random:54755-6638497 ...
    Testing query chr13_random:5891419-7679795 ...
    Testing query chr12:1730038-8775120 ...
    Testing query chr10:3971454-8725046 ...
    Testing query chr13_random:2420218-3946730 ...
    Testing query chr16_random:6268326-9602951 ...
    Testing query chr15_random:6201359-7624324 ...
    Testing query chr8_random:1897294-5156982 ...
    Testing query chr1:2597385-4514890 ...
    Testing query chrX_random:338730-7953560 ...
    Testing query chr7:5484367-7925032 ...
    Testing query chr5_random:6298235-7470139 ...
    Testing query chr21_random:3834366-4459713 ...
    Testing query chr5:2361767-8905807 ...
    Testing query chrM:3162105-9086123 ...
    Testing query chrX_random:4940689-6482079 ...
    Testing query chr4:4948264-5128137 ...
    Testing query chr3:4207686-7342748 ...
    Testing query chr19_random:2021389-9994958 ...
    Testing query chr18:3680011-9706840 ...
    Testing query chr17_random:5951397-8238603 ...
    Testing query chr15_random:4175461-7481270 ...
    Testing query chr4:498362-9165782 ...
    Testing query chr21:4179687-5159563 ...
    Testing query chr1:5178637-7992880 ...
    Testing query chr15_random:6053128-8149868 ...
    Testing query chr5:4008322-7971530 ...
    Testing query chr19_random:1097409-1939223 ...
    Testing query chr15:7469377-8821183 ...
    Testing query chr11_random:1627957-5387469 ...
    Testing query chr9:5855393-7238773 ...
    Testing query chr22:3055704-4751301 ...
    Testing query chr18_random:2752026-7569770 ...
    Testing query chr6:2659325-3383321 ...
    Testing query chr19_random:6031799-9193165 ...
    Testing query chr10:2867928-7456748 ...
    Testing query chr17:803521-2016747 ...
    Testing query chr11_random:2756837-9309974 ...
    Testing query chr9_random:4932323-6215308 ...
    Testing query chr19_random:1738738-9429398 ...
    Testing query chr4_random:162435-8328176 ...
    Testing query chr17:138893-2694455 ...
    Testing query chrX_random:4137996-9339319 ...
    Testing query chr19:2497402-8914940 ...
    Testing query chr13_random:3513964-5910759 ...
    Testing query chrX:1099583-2639169 ...
    Testing query chr11_random:6266637-8387131 ...
    Testing query chr8_random:3059827-5229064 ...
    Testing query chr6:380960-2560436 ...
    Testing query chr15_random:5618328-6876961 ...
    Testing query chr2_random:3878460-5680854 ...
    Testing query chr8_random:2477614-4148075 ...
    Testing query chr18_random:5415785-8338387 ...
    Testing query chr10_random:8209397-8355863 ...
    Testing query chr11_random:4475489-6604223 ...
    Testing query chr1_random:754948-7226484 ...
    Testing query chr9:2946100-8357028 ...
    Testing query chr15:7199317-8245905 ...
    Testing query chr7_random:7269507-8820498 ...
    Testing query chr16:1621267-2368637 ...
    Testing query chr7_random:2996833-9854987 ...
    Testing query chrM:6484003-6911983 ...
    Testing query chr13:1771424-4738191 ...
    Testing query chr13_random:1828228-4302873 ...
    Testing query chrM:2962858-5957962 ...
    Testing query chr6_random:4242794-9824359 ...
    Testing query chr13:415874-9331256 ...
    Testing query chr8:7417568-9299672 ...
    Testing query chr5_random:6880184-8188312 ...
    Testing query chr10_random:1892176-5188920 ...
    Testing query chr21_random:4076206-6101050 ...
    Testing query chr20:5126731-9990106 ...
    Testing query chr4:3133535-3261569 ...

Gradle suite > Gradle test > htsjdk.samtools.BAMFileReaderTest.testGetIndexTypeOK STANDARD_OUT
    chrM length=	16571	Aligned= 23	Unaligned= 0
    chr1 length=	247249719	Aligned= 885	Unaligned= 0
    chr2 length=	242951149	Aligned= 837	Unaligned= 0
    chr3 length=	199501827	Aligned= 683	Unaligned= 0
    chr4 length=	191273063	Aligned= 633	Unaligned= 0
    chr5 length=	180857866	Aligned= 611	Unaligned= 0
    chr6 length=	170899992	Aligned= 585	Unaligned= 0
    chr7 length=	158821424	Aligned= 521	Unaligned= 0
    chr8 length=	146274826	Aligned= 507	Unaligned= 0
    chr9 length=	140273252	Aligned= 388	Unaligned= 0
    chr10 length=	135374737	Aligned= 477	Unaligned= 0
    chr11 length=	134452384	Aligned= 467	Unaligned= 0
    chr12 length=	132349534	Aligned= 459	Unaligned= 0
    chr13 length=	114142980	Aligned= 327	Unaligned= 0
    chr14 length=	106368585	Aligned= 310	Unaligned= 0
    chr15 length=	100338915	Aligned= 280	Unaligned= 0
    chr16 length=	88827254	Aligned= 278	Unaligned= 0
    chr17 length=	78774742	Aligned= 269	Unaligned= 0
    chr18 length=	76117153	Aligned= 265	Unaligned= 0
    chr19 length=	63811651	Aligned= 178	Unaligned= 0
    chr20 length=	62435964	Aligned= 228	Unaligned= 0
    chr21 length=	46944323	Aligned= 123	Unaligned= 0
    chr22 length=	49691432	Aligned= 121	Unaligned= 0
    chrX length=	154913754	Aligned= 237	Unaligned= 0
    chrY length=	57772954	Aligned= 29	Unaligned= 0
    chr1_random length=	1663265	Aligned= 0	Unaligned= 0
    chr2_random length=	185571	Aligned= 0	Unaligned= 0
    chr3_random length=	749256	Aligned= 0	Unaligned= 0
    chr4_random length=	842648	Aligned= 0	Unaligned= 0
    chr5_random length=	143687	Aligned= 0	Unaligned= 0
    chr6_random length=	1875562	Aligned= 0	Unaligned= 0
    chr7_random length=	549659	Aligned= 0	Unaligned= 0
    chr8_random length=	943810	Aligned= 0	Unaligned= 0
    chr9_random length=	1146434	Aligned= 0	Unaligned= 0
    chr10_random length=	113275	Aligned= 0	Unaligned= 0
    chr11_random length=	215294	Aligned= 0	Unaligned= 0
    chr13_random length=	186858	Aligned= 0	Unaligned= 0
    chr15_random length=	784346	Aligned= 0	Unaligned= 0
    chr16_random length=	105485	Aligned= 0	Unaligned= 0
    chr17_random length=	2617613	Aligned= 0	Unaligned= 0
    chr18_random length=	4262	Aligned= 0	Unaligned= 0
    chr19_random length=	301858	Aligned= 0	Unaligned= 0
    chr21_random length=	1679693	Aligned= 0	Unaligned= 0
    chr22_random length=	257318	Aligned= 0	Unaligned= 0
    chrX_random length=	1719168	Aligned= 0	Unaligned= 0
    NoCoordinateCount= 279

Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT
    #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.6316202909726158902.bai
    #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.7214351699829047750.bai
    #BAMIndexWriterTest diff /tmp/javaBai.6316202909726158902.bai /tmp/cBai.7214351699829047750.bai

Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT
    #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.18264849658027721009.bai.txt
    #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.14892524488975637870java.bai
    #BAMIndexWriterTest diff /tmp/javaBai.14892524488975637870java.bai.txt /tmp/cBai.18264849658027721009.bai.txt

Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT
    1ms to write

Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT
    0ms to write

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT
    Creating file /tmp/BCOST.5822739436573525835.gz

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT
    Creating file /tmp/testCustomDeflater.12033676398621340617.gz

Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT
    Creating file /tmp/BCOST.9599970237255234216.gz

Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR
    WARNING	2023-04-15 20:37:59	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:37:59	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR
    WARNING	2023-04-15 20:37:59	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:37:59	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR
    WARNING	2023-04-15 20:37:59	CRAMReferenceRegion	The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12
    WARNING	2023-04-15 20:37:59	Slice	Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0.
    WARNING	2023-04-15 20:37:59	CRAMReferenceRegion	The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12
    WARNING	2023-04-15 20:37:59	Slice	Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR
    WARNING	2023-04-15 20:38:07	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:38:07	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR
    WARNING	2023-04-15 20:38:08	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:38:08	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR
    WARNING	2023-04-15 20:38:08	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:38:08	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR
    WARNING	2023-04-15 20:38:10	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:38:10	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR
    WARNING	2023-04-15 20:38:10	CRAMReferenceRegion	The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3
    WARNING	2023-04-15 20:38:10	Slice	Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0.
    WARNING	2023-04-15 20:38:10	CRAMReferenceRegion	The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3
    WARNING	2023-04-15 20:38:10	Slice	Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR
    WARNING	2023-04-15 20:38:10	CRAMReferenceRegion	The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2023-04-15 20:38:10	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0.
    WARNING	2023-04-15 20:38:10	CRAMReferenceRegion	The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2023-04-15 20:38:10	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0.
	Gradle is still running, please be patient...

Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR
    WARNING	2023-04-15 20:46:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:46:17	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR
    WARNING	2023-04-15 20:46:19	CRAMReferenceRegion	The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2023-04-15 20:46:19	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0.
    WARNING	2023-04-15 20:46:19	CRAMReferenceRegion	The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37
    WARNING	2023-04-15 20:46:19	Slice	Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0.
	Gradle is still running, please be patient...

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@582bd522, [Ljava.lang.String;@caa8f41) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44a3d299, [Ljava.lang.String;@6739668b) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@22a05d93, [Ljava.lang.String;@1c7e32d3) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c3c3131, [Ljava.lang.String;@407e5f5f) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2a427051, [Ljava.lang.String;@1ad770d0) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@356299bc, [Ljava.lang.String;@13f386b7) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@665925a6, [Ljava.lang.String;@25d00310) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5013d104, [Ljava.lang.String;@68e7a747) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3c19ceb1, [Ljava.lang.String;@10fad6f) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@af66f21, [Ljava.lang.String;@6601bbb3) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5216f766, [Ljava.lang.String;@431dd569) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@19e9e37c, [Ljava.lang.String;@2d3fa2a9) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b8f14fa, [Ljava.lang.String;@7b1dd40a) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@255f82f5, [Ljava.lang.String;@397b0ced) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3fdbfef1, [Ljava.lang.String;@7a5f00a6) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6703fec7, [Ljava.lang.String;@56a12882) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@9bfe307, [Ljava.lang.String;@65c486de) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@56772276, [Ljava.lang.String;@6997921) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e097677, [Ljava.lang.String;@45e781fc) STANDARD_ERROR
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:24	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7a83c7f4) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@794e275d) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@78bbba1) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5271537b) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@59e4b5b2) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5c940ea7) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@3414802c) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@52a54b30) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:25	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2023-04-15 20:57:26	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:26	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:26	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:26	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:26	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:26	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@1ae545a, [Ljava.lang.String;@4ff4f4f0) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@347bae9c, [Ljava.lang.String;@591f4285) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2f659f5e, [Ljava.lang.String;@48dc53ca) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2afbf9a, [Ljava.lang.String;@7f9610ec) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@32a9c94a, [Ljava.lang.String;@3f800989) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3162ce52, [Ljava.lang.String;@3f9ac4c) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@bedb76, [Ljava.lang.String;@60f6c95c) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@18eea31a, [Ljava.lang.String;@7b4fa584) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5e1c36ed, [Ljava.lang.String;@518fed20) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@20b5d878, [Ljava.lang.String;@65ac5755) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5ed5c0ca, [Ljava.lang.String;@496750eb) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@14a63d7b, [Ljava.lang.String;@63f855ce) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5685756a, [Ljava.lang.String;@535fe53f) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d357063, [Ljava.lang.String;@6c2f855a) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f6ddb7c, [Ljava.lang.String;@5e16fbf8) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@308a4181, [Ljava.lang.String;@605fde62) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26198406, [Ljava.lang.String;@144f32b) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@377e8ce5) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@31f6d002) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@23f41714) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@20082682) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7fcf1f25) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@23d3574e) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@2f14e089) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2a04d688) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@65278c46) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7afa3bb6) STANDARD_ERROR
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:27	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@4b412243) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@5402add2) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@51e088f8) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4d15fabd) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3745aaea) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@1ca87b0a) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5ee7c7c5) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@110c5a95) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7e9601ee) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@ccce94) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@6a0a53d4) STANDARD_ERROR
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:28	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@69d567f8) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@718b02c1) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3ac1db4c) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@32bf44) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@71db07a6) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@4d4c55f0) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5e6f56b4) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@543db009) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5bd86542) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.10856787199484071118.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@db50918) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7312ac5a, 5) STANDARD_ERROR
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:29	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR
    WARNING	2023-04-15 20:57:30	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:57:30	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR
    WARNING	2023-04-15 20:57:31	CRAMReferenceRegion	The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000

Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 2, Read name 20FUKAAXX100202:3:27:11250:128353, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 2, Read name 20FUKAAXX100202:3:27:11250:128353, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 3, Read name 20GAVAAXX100126:4:23:2251:22957, Mate Alignment start (9999692) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 3, Read name 20GAVAAXX100126:4:23:2251:22957, Mate Alignment start (9999692) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 4, Read name 20FUKAAXX100202:2:41:20497:197885, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 4, Read name 20FUKAAXX100202:2:41:20497:197885, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 5, Read name 20FUKAAXX100202:7:67:1995:131468, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 5, Read name 20FUKAAXX100202:7:67:1995:131468, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 6, Read name 20GAVAAXX100126:2:64:13726:30107, Mate Alignment start (10000306) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 6, Read name 20GAVAAXX100126:2:64:13726:30107, Mate Alignment start (10000306) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 7, Read name 20FUKAAXX100202:4:43:20796:59238, Mate Alignment start (9999709) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 7, Read name 20FUKAAXX100202:4:43:20796:59238, Mate Alignment start (9999709) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 8, Read name 20GAVAAXX100126:1:23:7794:118351, Mate Alignment start (10000299) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 8, Read name 20GAVAAXX100126:1:23:7794:118351, Mate Alignment start (10000299) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 9, Read name 20GAVAAXX100126:4:68:6400:174077, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 9, Read name 20GAVAAXX100126:4:68:6400:174077, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 10, Read name 20GAVAAXX100126:5:27:13558:117863, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 10, Read name 20GAVAAXX100126:5:27:13558:117863, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 11, Read name 20FUKAAXX100202:1:64:5977:190591, Mate Alignment start (10000296) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 11, Read name 20FUKAAXX100202:1:64:5977:190591, Mate Alignment start (10000296) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 12, Read name 20FUKAAXX100202:8:68:8163:66511, Mate Alignment start (10000285) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 12, Read name 20FUKAAXX100202:8:68:8163:66511, Mate Alignment start (10000285) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 13, Read name 20GAVAAXX100126:2:65:15310:41789, Mate Alignment start (9999670) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 13, Read name 20GAVAAXX100126:2:65:15310:41789, Mate Alignment start (9999670) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 14, Read name 20GAVAAXX100126:7:66:12507:22293, Mate Alignment start (10000236) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 14, Read name 20GAVAAXX100126:7:66:12507:22293, Mate Alignment start (10000236) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 15, Read name 20FUKAAXX100202:4:28:1593:6464, Mate Alignment start (9999607) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 15, Read name 20FUKAAXX100202:4:28:1593:6464, Mate Alignment start (9999607) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 16, Read name 20FUKAAXX100202:3:43:19691:103757, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 16, Read name 20FUKAAXX100202:3:43:19691:103757, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 17, Read name 20FUKAAXX100202:5:24:20426:8780, Mate Alignment start (10000318) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 17, Read name 20FUKAAXX100202:5:24:20426:8780, Mate Alignment start (10000318) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 18, Read name 20GAVAAXX100126:3:43:6705:167739, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 18, Read name 20GAVAAXX100126:3:43:6705:167739, Mate Alignment start (10000257) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 19, Read name 20GAVAAXX100126:3:66:17154:191764, Mate Alignment start (9999760) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 19, Read name 20GAVAAXX100126:3:66:17154:191764, Mate Alignment start (9999760) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 20, Read name 20GAVAAXX100126:6:66:18327:134560, Mate Alignment start (9999694) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 20, Read name 20GAVAAXX100126:6:66:18327:134560, Mate Alignment start (9999694) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 23, Read name 20FUKAAXX100202:5:64:19991:74214, Mate Alignment start (10000274) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 23, Read name 20FUKAAXX100202:5:64:19991:74214, Mate Alignment start (10000274) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 24, Read name 20FUKAAXX100202:2:41:7948:31113, Mate Alignment start (9999705) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 24, Read name 20FUKAAXX100202:2:41:7948:31113, Mate Alignment start (9999705) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 25, Read name 20GAVAAXX100126:8:67:6825:84706, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 25, Read name 20GAVAAXX100126:8:67:6825:84706, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 26, Read name 20FUKAAXX100202:5:46:8200:95675, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 26, Read name 20FUKAAXX100202:5:46:8200:95675, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 27, Read name 20FUKAAXX100202:5:46:8201:95696, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 27, Read name 20FUKAAXX100202:5:46:8201:95696, Mate Alignment start (10000307) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 28, Read name 20FUKAAXX100202:6:5:15635:154535, Mate Alignment start (10000315) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 28, Read name 20FUKAAXX100202:6:5:15635:154535, Mate Alignment start (10000315) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 29, Read name 20FUKAAXX100202:7:41:10752:140666, Mate Alignment start (9999753) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 29, Read name 20FUKAAXX100202:7:41:10752:140666, Mate Alignment start (9999753) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 30, Read name 20GAVAAXX100126:2:23:4627:33063, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 30, Read name 20GAVAAXX100126:2:23:4627:33063, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 31, Read name 20GAVAAXX100126:2:23:4640:33082, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 31, Read name 20GAVAAXX100126:2:23:4640:33082, Mate Alignment start (10000346) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 32, Read name 20GAVAAXX100126:3:25:2015:120007, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 32, Read name 20GAVAAXX100126:3:25:2015:120007, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 33, Read name 20GAVAAXX100126:3:25:2028:120028, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 33, Read name 20GAVAAXX100126:3:25:2028:120028, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 34, Read name 20FUKAAXX100202:5:41:14163:52829, Mate Alignment start (10000260) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 34, Read name 20FUKAAXX100202:5:41:14163:52829, Mate Alignment start (10000260) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 35, Read name 20GAVAAXX100126:7:46:18099:135243, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 35, Read name 20GAVAAXX100126:7:46:18099:135243, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 36, Read name 20GAVAAXX100126:2:47:15498:55100, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 36, Read name 20GAVAAXX100126:2:47:15498:55100, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 37, Read name 20FUKAAXX100202:8:21:4919:132430, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 37, Read name 20FUKAAXX100202:8:21:4919:132430, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 38, Read name 20FUKAAXX100202:3:67:3748:19953, Mate Alignment start (10000279) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 38, Read name 20FUKAAXX100202:3:67:3748:19953, Mate Alignment start (10000279) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 39, Read name 20FUKAAXX100202:2:2:3418:95829, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 39, Read name 20FUKAAXX100202:2:2:3418:95829, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 40, Read name 20FUKAAXX100202:6:5:5332:102974, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 40, Read name 20FUKAAXX100202:6:5:5332:102974, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 41, Read name 20FUKAAXX100202:2:8:7024:145363, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 41, Read name 20FUKAAXX100202:2:8:7024:145363, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 42, Read name 20GAVAAXX100126:3:25:20036:5188, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 42, Read name 20GAVAAXX100126:3:25:20036:5188, Mate Alignment start (9999721) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 43, Read name 20FUKAAXX100202:5:2:4432:167162, Mate Alignment start (9999749) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 43, Read name 20FUKAAXX100202:5:2:4432:167162, Mate Alignment start (9999749) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 44, Read name 20GAVAAXX100126:3:63:6482:2143, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 44, Read name 20GAVAAXX100126:3:63:6482:2143, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 45, Read name 20GAVAAXX100126:3:63:6488:2160, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 45, Read name 20GAVAAXX100126:3:63:6488:2160, Mate Alignment start (10000263) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 48, Read name 20FUKAAXX100202:1:21:2273:66026, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 48, Read name 20FUKAAXX100202:1:21:2273:66026, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 49, Read name 20FUKAAXX100202:1:21:2285:66012, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 49, Read name 20FUKAAXX100202:1:21:2285:66012, Mate Alignment start (10000322) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 50, Read name 20FUKAAXX100202:4:8:13315:108160, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 50, Read name 20FUKAAXX100202:4:8:13315:108160, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 51, Read name 20FUKAAXX100202:2:21:15808:57403, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 51, Read name 20FUKAAXX100202:2:21:15808:57403, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 52, Read name 20FUKAAXX100202:8:41:10876:123643, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 52, Read name 20FUKAAXX100202:8:41:10876:123643, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 53, Read name 20FUKAAXX100202:8:41:10891:123658, Mate Alignment start (10000357) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 53, Read name 20FUKAAXX100202:8:41:10891:123658, Mate Alignment start (10000357) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 54, Read name 20FUKAAXX100202:1:8:10582:193735, Mate Alignment start (9999814) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 54, Read name 20FUKAAXX100202:1:8:10582:193735, Mate Alignment start (9999814) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 55, Read name 20FUKAAXX100202:4:23:20668:198863, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 55, Read name 20FUKAAXX100202:4:23:20668:198863, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 56, Read name 20FUKAAXX100202:3:27:18714:174324, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 56, Read name 20FUKAAXX100202:3:27:18714:174324, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 57, Read name 20GAVAAXX100126:3:3:7922:39057, Mate Alignment start (9999758) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 57, Read name 20GAVAAXX100126:3:3:7922:39057, Mate Alignment start (9999758) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 58, Read name 20GAVAAXX100126:3:26:15712:87893, Mate Alignment start (10000309) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 58, Read name 20GAVAAXX100126:3:26:15712:87893, Mate Alignment start (10000309) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 59, Read name 20GAVAAXX100126:4:23:3530:147535, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 59, Read name 20GAVAAXX100126:4:23:3530:147535, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 60, Read name 20GAVAAXX100126:5:24:17054:156839, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 60, Read name 20GAVAAXX100126:5:24:17054:156839, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 61, Read name 20GAVAAXX100126:5:24:17070:156829, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 61, Read name 20GAVAAXX100126:5:24:17070:156829, Mate Alignment start (10000359) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 62, Read name 20GAVAAXX100126:5:28:14493:46327, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 62, Read name 20GAVAAXX100126:5:28:14493:46327, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 63, Read name 20GAVAAXX100126:5:28:14509:46338, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 63, Read name 20GAVAAXX100126:5:28:14509:46338, Mate Alignment start (10000381) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 64, Read name 20FUKAAXX100202:3:3:19592:17448, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 64, Read name 20FUKAAXX100202:3:3:19592:17448, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 65, Read name 20FUKAAXX100202:5:61:14815:105709, Mate Alignment start (9999813) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 65, Read name 20FUKAAXX100202:5:61:14815:105709, Mate Alignment start (9999813) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 66, Read name 20GAVAAXX100126:2:1:17704:50462, Mate Alignment start (9999830) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 66, Read name 20GAVAAXX100126:2:1:17704:50462, Mate Alignment start (9999830) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 67, Read name 20GAVAAXX100126:2:5:19558:132530, Mate Alignment start (10000310) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 67, Read name 20GAVAAXX100126:2:5:19558:132530, Mate Alignment start (10000310) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 68, Read name 20FUKAAXX100202:2:42:6225:11993, Mate Alignment start (10000403) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 68, Read name 20FUKAAXX100202:2:42:6225:11993, Mate Alignment start (10000403) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 69, Read name 20FUKAAXX100202:1:6:12511:73800, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 69, Read name 20FUKAAXX100202:1:6:12511:73800, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 70, Read name 20FUKAAXX100202:3:3:7237:174227, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 70, Read name 20FUKAAXX100202:3:3:7237:174227, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 71, Read name 20GAVAAXX100126:2:44:2924:108763, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 71, Read name 20GAVAAXX100126:2:44:2924:108763, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 72, Read name 20FUKAAXX100202:5:46:18326:99323, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 72, Read name 20FUKAAXX100202:5:46:18326:99323, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 73, Read name 20FUKAAXX100202:1:41:13026:43433, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 73, Read name 20FUKAAXX100202:1:41:13026:43433, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 74, Read name 20FUKAAXX100202:7:41:10475:81635, Mate Alignment start (10000316) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 74, Read name 20FUKAAXX100202:7:41:10475:81635, Mate Alignment start (10000316) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 75, Read name 20FUKAAXX100202:6:7:6837:63100, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 75, Read name 20FUKAAXX100202:6:7:6837:63100, Mate Alignment start (10000335) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 76, Read name 20FUKAAXX100202:8:41:15613:40512, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 76, Read name 20FUKAAXX100202:8:41:15613:40512, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 77, Read name 20GAVAAXX100126:4:66:5628:46560, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 77, Read name 20GAVAAXX100126:4:66:5628:46560, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 78, Read name 20GAVAAXX100126:2:43:11751:59743, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 78, Read name 20GAVAAXX100126:2:43:11751:59743, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 79, Read name 20GAVAAXX100126:4:6:17284:168594, Mate Alignment start (9999791) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 79, Read name 20GAVAAXX100126:4:6:17284:168594, Mate Alignment start (9999791) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 80, Read name 20FUKAAXX100202:8:41:1273:146353, Mate Alignment start (10000404) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 80, Read name 20FUKAAXX100202:8:41:1273:146353, Mate Alignment start (10000404) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 81, Read name 20FUKAAXX100202:5:43:11657:127515, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 81, Read name 20FUKAAXX100202:5:43:11657:127515, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 82, Read name 20FUKAAXX100202:5:43:11665:127498, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 82, Read name 20FUKAAXX100202:5:43:11665:127498, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 83, Read name 20FUKAAXX100202:1:48:13750:136932, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 83, Read name 20FUKAAXX100202:1:48:13750:136932, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 84, Read name 20FUKAAXX100202:1:2:3754:138352, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 84, Read name 20FUKAAXX100202:1:2:3754:138352, Mate Alignment start (10000379) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 85, Read name 20GAVAAXX100126:7:46:18080:135229, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 85, Read name 20GAVAAXX100126:7:46:18080:135229, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 86, Read name 20FUKAAXX100202:7:22:18885:27661, Mate Alignment start (9999857) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 86, Read name 20FUKAAXX100202:7:22:18885:27661, Mate Alignment start (9999857) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 87, Read name 20GAVAAXX100126:2:68:19001:156273, Mate Alignment start (9999800) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 87, Read name 20GAVAAXX100126:2:68:19001:156273, Mate Alignment start (9999800) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 88, Read name 20GAVAAXX100126:7:23:12948:100075, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 88, Read name 20GAVAAXX100126:7:23:12948:100075, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 89, Read name 20GAVAAXX100126:3:44:17022:23968, Mate Alignment start (9999797) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 89, Read name 20GAVAAXX100126:3:44:17022:23968, Mate Alignment start (9999797) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 90, Read name 20FUKAAXX100202:1:21:6910:153058, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 90, Read name 20FUKAAXX100202:1:21:6910:153058, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 91, Read name 20GAVAAXX100126:4:43:14464:8329, Mate Alignment start (10000409) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 91, Read name 20GAVAAXX100126:4:43:14464:8329, Mate Alignment start (10000409) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 92, Read name 20GAVAAXX100126:4:43:14480:8346, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 92, Read name 20GAVAAXX100126:4:43:14480:8346, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 93, Read name 20FUKAAXX100202:6:27:18144:27680, Mate Alignment start (10000498) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 93, Read name 20FUKAAXX100202:6:27:18144:27680, Mate Alignment start (10000498) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 94, Read name 20GAVAAXX100126:8:44:5555:179202, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 94, Read name 20GAVAAXX100126:8:44:5555:179202, Mate Alignment start (9999834) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 95, Read name 20GAVAAXX100126:5:63:15490:26472, Mate Alignment start (10000395) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 95, Read name 20GAVAAXX100126:5:63:15490:26472, Mate Alignment start (10000395) must be <= reference sequence length (200) on reference 20
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 96, Read name 20FUKAAXX100202:6:24:17640:150063, Mate Alignment start (9999667) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 96, Read name 20FUKAAXX100202:6:24:17640:150063, Mate Alignment start (9999667) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 97, Read name 20FUKAAXX100202:2:46:7154:171464, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 97, Read name 20FUKAAXX100202:2:46:7154:171464, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 98, Read name 20FUKAAXX100202:2:46:7154:171487, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 98, Read name 20FUKAAXX100202:2:46:7154:171487, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 99, Read name 20FUKAAXX100202:3:4:1882:78979, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 99, Read name 20FUKAAXX100202:3:4:1882:78979, Mate Alignment start (10000344) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 100, Read name 20FUKAAXX100202:4:5:13072:190773, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 100, Read name 20FUKAAXX100202:4:5:13072:190773, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 101, Read name 20FUKAAXX100202:8:63:5291:16081, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 101, Read name 20FUKAAXX100202:8:63:5291:16081, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 102, Read name 20GAVAAXX100126:5:48:11843:159383, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 102, Read name 20GAVAAXX100126:5:48:11843:159383, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 103, Read name 20GAVAAXX100126:6:21:4070:89543, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 103, Read name 20GAVAAXX100126:6:21:4070:89543, Mate Alignment start (9999671) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 104, Read name 20GAVAAXX100126:7:44:7446:1891, Mate Alignment start (9999669) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 104, Read name 20GAVAAXX100126:7:44:7446:1891, Mate Alignment start (9999669) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 105, Read name 20FUKAAXX100202:6:67:17100:172461, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 105, Read name 20FUKAAXX100202:6:67:17100:172461, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 106, Read name 20GAVAAXX100126:6:64:2441:17495, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 106, Read name 20GAVAAXX100126:6:64:2441:17495, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 107, Read name 20FUKAAXX100202:1:5:14642:152032, Mate Alignment start (10000246) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 107, Read name 20FUKAAXX100202:1:5:14642:152032, Mate Alignment start (10000246) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 108, Read name 20FUKAAXX100202:4:6:12695:123335, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 108, Read name 20FUKAAXX100202:4:6:12695:123335, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 109, Read name 20FUKAAXX100202:1:61:11336:198565, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 109, Read name 20FUKAAXX100202:1:61:11336:198565, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 110, Read name 20GAVAAXX100126:7:48:10601:51282, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 110, Read name 20GAVAAXX100126:7:48:10601:51282, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 111, Read name 20GAVAAXX100126:8:62:18437:38607, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 111, Read name 20GAVAAXX100126:8:62:18437:38607, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 112, Read name 20GAVAAXX100126:4:7:20111:148814, Mate Alignment start (10000281) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 112, Read name 20GAVAAXX100126:4:7:20111:148814, Mate Alignment start (10000281) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 113, Read name 20FUKAAXX100202:8:43:12077:86650, Mate Alignment start (9999682) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 113, Read name 20FUKAAXX100202:8:43:12077:86650, Mate Alignment start (9999682) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 114, Read name 20GAVAAXX100126:5:25:17399:72164, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 114, Read name 20GAVAAXX100126:5:25:17399:72164, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 117, Read name 20FUKAAXX100202:3:48:16538:10482, Mate Alignment start (10000457) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 117, Read name 20FUKAAXX100202:3:48:16538:10482, Mate Alignment start (10000457) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 118, Read name 20GAVAAXX100126:7:46:11904:195602, Mate Alignment start (10000293) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 118, Read name 20GAVAAXX100126:7:46:11904:195602, Mate Alignment start (10000293) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 121, Read name 20GAVAAXX100126:4:21:14134:132604, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 121, Read name 20GAVAAXX100126:4:21:14134:132604, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 122, Read name 20FUKAAXX100202:5:47:2763:24217, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 122, Read name 20FUKAAXX100202:5:47:2763:24217, Mate Alignment start (9999701) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 123, Read name 20GAVAAXX100126:8:21:2096:123816, Mate Alignment start (9999768) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 123, Read name 20GAVAAXX100126:8:21:2096:123816, Mate Alignment start (9999768) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 126, Read name 20FUKAAXX100202:4:23:7470:195860, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 126, Read name 20FUKAAXX100202:4:23:7470:195860, Mate Alignment start (10000353) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 127, Read name 20GAVAAXX100126:5:5:9475:54882, Mate Alignment start (10000264) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 127, Read name 20GAVAAXX100126:5:5:9475:54882, Mate Alignment start (10000264) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 128, Read name 20GAVAAXX100126:6:68:9971:99340, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 128, Read name 20GAVAAXX100126:6:68:9971:99340, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 20GAVAAXX100126:8:4:2514:172766, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 20GAVAAXX100126:8:4:2514:172766, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 20FUKAAXX100202:8:45:1989:15113, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, Read name 20FUKAAXX100202:8:45:1989:15113, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 131, Read name 20FUKAAXX100202:5:43:9081:11499, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 131, Read name 20FUKAAXX100202:5:43:9081:11499, Mate Alignment start (9999706) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 132, Read name 20GAVAAXX100126:6:2:3042:60022, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 132, Read name 20GAVAAXX100126:6:2:3042:60022, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 133, Read name 20FUKAAXX100202:1:25:16659:142466, Mate Alignment start (9999713) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 133, Read name 20FUKAAXX100202:1:25:16659:142466, Mate Alignment start (9999713) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 134, Read name 20GAVAAXX100126:7:47:6583:18921, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 134, Read name 20GAVAAXX100126:7:47:6583:18921, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 135, Read name 20FUKAAXX100202:8:25:6061:158813, Mate Alignment start (9999688) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 135, Read name 20FUKAAXX100202:8:25:6061:158813, Mate Alignment start (9999688) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 136, Read name 20GAVAAXX100126:8:65:19600:82097, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 136, Read name 20GAVAAXX100126:8:65:19600:82097, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 137, Read name 20GAVAAXX100126:8:65:19610:82077, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 137, Read name 20GAVAAXX100126:8:65:19610:82077, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 138, Read name 20FUKAAXX100202:2:22:8993:175344, Mate Alignment start (9999717) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 138, Read name 20FUKAAXX100202:2:22:8993:175344, Mate Alignment start (9999717) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 139, Read name 20GAVAAXX100126:1:21:7801:54762, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 139, Read name 20GAVAAXX100126:1:21:7801:54762, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 140, Read name 20GAVAAXX100126:4:1:13342:97110, Mate Alignment start (9999743) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 140, Read name 20GAVAAXX100126:4:1:13342:97110, Mate Alignment start (9999743) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 141, Read name 20FUKAAXX100202:3:2:9552:27284, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 141, Read name 20FUKAAXX100202:3:2:9552:27284, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 142, Read name 20FUKAAXX100202:4:3:6934:181831, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 142, Read name 20FUKAAXX100202:4:3:6934:181831, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 143, Read name 20GAVAAXX100126:8:7:2115:102977, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 143, Read name 20GAVAAXX100126:8:7:2115:102977, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 144, Read name 20FUKAAXX100202:5:45:17899:193943, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 144, Read name 20FUKAAXX100202:5:45:17899:193943, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 145, Read name 20FUKAAXX100202:7:24:21385:130712, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 145, Read name 20FUKAAXX100202:7:24:21385:130712, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 146, Read name 20FUKAAXX100202:7:2:15287:105342, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 146, Read name 20FUKAAXX100202:7:2:15287:105342, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 147, Read name 20FUKAAXX100202:2:61:15800:106937, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 147, Read name 20FUKAAXX100202:2:61:15800:106937, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 148, Read name 20GAVAAXX100126:8:41:3599:9555, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 148, Read name 20GAVAAXX100126:8:41:3599:9555, Mate Alignment start (9999698) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 149, Read name 20FUKAAXX100202:1:44:3588:13144, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 149, Read name 20FUKAAXX100202:1:44:3588:13144, Mate Alignment start (10000326) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 150, Read name 20GAVAAXX100126:2:8:6126:168407, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 150, Read name 20GAVAAXX100126:2:8:6126:168407, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 151, Read name 20GAVAAXX100126:2:8:6143:168418, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 151, Read name 20GAVAAXX100126:2:8:6143:168418, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 152, Read name 20FUKAAXX100202:3:28:12160:117165, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 152, Read name 20FUKAAXX100202:3:28:12160:117165, Mate Alignment start (9999722) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 153, Read name 20GAVAAXX100126:4:45:8053:140082, Mate Alignment start (9999604) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 153, Read name 20GAVAAXX100126:4:45:8053:140082, Mate Alignment start (9999604) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 154, Read name 20GAVAAXX100126:6:28:11134:174564, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 154, Read name 20GAVAAXX100126:6:28:11134:174564, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 155, Read name 20GAVAAXX100126:6:28:11146:174578, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 155, Read name 20GAVAAXX100126:6:28:11146:174578, Mate Alignment start (9999697) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 156, Read name 20FUKAAXX100202:8:2:10382:194128, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 156, Read name 20FUKAAXX100202:8:2:10382:194128, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 157, Read name 20FUKAAXX100202:3:61:14021:185070, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 157, Read name 20FUKAAXX100202:3:61:14021:185070, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 158, Read name 20FUKAAXX100202:5:62:19690:9570, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 158, Read name 20FUKAAXX100202:5:62:19690:9570, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 159, Read name 20GAVAAXX100126:1:63:20142:132241, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 159, Read name 20GAVAAXX100126:1:63:20142:132241, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 160, Read name 20GAVAAXX100126:5:5:16399:184379, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 160, Read name 20GAVAAXX100126:5:5:16399:184379, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 161, Read name 20GAVAAXX100126:2:8:11075:186130, Mate Alignment start (10000336) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 161, Read name 20GAVAAXX100126:2:8:11075:186130, Mate Alignment start (10000336) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 162, Read name 20FUKAAXX100202:3:64:18891:180836, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 162, Read name 20FUKAAXX100202:3:64:18891:180836, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 163, Read name 20GAVAAXX100126:6:41:1651:77368, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 163, Read name 20GAVAAXX100126:6:41:1651:77368, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 164, Read name 20FUKAAXX100202:4:24:12641:3924, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 164, Read name 20FUKAAXX100202:4:24:12641:3924, Mate Alignment start (9999704) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 165, Read name 20GAVAAXX100126:1:67:21027:67363, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 165, Read name 20GAVAAXX100126:1:67:21027:67363, Mate Alignment start (9999730) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 166, Read name 20GAVAAXX100126:6:23:2944:66430, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 166, Read name 20GAVAAXX100126:6:23:2944:66430, Mate Alignment start (9999718) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 167, Read name 20FUKAAXX100202:5:27:9785:178062, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 167, Read name 20FUKAAXX100202:5:27:9785:178062, Mate Alignment start (10000338) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 168, Read name 20FUKAAXX100202:7:25:3261:114933, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 168, Read name 20FUKAAXX100202:7:25:3261:114933, Mate Alignment start (9999772) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 169, Read name 20FUKAAXX100202:7:68:14596:106064, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 169, Read name 20FUKAAXX100202:7:68:14596:106064, Mate Alignment start (9999731) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 170, Read name 20GAVAAXX100126:3:27:20408:42852, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 170, Read name 20GAVAAXX100126:3:27:20408:42852, Mate Alignment start (9999751) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 171, Read name 20GAVAAXX100126:5:27:19872:165078, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 171, Read name 20GAVAAXX100126:5:27:19872:165078, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 172, Read name 20GAVAAXX100126:8:46:5544:82405, Mate Alignment start (9999696) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 172, Read name 20GAVAAXX100126:8:46:5544:82405, Mate Alignment start (9999696) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 173, Read name 20FUKAAXX100202:6:5:13733:127380, Mate Alignment start (10000378) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 173, Read name 20FUKAAXX100202:6:5:13733:127380, Mate Alignment start (10000378) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 174, Read name 20FUKAAXX100202:6:61:9436:123634, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 174, Read name 20FUKAAXX100202:6:61:9436:123634, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 175, Read name 20FUKAAXX100202:1:4:6802:198636, Mate Alignment start (9999734) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 175, Read name 20FUKAAXX100202:1:4:6802:198636, Mate Alignment start (9999734) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 176, Read name 20FUKAAXX100202:3:61:2345:190213, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 176, Read name 20FUKAAXX100202:3:61:2345:190213, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 177, Read name 20FUKAAXX100202:7:66:18422:38530, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 177, Read name 20FUKAAXX100202:7:66:18422:38530, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 178, Read name 20FUKAAXX100202:1:1:11716:63554, Mate Alignment start (10000217) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 178, Read name 20FUKAAXX100202:1:1:11716:63554, Mate Alignment start (10000217) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 179, Read name 20FUKAAXX100202:7:2:20791:62084, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 179, Read name 20FUKAAXX100202:7:2:20791:62084, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 180, Read name 20FUKAAXX100202:8:7:11983:56692, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 180, Read name 20FUKAAXX100202:8:7:11983:56692, Mate Alignment start (10000329) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 181, Read name 20GAVAAXX100126:4:62:3221:106888, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 181, Read name 20GAVAAXX100126:4:62:3221:106888, Mate Alignment start (9999712) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 182, Read name 20GAVAAXX100126:4:8:17348:119983, Mate Alignment start (9999711) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 182, Read name 20GAVAAXX100126:4:8:17348:119983, Mate Alignment start (9999711) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 183, Read name 20FUKAAXX100202:4:5:8921:109860, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 183, Read name 20FUKAAXX100202:4:5:8921:109860, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 184, Read name 20FUKAAXX100202:3:61:5334:12201, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 184, Read name 20FUKAAXX100202:3:61:5334:12201, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 185, Read name 20FUKAAXX100202:6:25:20343:31574, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 185, Read name 20FUKAAXX100202:6:25:20343:31574, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 186, Read name 20FUKAAXX100202:6:25:20360:31581, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 186, Read name 20FUKAAXX100202:6:25:20360:31581, Mate Alignment start (9999767) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 187, Read name 20GAVAAXX100126:3:7:12571:28928, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 187, Read name 20GAVAAXX100126:3:7:12571:28928, Mate Alignment start (9999729) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 188, Read name 20GAVAAXX100126:7:45:8702:45252, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 188, Read name 20GAVAAXX100126:7:45:8702:45252, Mate Alignment start (10000303) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 189, Read name 20FUKAAXX100202:4:26:8462:86912, Mate Alignment start (10000373) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 189, Read name 20FUKAAXX100202:4:26:8462:86912, Mate Alignment start (10000373) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 190, Read name 20GAVAAXX100126:8:45:6375:103133, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 190, Read name 20GAVAAXX100126:8:45:6375:103133, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 191, Read name 20FUKAAXX100202:4:23:21082:72960, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 191, Read name 20FUKAAXX100202:4:23:21082:72960, Mate Alignment start (9999741) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 192, Read name 20FUKAAXX100202:4:5:5992:35455, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 192, Read name 20FUKAAXX100202:4:5:5992:35455, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 193, Read name 20GAVAAXX100126:6:4:12978:135278, Mate Alignment start (10000348) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 193, Read name 20GAVAAXX100126:6:4:12978:135278, Mate Alignment start (10000348) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 194, Read name 20GAVAAXX100126:2:5:1838:180237, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 194, Read name 20GAVAAXX100126:2:5:1838:180237, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 195, Read name 20GAVAAXX100126:7:63:11003:164288, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 195, Read name 20GAVAAXX100126:7:63:11003:164288, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 196, Read name 20FUKAAXX100202:3:48:15406:75661, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 196, Read name 20FUKAAXX100202:3:48:15406:75661, Mate Alignment start (10000347) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 197, Read name 20GAVAAXX100126:8:65:18514:117061, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 197, Read name 20GAVAAXX100126:8:65:18514:117061, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 200, Read name 20FUKAAXX100202:4:46:4678:167193, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 200, Read name 20FUKAAXX100202:4:46:4678:167193, Mate Alignment start (9999725) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 201, Read name 20GAVAAXX100126:4:27:15355:60703, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 201, Read name 20GAVAAXX100126:4:27:15355:60703, Mate Alignment start (9999746) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 202, Read name 20FUKAAXX100202:4:63:3107:142967, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 202, Read name 20FUKAAXX100202:4:63:3107:142967, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 203, Read name 20GAVAAXX100126:1:46:17524:10808, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 203, Read name 20GAVAAXX100126:1:46:17524:10808, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 204, Read name 20GAVAAXX100126:2:45:9532:172440, Mate Alignment start (10000366) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 204, Read name 20GAVAAXX100126:2:45:9532:172440, Mate Alignment start (10000366) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 205, Read name 20FUKAAXX100202:4:43:4771:2441, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 205, Read name 20FUKAAXX100202:4:43:4771:2441, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 206, Read name 20FUKAAXX100202:1:23:16512:3262, Mate Alignment start (9999728) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 206, Read name 20FUKAAXX100202:1:23:16512:3262, Mate Alignment start (9999728) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 207, Read name 20GAVAAXX100126:6:66:6108:99558, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 207, Read name 20GAVAAXX100126:6:66:6108:99558, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 208, Read name 20FUKAAXX100202:3:23:19248:42689, Mate Alignment start (10000341) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 208, Read name 20FUKAAXX100202:3:23:19248:42689, Mate Alignment start (10000341) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 209, Read name 20FUKAAXX100202:4:67:19946:84115, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 209, Read name 20FUKAAXX100202:4:67:19946:84115, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 210, Read name 20FUKAAXX100202:4:67:19957:84130, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 210, Read name 20FUKAAXX100202:4:67:19957:84130, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 211, Read name 20GAVAAXX100126:8:46:6721:107141, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 211, Read name 20GAVAAXX100126:8:46:6721:107141, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 212, Read name 20FUKAAXX100202:2:44:11476:56122, Mate Alignment start (10000402) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 212, Read name 20FUKAAXX100202:2:44:11476:56122, Mate Alignment start (10000402) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 213, Read name 20FUKAAXX100202:2:62:3370:172539, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 213, Read name 20FUKAAXX100202:2:62:3370:172539, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 214, Read name 20FUKAAXX100202:5:27:20510:84577, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 214, Read name 20FUKAAXX100202:5:27:20510:84577, Mate Alignment start (9999762) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 215, Read name 20FUKAAXX100202:5:43:10418:69609, Mate Alignment start (10000351) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 215, Read name 20FUKAAXX100202:5:43:10418:69609, Mate Alignment start (10000351) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 216, Read name 20FUKAAXX100202:8:22:10804:10935, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 216, Read name 20FUKAAXX100202:8:22:10804:10935, Mate Alignment start (10000400) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 217, Read name 20FUKAAXX100202:8:28:12970:89358, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 217, Read name 20FUKAAXX100202:8:28:12970:89358, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 218, Read name 20GAVAAXX100126:1:3:9885:16197, Mate Alignment start (10000221) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 218, Read name 20GAVAAXX100126:1:3:9885:16197, Mate Alignment start (10000221) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 219, Read name 20GAVAAXX100126:5:41:2927:129979, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 219, Read name 20GAVAAXX100126:5:41:2927:129979, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 220, Read name 20FUKAAXX100202:6:3:13871:76745, Mate Alignment start (9999759) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 220, Read name 20FUKAAXX100202:6:3:13871:76745, Mate Alignment start (9999759) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 221, Read name 20GAVAAXX100126:8:8:9677:53860, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 221, Read name 20GAVAAXX100126:8:8:9677:53860, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 222, Read name 20GAVAAXX100126:2:7:6406:190923, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 222, Read name 20GAVAAXX100126:2:7:6406:190923, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 225, Read name 20GAVAAXX100126:5:45:7084:89817, Mate Alignment start (9999773) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 225, Read name 20GAVAAXX100126:5:45:7084:89817, Mate Alignment start (9999773) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 226, Read name 20FUKAAXX100202:2:8:8921:13714, Mate Alignment start (9999637) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 226, Read name 20FUKAAXX100202:2:8:8921:13714, Mate Alignment start (9999637) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 227, Read name 20FUKAAXX100202:3:25:5393:174013, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 227, Read name 20FUKAAXX100202:3:25:5393:174013, Mate Alignment start (9999699) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 228, Read name 20GAVAAXX100126:4:61:19483:178175, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 228, Read name 20GAVAAXX100126:4:61:19483:178175, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 229, Read name 20FUKAAXX100202:6:61:13597:167016, Mate Alignment start (9999733) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 229, Read name 20FUKAAXX100202:6:61:13597:167016, Mate Alignment start (9999733) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 230, Read name 20GAVAAXX100126:2:46:9819:189801, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 230, Read name 20GAVAAXX100126:2:46:9819:189801, Mate Alignment start (9999723) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 231, Read name 20GAVAAXX100126:1:47:11960:43085, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 231, Read name 20GAVAAXX100126:1:47:11960:43085, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 232, Read name 20FUKAAXX100202:8:61:8547:37887, Mate Alignment start (10000431) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 232, Read name 20FUKAAXX100202:8:61:8547:37887, Mate Alignment start (10000431) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 233, Read name 20GAVAAXX100126:1:64:13278:136055, Mate Alignment start (10000387) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 233, Read name 20GAVAAXX100126:1:64:13278:136055, Mate Alignment start (10000387) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 234, Read name 20GAVAAXX100126:8:8:10069:1815, Mate Alignment start (10000360) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 234, Read name 20GAVAAXX100126:8:8:10069:1815, Mate Alignment start (10000360) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 235, Read name 20FUKAAXX100202:6:43:12464:95867, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 235, Read name 20FUKAAXX100202:6:43:12464:95867, Mate Alignment start (9999715) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 236, Read name 20GAVAAXX100126:8:4:3360:104730, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 236, Read name 20GAVAAXX100126:8:4:3360:104730, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 237, Read name 20GAVAAXX100126:7:23:5527:173596, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 237, Read name 20GAVAAXX100126:7:23:5527:173596, Mate Alignment start (10000333) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 238, Read name 20FUKAAXX100202:3:63:15601:87681, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 238, Read name 20FUKAAXX100202:3:63:15601:87681, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 239, Read name 20GAVAAXX100126:8:7:19780:99577, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 239, Read name 20GAVAAXX100126:8:7:19780:99577, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 240, Read name 20FUKAAXX100202:7:64:11274:28663, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 240, Read name 20FUKAAXX100202:7:64:11274:28663, Mate Alignment start (10000350) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 241, Read name 20FUKAAXX100202:5:46:7034:130269, Mate Alignment start (9999775) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 241, Read name 20FUKAAXX100202:5:46:7034:130269, Mate Alignment start (9999775) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 242, Read name 20FUKAAXX100202:6:42:13864:97949, Mate Alignment start (9999770) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 242, Read name 20FUKAAXX100202:6:42:13864:97949, Mate Alignment start (9999770) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 243, Read name 20FUKAAXX100202:7:63:12812:59167, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 243, Read name 20FUKAAXX100202:7:63:12812:59167, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 244, Read name 20FUKAAXX100202:3:42:10889:9286, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 244, Read name 20FUKAAXX100202:3:42:10889:9286, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 245, Read name 20FUKAAXX100202:7:44:10464:154941, Mate Alignment start (9999777) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 245, Read name 20FUKAAXX100202:7:44:10464:154941, Mate Alignment start (9999777) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 246, Read name 20GAVAAXX100126:2:62:9149:111864, Mate Alignment start (10000382) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 246, Read name 20GAVAAXX100126:2:62:9149:111864, Mate Alignment start (10000382) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 247, Read name 20GAVAAXX100126:3:6:21157:147419, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 247, Read name 20GAVAAXX100126:3:6:21157:147419, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 248, Read name 20FUKAAXX100202:2:6:7367:104244, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 248, Read name 20FUKAAXX100202:2:6:7367:104244, Mate Alignment start (10000408) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 249, Read name 20GAVAAXX100126:8:23:12150:79883, Mate Alignment start (10000363) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 249, Read name 20GAVAAXX100126:8:23:12150:79883, Mate Alignment start (10000363) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 250, Read name 20GAVAAXX100126:2:66:8843:33721, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 250, Read name 20GAVAAXX100126:2:66:8843:33721, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 251, Read name 20GAVAAXX100126:2:66:8848:33740, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 251, Read name 20GAVAAXX100126:2:66:8848:33740, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 252, Read name 20GAVAAXX100126:2:66:8861:33717, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 252, Read name 20GAVAAXX100126:2:66:8861:33717, Mate Alignment start (10000388) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 253, Read name 20FUKAAXX100202:6:24:9789:119768, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 253, Read name 20FUKAAXX100202:6:24:9789:119768, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 254, Read name 20GAVAAXX100126:4:48:13006:180541, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 254, Read name 20GAVAAXX100126:4:48:13006:180541, Mate Alignment start (9999739) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 255, Read name 20FUKAAXX100202:4:61:14645:192554, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 255, Read name 20FUKAAXX100202:4:61:14645:192554, Mate Alignment start (10000352) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 256, Read name 20GAVAAXX100126:2:27:18806:87123, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 256, Read name 20GAVAAXX100126:2:27:18806:87123, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 257, Read name 20GAVAAXX100126:2:66:8554:80197, Mate Alignment start (9999742) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 257, Read name 20GAVAAXX100126:2:66:8554:80197, Mate Alignment start (9999742) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 258, Read name 20FUKAAXX100202:5:44:18607:97922, Mate Alignment start (10000375) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 258, Read name 20FUKAAXX100202:5:44:18607:97922, Mate Alignment start (10000375) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 259, Read name 20FUKAAXX100202:6:7:20029:86575, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 259, Read name 20FUKAAXX100202:6:7:20029:86575, Mate Alignment start (9999724) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 262, Read name 20GAVAAXX100126:7:28:19343:119692, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 262, Read name 20GAVAAXX100126:7:28:19343:119692, Mate Alignment start (10000324) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 263, Read name 20GAVAAXX100126:8:3:19154:172785, Mate Alignment start (10000444) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 263, Read name 20GAVAAXX100126:8:3:19154:172785, Mate Alignment start (10000444) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 264, Read name 20FUKAAXX100202:4:2:11323:157919, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 264, Read name 20FUKAAXX100202:4:2:11323:157919, Mate Alignment start (9999727) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 265, Read name 20FUKAAXX100202:4:24:20755:63383, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 265, Read name 20FUKAAXX100202:4:24:20755:63383, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 266, Read name 20GAVAAXX100126:6:41:12737:140458, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 266, Read name 20GAVAAXX100126:6:41:12737:140458, Mate Alignment start (10000391) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 267, Read name 20FUKAAXX100202:1:41:8855:77865, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 267, Read name 20FUKAAXX100202:1:41:8855:77865, Mate Alignment start (10000406) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 268, Read name 20FUKAAXX100202:2:7:20289:162172, Mate Alignment start (10000401) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 268, Read name 20FUKAAXX100202:2:7:20289:162172, Mate Alignment start (10000401) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 269, Read name 20FUKAAXX100202:3:5:15184:151247, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 269, Read name 20FUKAAXX100202:3:5:15184:151247, Mate Alignment start (10000349) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 270, Read name 20GAVAAXX100126:5:8:18245:6953, Mate Alignment start (10000327) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 270, Read name 20GAVAAXX100126:5:8:18245:6953, Mate Alignment start (10000327) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 271, Read name 20FUKAAXX100202:3:24:9989:45675, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 271, Read name 20FUKAAXX100202:3:24:9989:45675, Mate Alignment start (9999781) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 272, Read name 20FUKAAXX100202:3:25:21206:43648, Mate Alignment start (9999754) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 272, Read name 20FUKAAXX100202:3:25:21206:43648, Mate Alignment start (9999754) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 273, Read name 20GAVAAXX100126:8:7:10416:22501, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 273, Read name 20GAVAAXX100126:8:7:10416:22501, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 20GAVAAXX100126:8:7:10417:22480, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 20GAVAAXX100126:8:7:10417:22480, Mate Alignment start (9999744) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 20FUKAAXX100202:2:23:12195:137492, Mate Alignment start (10000417) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 275, Read name 20FUKAAXX100202:2:23:12195:137492, Mate Alignment start (10000417) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 276, Read name 20FUKAAXX100202:2:68:14803:9019, Mate Alignment start (10000435) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 276, Read name 20FUKAAXX100202:2:68:14803:9019, Mate Alignment start (10000435) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 277, Read name 20FUKAAXX100202:2:68:1649:5921, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 277, Read name 20FUKAAXX100202:2:68:1649:5921, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 278, Read name 20GAVAAXX100126:6:67:14138:53447, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 278, Read name 20GAVAAXX100126:6:67:14138:53447, Mate Alignment start (10000369) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 279, Read name 20GAVAAXX100126:6:27:17917:125886, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 279, Read name 20GAVAAXX100126:6:27:17917:125886, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 280, Read name 20GAVAAXX100126:6:27:17919:125864, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 280, Read name 20GAVAAXX100126:6:27:17919:125864, Mate Alignment start (10000392) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 281, Read name 20GAVAAXX100126:4:23:11820:142520, Mate Alignment start (9999792) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 281, Read name 20GAVAAXX100126:4:23:11820:142520, Mate Alignment start (9999792) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 282, Read name 20FUKAAXX100202:3:22:1789:82621, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 282, Read name 20FUKAAXX100202:3:22:1789:82621, Mate Alignment start (10000372) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 283, Read name 20GAVAAXX100126:6:21:6652:178712, Mate Alignment start (10000425) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 283, Read name 20GAVAAXX100126:6:21:6652:178712, Mate Alignment start (10000425) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 284, Read name 20FUKAAXX100202:4:43:6140:91204, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 284, Read name 20FUKAAXX100202:4:43:6140:91204, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 285, Read name 20FUKAAXX100202:4:43:6159:91203, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 285, Read name 20FUKAAXX100202:4:43:6159:91203, Mate Alignment start (9999747) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 288, Read name 20GAVAAXX100126:4:28:9009:173490, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 288, Read name 20GAVAAXX100126:4:28:9009:173490, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 289, Read name 20FUKAAXX100202:8:45:1884:47673, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 289, Read name 20FUKAAXX100202:8:45:1884:47673, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 290, Read name 20FUKAAXX100202:8:45:1902:47680, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 290, Read name 20FUKAAXX100202:8:45:1902:47680, Mate Alignment start (9999784) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 293, Read name 20FUKAAXX100202:5:26:19959:88445, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 293, Read name 20FUKAAXX100202:5:26:19959:88445, Mate Alignment start (9999764) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 294, Read name 20FUKAAXX100202:6:26:12485:190127, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 294, Read name 20FUKAAXX100202:6:26:12485:190127, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 295, Read name 20FUKAAXX100202:6:26:12497:190143, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 295, Read name 20FUKAAXX100202:6:26:12497:190143, Mate Alignment start (9999750) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 296, Read name 20FUKAAXX100202:7:67:18360:176157, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 296, Read name 20FUKAAXX100202:7:67:18360:176157, Mate Alignment start (10000361) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 297, Read name 20GAVAAXX100126:3:7:6468:165793, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 297, Read name 20GAVAAXX100126:3:7:6468:165793, Mate Alignment start (10000368) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 298, Read name 20FUKAAXX100202:3:63:14607:69414, Mate Alignment start (10000374) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 298, Read name 20FUKAAXX100202:3:63:14607:69414, Mate Alignment start (10000374) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 299, Read name 20FUKAAXX100202:4:66:18078:75058, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 299, Read name 20FUKAAXX100202:4:66:18078:75058, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 300, Read name 20FUKAAXX100202:4:66:18086:75040, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 300, Read name 20FUKAAXX100202:4:66:18086:75040, Mate Alignment start (10000422) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 301, Read name 20GAVAAXX100126:6:62:12722:64586, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 301, Read name 20GAVAAXX100126:6:62:12722:64586, Mate Alignment start (10000424) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 304, Read name 20FUKAAXX100202:2:65:8299:177086, Mate Alignment start (10000414) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 304, Read name 20FUKAAXX100202:2:65:8299:177086, Mate Alignment start (10000414) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 305, Read name 20FUKAAXX100202:5:1:12372:198214, Mate Alignment start (10000442) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 305, Read name 20FUKAAXX100202:5:1:12372:198214, Mate Alignment start (10000442) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 306, Read name 20GAVAAXX100126:7:44:13710:11047, Mate Alignment start (10000383) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 306, Read name 20GAVAAXX100126:7:44:13710:11047, Mate Alignment start (10000383) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 309, Read name 20FUKAAXX100202:6:27:15343:160627, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 309, Read name 20FUKAAXX100202:6:27:15343:160627, Mate Alignment start (9999796) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 310, Read name 20FUKAAXX100202:8:21:1790:48091, Mate Alignment start (9999943) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 310, Read name 20FUKAAXX100202:8:21:1790:48091, Mate Alignment start (9999943) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 311, Read name 20GAVAAXX100126:4:67:14214:45473, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 311, Read name 20GAVAAXX100126:4:67:14214:45473, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 312, Read name 20GAVAAXX100126:7:45:7524:110161, Mate Alignment start (9999815) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 312, Read name 20GAVAAXX100126:7:45:7524:110161, Mate Alignment start (9999815) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 313, Read name 20GAVAAXX100126:5:27:11481:127142, Mate Alignment start (10000390) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 313, Read name 20GAVAAXX100126:5:27:11481:127142, Mate Alignment start (10000390) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 314, Read name 20GAVAAXX100126:6:41:19998:100609, Mate Alignment start (10000440) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 314, Read name 20GAVAAXX100126:6:41:19998:100609, Mate Alignment start (10000440) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 315, Read name 20GAVAAXX100126:2:41:5807:152808, Mate Alignment start (10000365) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 315, Read name 20GAVAAXX100126:2:41:5807:152808, Mate Alignment start (10000365) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 316, Read name 20GAVAAXX100126:5:67:8769:184399, Mate Alignment start (10000413) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 316, Read name 20GAVAAXX100126:5:67:8769:184399, Mate Alignment start (10000413) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 317, Read name 20GAVAAXX100126:1:1:8996:5944, Mate Alignment start (9999798) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 317, Read name 20GAVAAXX100126:1:1:8996:5944, Mate Alignment start (9999798) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 318, Read name 20GAVAAXX100126:5:42:12694:142155, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 318, Read name 20GAVAAXX100126:5:42:12694:142155, Mate Alignment start (10000420) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 319, Read name 20GAVAAXX100126:7:44:8840:83089, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 319, Read name 20GAVAAXX100126:7:44:8840:83089, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 320, Read name 20FUKAAXX100202:7:26:12026:80165, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 320, Read name 20FUKAAXX100202:7:26:12026:80165, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 321, Read name 20GAVAAXX100126:1:4:21009:20022, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 321, Read name 20GAVAAXX100126:1:4:21009:20022, Mate Alignment start (10000385) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 322, Read name 20FUKAAXX100202:2:68:3792:94879, Mate Alignment start (10000432) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 322, Read name 20FUKAAXX100202:2:68:3792:94879, Mate Alignment start (10000432) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 323, Read name 20GAVAAXX100126:8:25:12361:154123, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 323, Read name 20GAVAAXX100126:8:25:12361:154123, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 324, Read name 20GAVAAXX100126:8:25:12382:154125, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 324, Read name 20GAVAAXX100126:8:25:12382:154125, Mate Alignment start (9999756) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 325, Read name 20GAVAAXX100126:3:65:18493:115113, Mate Alignment start (10000436) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 325, Read name 20GAVAAXX100126:3:65:18493:115113, Mate Alignment start (10000436) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 326, Read name 20FUKAAXX100202:7:67:21244:6474, Mate Alignment start (10000458) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 326, Read name 20FUKAAXX100202:7:67:21244:6474, Mate Alignment start (10000458) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 327, Read name 20FUKAAXX100202:4:46:2349:67300, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 327, Read name 20FUKAAXX100202:4:46:2349:67300, Mate Alignment start (9999771) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 328, Read name 20FUKAAXX100202:4:64:17702:39209, Mate Alignment start (9999785) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 328, Read name 20FUKAAXX100202:4:64:17702:39209, Mate Alignment start (9999785) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 329, Read name 20FUKAAXX100202:1:43:15726:132914, Mate Alignment start (10000377) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 329, Read name 20FUKAAXX100202:1:43:15726:132914, Mate Alignment start (10000377) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 330, Read name 20FUKAAXX100202:6:64:3811:167383, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 330, Read name 20FUKAAXX100202:6:64:3811:167383, Mate Alignment start (10000412) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 331, Read name 20FUKAAXX100202:8:27:7323:75566, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 331, Read name 20FUKAAXX100202:8:27:7323:75566, Mate Alignment start (10000393) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 332, Read name 20GAVAAXX100126:2:28:15360:131557, Mate Alignment start (10000418) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 332, Read name 20GAVAAXX100126:2:28:15360:131557, Mate Alignment start (10000418) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 333, Read name 20GAVAAXX100126:2:66:5383:81213, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 333, Read name 20GAVAAXX100126:2:66:5383:81213, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 334, Read name 20GAVAAXX100126:6:22:11440:95696, Mate Alignment start (9999766) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 334, Read name 20GAVAAXX100126:6:22:11440:95696, Mate Alignment start (9999766) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 335, Read name 20GAVAAXX100126:6:67:12425:123302, Mate Alignment start (9999799) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 335, Read name 20GAVAAXX100126:6:67:12425:123302, Mate Alignment start (9999799) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 336, Read name 20FUKAAXX100202:1:41:1662:13912, Mate Alignment start (10000331) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 336, Read name 20FUKAAXX100202:1:41:1662:13912, Mate Alignment start (10000331) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 337, Read name 20FUKAAXX100202:3:21:19677:162487, Mate Alignment start (10000332) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 337, Read name 20FUKAAXX100202:3:21:19677:162487, Mate Alignment start (10000332) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 340, Read name 20FUKAAXX100202:6:46:13213:95672, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 340, Read name 20FUKAAXX100202:6:46:13213:95672, Mate Alignment start (10000321) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 20GAVAAXX100126:2:67:11830:144272, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 341, Read name 20GAVAAXX100126:2:67:11830:144272, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 342, Read name 20GAVAAXX100126:6:25:11700:156967, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 342, Read name 20GAVAAXX100126:6:25:11700:156967, Mate Alignment start (10000423) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 343, Read name 20GAVAAXX100126:8:2:1530:90452, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 343, Read name 20GAVAAXX100126:8:2:1530:90452, Mate Alignment start (10000415) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 344, Read name 20FUKAAXX100202:1:41:15735:31577, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 344, Read name 20FUKAAXX100202:1:41:15735:31577, Mate Alignment start (9999745) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 345, Read name 20FUKAAXX100202:7:67:19743:72886, Mate Alignment start (10000397) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 345, Read name 20FUKAAXX100202:7:67:19743:72886, Mate Alignment start (10000397) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 346, Read name 20GAVAAXX100126:2:62:5242:113457, Mate Alignment start (10000452) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 346, Read name 20GAVAAXX100126:2:62:5242:113457, Mate Alignment start (10000452) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 347, Read name 20FUKAAXX100202:7:41:10114:15727, Mate Alignment start (9999528) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 347, Read name 20FUKAAXX100202:7:41:10114:15727, Mate Alignment start (9999528) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 348, Read name 20FUKAAXX100202:5:27:14631:113616, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 348, Read name 20FUKAAXX100202:5:27:14631:113616, Mate Alignment start (10000394) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 349, Read name 20FUKAAXX100202:8:26:8051:103852, Mate Alignment start (10000399) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 349, Read name 20FUKAAXX100202:8:26:8051:103852, Mate Alignment start (10000399) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 350, Read name 20GAVAAXX100126:4:1:11639:105967, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 350, Read name 20GAVAAXX100126:4:1:11639:105967, Mate Alignment start (9999769) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21
    Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR
    WARNING	2023-04-15 20:57:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR
    WARNING	2023-04-15 20:57:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:57:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_first_3_bytes STANDARD_ERROR
    Adding chunk: 0 - 1
    Adding chunk: 1 - 2
    Adding chunk: 2 - 3

Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_range_read STANDARD_ERROR
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576
    Adding chunk: 0 - 100
    Adding chunk: 10 - 20
    Adding chunk: 100 - 200
    Adding chunk: 1048575 - 1048576

Gradle suite > Gradle test > htsjdk.samtools.cram.build.CramIOTest.testCheckHeaderAndEOF SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.build.CramIOTest.testRejectUnknownCRAMVersion SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest STANDARD_ERROR
    Resetting tmpdir

Gradle suite > Gradle test STANDARD_ERROR
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.2612924213616438796.tmp
    Resetting tmpdir

Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    WARNING	2023-04-15 20:58:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR
    WARNING	2023-04-15 20:58:27	AsciiLineReader	Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2023-04-15 20:58:30	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2023-04-15 20:58:30	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200
    WARNING	2023-04-15 20:58:31	Gff3Codec	ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200

Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR
    WARNING	2023-04-15 20:58:32	ExperimentalEncoding	Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec

Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR
    WARNING	2023-04-15 20:58:32	ExperimentalEncoding	Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79db7c6d, [Ljava.lang.String;@4a2a265c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15624c9b, [Ljava.lang.String;@f6d62d0) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@1b222438) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@b4e9a3a) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@168699c3) STANDARD_ERROR
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:33	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@448239e6) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@22888154) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7f6da889) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@78132c4c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3a043e0) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@2df01754, [Ljava.lang.String;@36afe5c4) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5ea9bc27, [Ljava.lang.String;@2bac3d16) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4c355044, [Ljava.lang.String;@1ac84b6) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@b8b881f, [Ljava.lang.String;@53a7f48a) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1ce93e47, [Ljava.lang.String;@4cc79d2) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@54423633, [Ljava.lang.String;@45155037) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@64154380, [Ljava.lang.String;@6458657c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@76b8d38e, [Ljava.lang.String;@2f71501c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1418f2b0, [Ljava.lang.String;@162c2e72) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@65bd22e6, [Ljava.lang.String;@4f768f74) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b64b8a2, [Ljava.lang.String;@2b423f1d) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2880d433, [Ljava.lang.String;@1cf5d635) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f85abc6, [Ljava.lang.String;@6a20d0a6) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c1068bd, [Ljava.lang.String;@1dd9c531) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2dcc17ec, [Ljava.lang.String;@380eb6b9) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a373b2, [Ljava.lang.String;@76347cd0) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4590f798, [Ljava.lang.String;@316d71bd) STANDARD_ERROR
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:34	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:35	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:36	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@474b67ea) STANDARD_ERROR
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@5fd0ac6f) STANDARD_ERROR
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@31dff7e9) STANDARD_ERROR
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@5a38aa93) STANDARD_ERROR
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1c84442e) STANDARD_ERROR
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:37	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@756d08d1, [Ljava.lang.String;@7c5944f3) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@24aaa8d7, [Ljava.lang.String;@5a19531b) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36adce57, [Ljava.lang.String;@1d70329a) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@253d84d5, [Ljava.lang.String;@73d78946) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@300df2a0, [Ljava.lang.String;@6678e314) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@75c28e90, [Ljava.lang.String;@1f773ee8) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6cf78ce4, [Ljava.lang.String;@5e91d944) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d33396d, [Ljava.lang.String;@4ca9622e) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3db7994, [Ljava.lang.String;@331b9573) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d3a2727, [Ljava.lang.String;@7e25134d) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d55d3bc, [Ljava.lang.String;@3382b8fa) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68e4c3d2, [Ljava.lang.String;@1f54b7b2) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@19818297, [Ljava.lang.String;@33e74bbc) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6c96caf1, [Ljava.lang.String;@5b42fa37) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1cc19288, [Ljava.lang.String;@7f91c020) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b47d139, [Ljava.lang.String;@25da8d79) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@590e97c8, [Ljava.lang.String;@39676360) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@b43a0df) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@9b92374) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@65b18042) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@3636382d) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@634f4b23) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@6d424968) STANDARD_ERROR
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:38	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@7f9ffa5c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.11905955962839757178.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@279d063c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@263878a7) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5e7e2436) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@54dc03f5) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@40322c5b) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@5f6f17b0) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@66361e3c) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@249ece71) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@38c2aa61) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4e2ce77) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@23478cd6, 5) STANDARD_ERROR
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:39	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 20:58:40	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 20:58:40	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27569801, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3be86de5], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2023-04-15 20:58:40	HtsCodecResolver	The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2023-04-15 20:58:40	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@521a8e42, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@c5571, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@37e8e1f4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@d204f1e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@43e4ebde], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2023-04-15 20:58:40	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@521a8e42, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@c5571, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@37e8e1f4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@d204f1e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@43e4ebde], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2023-04-15 20:58:40	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)

Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@521a8e42, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@c5571, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@37e8e1f4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@d204f1e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@43e4ebde], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR
    WARNING	2023-04-15 20:58:40	HtsCodecResolver	The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS)
some stuff
Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR
    Could not delete file tmp
    Could not delete file file9227409577832541277.bad

Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT
    Time to construct a tree with 50000 nodes: 69 milliseconds
    Queried for the same 100-length mapping 82793780 times in 10 seconds.

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95)
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95)

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051	+	.) STANDARD_OUT
    Diagnosing chr3:50911035-50911051	+	. (len 17)
    chr3:50911035-50911051	+	null intersection null (len 17)=>chr3:50936014-50936030	+	.(+) using chain 3 ; pct matched 0.9411765

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[1](chr2:111013693-111013832	+	.) STANDARD_OUT
    Diagnosing chr2:111013693-111013832	+	. (len 140)
    chr2:111013693-111013832	+	null intersection null (len 140)=>null using chain 1
    chr2:111013693-111013832	+	null intersection null (len 140)=>chr2:108482693-108482783	-	.(-) using chain 53 ; pct matched 0.65
    chr2:111013693-111013832	+	null intersection null (len 140)=>chr2:113152284-113152332	+	.(+) using chain 310 ; pct matched 0.35

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[2](chr3:14174511-14175398	+	.) STANDARD_OUT
    Diagnosing chr3:14174511-14175398	+	. (len 888)
    chr3:14174511-14175398	+	null intersection null (len 888)=>chr3:14199509-14200394	+	.(+) using chain 3 ; pct matched 0.9166667

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[3](chr3:50911035-50911051	+	.) STANDARD_OUT
    Diagnosing chr3:50911035-50911051	+	. (len 17)
    chr3:50911035-50911051	+	null intersection null (len 17)=>chr3:50936014-50936030	+	.(+) using chain 3 ; pct matched 0.9411765

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[4](chr6:32071709-32071869	+	.) STANDARD_OUT
    Diagnosing chr6:32071709-32071869	+	. (len 161)
    chr6:32071709-32071869	+	null intersection null (len 161)=>chr6:31963730-31963890	+	.(+) using chain 6 ; pct matched 0.89440995

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[5](chr6:32072183-32072358	+	.) STANDARD_OUT
    Diagnosing chr6:32072183-32072358	+	. (len 176)
    chr6:32072183-32072358	+	null intersection null (len 176)=>chr6:31964204-31964379	+	.(+) using chain 6 ; pct matched 0.90909094

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[6](chr6:32104446-32104606	+	.) STANDARD_OUT
    Diagnosing chr6:32104446-32104606	+	. (len 161)
    chr6:32104446-32104606	+	null intersection null (len 161)=>chr6:31996468-31996628	+	.(+) using chain 6 ; pct matched 0.89440995

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[7](chr6:32104920-32105095	+	.) STANDARD_OUT
    Diagnosing chr6:32104920-32105095	+	. (len 176)
    chr6:32104920-32105095	+	null intersection null (len 176)=>chr6:31996942-31997117	+	.(+) using chain 6 ; pct matched 0.90909094

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[8](chr7:101995561-101995739	+	.) STANDARD_OUT
    Diagnosing chr7:101995561-101995739	+	. (len 179)
    chr7:101995561-101995739	+	null intersection null (len 179)=>chr7:102208488-102208633	+	.(+) using chain 7 ; pct matched 0.8156425

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[9](chr7:142178782-142178825	+	.) STANDARD_OUT
    Diagnosing chr7:142178782-142178825	+	. (len 44)
    chr7:142178782-142178825	+	null intersection null (len 44)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[10](chr7:142179850-142180013	+	.) STANDARD_OUT
    Diagnosing chr7:142179850-142180013	+	. (len 164)
    chr7:142179850-142179857	+	null intersection null (len 8)=>chr7:142479907-142479914	+	.(+) using chain 31548103 ; pct matched 0.048780486
    chr7:142179946-142180009	+	null intersection null (len 64)=>chr7:142480003-142480066	+	.(+) using chain 30171758 ; pct matched 0.3902439
    chr7:142179850-142180013	+	null intersection null (len 164)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[11](chr7:142181067-142181324	+	.) STANDARD_OUT
    Diagnosing chr7:142181067-142181324	+	. (len 258)
    chr7:142181067-142181324	+	null intersection null (len 258)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[12](chr7:142181720-142181860	+	.) STANDARD_OUT
    Diagnosing chr7:142181720-142181860	+	. (len 141)
    chr7:142181720-142181860	+	null intersection null (len 141)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[13](chr7:142182157-142182313	+	.) STANDARD_OUT
    Diagnosing chr7:142182157-142182313	+	. (len 157)
    chr7:142182157-142182313	+	null intersection null (len 157)=>null using chain 7

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[14](chr15:19335778-19336302	+	.) STANDARD_OUT
    Diagnosing chr15:19335778-19336302	+	. (len 525)
    chr15:19335778-19336302	+	null intersection null (len 525)=>chr15:21071199-21071612	+	.(+) using chain 16 ; pct matched 0.7885714
    chr15:19335778-19336302	+	null intersection null (len 525)=>null using chain 110

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[15](chr17:33364376-33364428	+	.) STANDARD_OUT
    Diagnosing chr17:33364376-33364428	+	. (len 53)
    chr17:33364376-33364428	+	null intersection null (len 53)=>chr17:36289992-36290044	+	.(+) using chain 18 ; pct matched 0.3207547
    chr17:33364385-33364428	+	null intersection null (len 44)=>chr17:36342590-36342625	-	.(-) using chain 363 ; pct matched 0.6792453

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[16](chr17:33546162-33546214	+	.) STANDARD_OUT
    Diagnosing chr17:33546162-33546214	+	. (len 53)
    chr17:33546162-33546214	+	null intersection null (len 53)=>null using chain 18
    chr17:33546162-33546214	+	null intersection null (len 53)=>null using chain 1564
    chr17:33546162-33546214	+	null intersection null (len 53)=>chr17:36289992-36290044	-	.(-) using chain 363 ; pct matched 0.3207547
    chr17:33546162-33546214	+	null intersection null (len 53)=>chr17:36342590-36342625	+	.(+) using chain 1571 ; pct matched 0.6792453

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[17](chr17:33706667-33706736	+	.) STANDARD_OUT
    Diagnosing chr17:33706667-33706736	+	. (len 70)
    chr17:33706667-33706736	+	null intersection null (len 70)=>chr17:36453148-36453217	+	.(+) using chain 18 ; pct matched 0.75714284

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[18](chr17:59772721-59772781	+	.) STANDARD_OUT
    Diagnosing chr17:59772721-59772781	+	. (len 61)
    chr17:59772721-59772781	+	null intersection null (len 61)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[19](chr17:59779355-59779421	+	.) STANDARD_OUT
    Diagnosing chr17:59779355-59779421	+	. (len 67)
    chr17:59779355-59779421	+	null intersection null (len 67)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[20](chr17:59781483-59781540	+	.) STANDARD_OUT
    Diagnosing chr17:59781483-59781540	+	. (len 58)
    chr17:59781483-59781540	+	null intersection null (len 58)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[21](chr17:59783488-59783565	+	.) STANDARD_OUT
    Diagnosing chr17:59783488-59783565	+	. (len 78)
    chr17:59783488-59783565	+	null intersection null (len 78)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[22](chr17:59784584-59784615	+	.) STANDARD_OUT
    Diagnosing chr17:59784584-59784615	+	. (len 32)
    chr17:59784584-59784615	+	null intersection null (len 32)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[23](chr17:59786025-59786136	+	.) STANDARD_OUT
    Diagnosing chr17:59786025-59786136	+	. (len 112)
    chr17:59786025-59786136	+	null intersection null (len 112)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[24](chr17:59787203-59787494	+	.) STANDARD_OUT
    Diagnosing chr17:59787203-59787494	+	. (len 292)
    chr17:59787203-59787494	+	null intersection null (len 292)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[25](chr17:59791235-59791514	+	.) STANDARD_OUT
    Diagnosing chr17:59791235-59791514	+	. (len 280)
    chr17:59791235-59791514	+	null intersection null (len 280)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[26](chr17:59794247-59794502	+	.) STANDARD_OUT
    Diagnosing chr17:59794247-59794502	+	. (len 256)
    chr17:59794247-59794502	+	null intersection null (len 256)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[27](chr17:59801884-59802193	+	.) STANDARD_OUT
    Diagnosing chr17:59801884-59802193	+	. (len 310)
    chr17:59801884-59802193	+	null intersection null (len 310)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[28](chr17:59804685-59804982	+	.) STANDARD_OUT
    Diagnosing chr17:59804685-59804982	+	. (len 298)
    chr17:59804685-59804982	+	null intersection null (len 298)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[29](chr17:59817352-59817382	+	.) STANDARD_OUT
    Diagnosing chr17:59817352-59817382	+	. (len 31)
    chr17:59817352-59817382	+	null intersection null (len 31)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[30](chr17:59817465-59817532	+	.) STANDARD_OUT
    Diagnosing chr17:59817465-59817532	+	. (len 68)
    chr17:59817465-59817532	+	null intersection null (len 68)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[31](chr17:59875754-59875812	+	.) STANDARD_OUT
    Diagnosing chr17:59875754-59875812	+	. (len 59)
    chr17:59875754-59875812	+	null intersection null (len 59)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[32](chr17:59875899-59875944	+	.) STANDARD_OUT
    Diagnosing chr17:59875899-59875944	+	. (len 46)
    chr17:59875899-59875944	+	null intersection null (len 46)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[33](chr17:59879183-59879456	+	.) STANDARD_OUT
    Diagnosing chr17:59879183-59879456	+	. (len 274)
    chr17:59879183-59879456	+	null intersection null (len 274)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[34](chr17:59883988-59884276	+	.) STANDARD_OUT
    Diagnosing chr17:59883988-59884276	+	. (len 289)
    chr17:59883988-59884276	+	null intersection null (len 289)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[35](chr17:59887398-59887512	+	.) STANDARD_OUT
    Diagnosing chr17:59887398-59887512	+	. (len 115)
    chr17:59887398-59887512	+	null intersection null (len 115)=>null using chain 18

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058	+	.) STANDARD_OUT
    Diagnosing chrX:48774611-48775058	+	. (len 448)
    chrX:48774611-48775058	+	null intersection null (len 448)=>null using chain 8

Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051	+	., null) STANDARD_ERROR
    INFO	2023-04-15 20:58:58	LiftOver	Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95)
	Gradle is still running, please be patient...

Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT
    read_28833_29006_6945	0	chr21	28833	255	36M	*	0	0	AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA	?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2<	RG:Z:1

    read_28833_29006_6945	0	chr21	30000	255	36M	*	0	0	AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA	?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2<	RG:Z:1

    read_28701_28881_323b	0	chrX	28834	255	36M	*	0	0	GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG	$>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O	RG:Z:1

    read_28701_28881_323b	0	chrX	28835	255	36M	*	0	0	GCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAG	$>8BE+:L!M$K(L*MQ>PO8N*8>;;=5IA>B,*O	RG:Z:1

    read_28701_28881_323c	0	chrX	28835	255	36M	*	0	0	CTCAACGTATTCATACAGGCCCTTTTCGAATAGCTG	%$=LPJ?D6&@R!"KJCOI+05?>>J9CJ)'@-O>K	RG:Z:1


Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaReadOrderMultiIterator STANDARD_OUT
    a
    b
    c
    d
    e

Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT
    d
    e
    b
    a
    c

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD	VN:1.0	SO:UNSORTED
) STANDARD_ERROR
    WARNING	2023-04-15 21:00:29	SAMTextHeaderCodec	Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD	VN:1.0	SO:FALSE
) STANDARD_ERROR
    WARNING	2023-04-15 21:00:29	SAMTextHeaderCodec	Found non-conforming header SO tag: FALSE. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD	VN:1.0	SO:COORDINATE
) STANDARD_ERROR
    WARNING	2023-04-15 21:00:29	SAMTextHeaderCodec	Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD	VN:1.0	SO:uNknOWn
) STANDARD_ERROR
    WARNING	2023-04-15 21:00:29	SAMTextHeaderCodec	Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD	VN:1.0	SO:cOoRdinate
) STANDARD_ERROR
    WARNING	2023-04-15 21:00:29	SAMTextHeaderCodec	Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'.

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR
    WARNING	2023-04-15 21:00:29	SAMFileWriterFactory	Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null
    WARNING	2023-04-15 21:00:29	SAMFileWriterFactory	Cannot create index for BAM because output file is not a regular file: file:///dev/null

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Reference fasta is not provided when writing CRAM file file:///tmp/tmp.18344873186284324105..cram
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Will attempt to use a default reference or download as set by defaults:
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension4191947237184900807.cram

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.1837960758651599533.bam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension8759017870903384463.cram
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Will attempt to use a default reference or download as set by defaults:
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension17379070012332037439

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension18381067932780119732.png

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://f6ffcda5-c652-4efb-834b-4ba68351f1f9/work/testMakeWriterPathsam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://a1e1f994-8e9f-4aac-9ad6-ecadb005e9d8/work/testMakeWriterPathbam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://90e577f5-6c12-41b8-93d6-61b880186b9c/work/testMakeWriterPathcram
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://8dd8f0d5-e53f-4711-9369-fc4803eb6146/work/testMakeWriterPathsam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://249a8ae5-d9ad-4d2d-9a89-31b601e88077/work/testMakeWriterPathbam
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR
    INFO	2023-04-15 21:00:29	SAMFileWriterFactory	Unknown file extension, assuming BAM format when writing file: jimfs://5f92455c-ffc1-4eb3-9f3a-dafc182a4a4b/work/testMakeWriterPathcram
    Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line:
    @RG	ID:1

Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR
    ERROR	2023-04-15 21:00:49	SAMSequenceDictionary	Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2.

Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR
    WARNING	2023-04-15 21:00:50	SamFiles	The index file /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam
    WARNING	2023-04-15 21:00:50	SamFiles	The index file /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR
    INFO	2023-04-15 21:00:53	CustomReaderFactory	Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory
    INFO	2023-04-15 21:00:53	CustomReaderFactory	Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory
    INFO	2023-04-15 21:00:53	CustomReaderFactory	Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from  this jar
    INFO	2023-04-15 21:00:53	SamReaderFactoryTest	Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR
    INFO	2023-04-15 21:00:53	SamReaderFactoryTest	Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ...

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR
    INFO	2023-04-15 21:00:54	SamReaderFactoryTest	Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ...
    INFO	2023-04-15 21:00:54	SamReaderFactoryTest	Finished queries in 114ms

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:54	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR
    WARNING	2023-04-15 21:00:54	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR
    WARNING	2023-04-15 21:00:54	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR
    WARNING	2023-04-15 21:00:54	SamReaderFactory	Unable to detect file format from input URL or stream, assuming SAM format.

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TN
    WARNING	2023-04-15 21:00:55	CompressionHeaderEncodingMap	Ignoring obsolete CRAM dataseries: TC

Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	BAMRecordCodec	Reference length is too large for BAM bin field.
    WARNING	2023-04-15 21:00:55	BAMRecordCodec	Reads on references longer than 536870912bp will have bin set to 0.

Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR
    WARNING	2023-04-15 21:00:55	BAMRecordCodec	Reference length is too large for BAM bin field.
    WARNING	2023-04-15 21:00:55	BAMRecordCodec	Reads on references longer than 536870912bp will have bin set to 0.

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED

Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index.
    WARNING	2023-04-15 21:00:56	CRAMCompressionRecord	CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index.

Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR
    WARNING	2023-04-15 21:00:56	CRAMReferenceRegion	The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20
    WARNING	2023-04-15 21:00:56	Slice	Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0.

Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR
    Resetting tmpdir

Gradle suite > Gradle test STANDARD_ERROR
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
    Resetting tmpdir
Gradle Test Executor 1 finished executing tests.
WARNING: A terminally deprecated method in java.lang.System has been called
WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar)
WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker
WARNING: System::setSecurityManager will be removed in a future release
Finished generating test XML results (0.51 secs) into: /build/htsjdk-3.0.4+dfsg/build/test-results/test
Generating HTML test report...
Finished generating test html results (0.62 secs) into: /build/htsjdk-3.0.4+dfsg/build/reports/tests/test
:test (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 31 mins 20.236 secs.

BUILD SUCCESSFUL in 32m 11s
7 actionable tasks: 5 executed, 2 up-to-date
make[1]: Map '/build/htsjdk-3.0.4+dfsg' wordt verlaten
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=gradle
   dh_prep -O--buildsystem=gradle
	rm -f -- debian/libhtsjdk-java.substvars debian/libhtsjdk-java-doc.substvars
	rm -fr -- debian/.debhelper/generated/libhtsjdk-java/ debian/libhtsjdk-java/ debian/tmp/ debian/.debhelper/generated/libhtsjdk-java-doc/ debian/libhtsjdk-java-doc/
   dh_auto_install -O--buildsystem=gradle
	install -m0755 -d /build/htsjdk-3.0.4\+dfsg/debian/tmp
   dh_install -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/usr/share/libhtsjdk-java
	cp --reflink=auto -a ./scripts/explain_sam_flags.py debian/libhtsjdk-java/usr/share/libhtsjdk-java/
   jh_installjavadoc -O--buildsystem=gradle
	Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java
	cp -r build/docs/javadoc debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/
	cat > debian/libhtsjdk-java-doc.doc-base.javadoc
   dh_installdocs -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java
	install -p -m0644 debian/libhtsjdk-java.README.Debian debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/README.Debian
	install -p -m0644 debian/copyright debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/copyright
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc
	install -p -m0644 debian/copyright debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/copyright
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc-base/
	install -p -m0644 debian/libhtsjdk-java-doc.doc-base.javadoc debian/libhtsjdk-java-doc/usr/share/doc-base/libhtsjdk-java-doc.libhtsjdk-java-doc
   dh_installchangelogs -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc
	install -p -m0644 debian/.debhelper/generated/libhtsjdk-java-doc/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian
	install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java
	install -p -m0644 debian/.debhelper/generated/libhtsjdk-java/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian
   dh_installsystemduser -O--buildsystem=gradle
   dh_lintian -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java-doc/usr/share/lintian/overrides
	install -p -m0644 debian/libhtsjdk-java-doc.lintian-overrides debian/libhtsjdk-java-doc/usr/share/lintian/overrides/libhtsjdk-java-doc
   dh_perl -O--buildsystem=gradle
   dh_link -O--buildsystem=gradle
	rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log
   debian/rules override_jh_installlibs
make[1]: Map '/build/htsjdk-3.0.4+dfsg' wordt binnengegaan
jh_installlibs --version-strip='[+]dfsg[.0-9]*'
	install -m0755 -d debian/libhtsjdk-java/usr/share/java
	install -p -m0644 ./build/libs/htsjdk-3.0.4.jar debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar
	rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	ln -s htsjdk-3.0.4.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar
make[1]: Map '/build/htsjdk-3.0.4+dfsg' wordt verlaten
   jh_classpath -O--buildsystem=gradle
	jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/mjson.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	Updating symlinked /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar)
	Reading manifest from /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar
	Updating manifest in /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar
   jh_manifest -O--buildsystem=gradle
	find debian/libhtsjdk-java  -name '*.jar'
	Found usr/share/java/htsjdk-3.0.4.jar
	Found symlink usr/share/java/htsjdk.jar
	Reading manifest from debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar
	No update of debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar required.
	find debian/libhtsjdk-java-doc  -name '*.jar'
   jh_exec -O--buildsystem=gradle
   jh_depends -O--buildsystem=gradle
Searching /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java for libhtsjdk-java
Searching /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar
Found Jars: /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/mjson.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/commons-compress.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-compress.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/commons-jexl2.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-jexl2.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/mjson.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc/usr/share/java/mjson.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/ngs-java-3.0.3.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc/usr/share/java/ngs-java-3.0.3.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/js-1.7.7.2.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc/usr/share/java/js-1.7.7.2.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java/usr/share/java/snappy-java.jar
Checking:  /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc/usr/share/java/snappy-java.jar
Found Debs: libcommons-compress-java libcommons-jexl2-java libmjson-java libngs-java librhino-java libsnappy-java
Adding substvars: java:Depends=libcommons-compress-java,  libcommons-jexl2-java,  libmjson-java,  libngs-java,  librhino-java,  libsnappy-java java:Recommends=
Searching /build/htsjdk-3.0.4+dfsg/debian/libhtsjdk-java-doc for libhtsjdk-java-doc
Searching
Found Jars:
Found Debs:
Adding substvars: java:Depends= java:Recommends=
   mh_installpoms -O--buildsystem=gradle
	mh_installpom   --package=libhtsjdk-java            --has-package-version --usj-name=htsjdk         debian/htsjdk.pom
	mh_cleanpom   --package=libhtsjdk-java    --has-package-version   --rules=debian/maven.rules      debian/htsjdk.pom debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/pom.properties
	mv debian/.debhelper/.mh/pom.xml debian/.debhelper/.mh/htsjdk-debian.pom
	install -m 644 -D debian/.debhelper/.mh/htsjdk-3.0.2.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.pom
	install -m 644 -D debian/.debhelper/.mh/htsjdk-debian.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.pom
   mh_linkjars --skip-clean-poms -O--buildsystem=gradle
	mh_linkjar --has-package-version            --package=libhtsjdk-java    --skip-clean-pom debian/htsjdk.pom /usr/share/java/htsjdk.jar
	dh_link   -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	ln -s htsjdk-3.0.4.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	install -m0755 -d debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2
	rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	dh_link   -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar
	rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	ln -s htsjdk-3.0.4.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar
	rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/3.0.2/htsjdk-3.0.2.jar
	install -m0755 -d debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian
	rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar
	ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar
   dh_strip_nondeterminism -O--buildsystem=gradle
	Using 1674530174 as canonical time
	Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar using File::StripNondeterminism::handlers::jar
	Using 1674530174 as canonical time
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/u	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/lib	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::ha	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Insertion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Bases.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/l	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.SetMateInfoIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.PairOrientation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.AssertingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMLineParser.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamInputResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamIndexes.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMHeaderRecordComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFormatException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFlagField.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.SortOrder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/QueryInterval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/NotPrimarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/MergingSamRecordIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/IndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/GenomicIndexUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/FileTruncatedException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSetIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSet.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.Strategy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsj	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/help-doc.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/glass.png using File::StripNondeterminism::handlers::png
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/BetaAPI.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkUnsupportedOperationException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkPluginException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/Upgradeable.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/IOUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsContentType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondetesr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/thtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontexndlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Severity.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.html using File::StripNondeterminisibhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/WholeReadClippedFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SamRecordFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/ReadNameFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/OverclippedReadFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/MappingQualityFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/JavascriptSamRecordFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InvertFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InsertSizeFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringSamIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AlignedFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsdk-java/api/htsjdk/samtools/DownsamplingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DiskBasedBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DefaultSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CSIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMBAIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarOperator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarElement.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Chunk.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.BinList.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinaryTagCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Bin.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStreamWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMSBIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileSpan.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamFileIoUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AlignmentBlock.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractSAMHeaderRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html us	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLoggerInterface.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLogger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PositionalOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekableIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/MergingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Log.LogLevel.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Log.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locus.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocationAware.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locatable.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ListMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.LazyInitializer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iterables.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableOnceIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableAdapter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iso8601Date.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IOUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTreeMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.ValuesIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.RevIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.OverlapIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.FwdIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.Bin.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/m::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextHeaderCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordSetBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordDuplicateComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.Option.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Type.html using File::StripNondeterminism::handlers::javadoc
ribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.html using File::StripNondeterminism::handlers::javadoc
ReadsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/IOPathUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/OutputStreamResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/IOPathResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/InputStreamResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleJSON.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/Bundle.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::Stript/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/SimpleAllele.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Allele.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc
jdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TrimmingUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TestUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TerminatorlessBlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingLongCollection.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.Codec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SolexaQualityConverter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SnappyLoader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.SequenceListsDifferException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordWithOrdinal.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordTrackingBuffer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SAMRecordPrefetchingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.LocusInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeScriptException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeIOException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc
ing File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc
Nondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc
rminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhdoc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.InvalidDateException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordMath.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.MultiMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CodeUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloseableIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BinaryCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsciiWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractProgressLogger.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractIterator.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractAsyncWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-tsjdk-java/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/EncodingFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc
java/api/htsjdk/samtools/util/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.Block.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequestField.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequest.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetFormat.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetErrorResponse.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetClass.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPUtils.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPStream.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPReply.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPClient.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/InflaterFactory.html using File::StripNondeterminism::handlers::javadoc
	Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/DeflaterFactory.html using File::StripNondeterminism::handlers::javadoc
   dh_compress -O--buildsystem=gradle
	cd debian/libhtsjdk-java
	cd debian/libhtsjdk-java-doc
	chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian
	gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian
	cd '/build/htsjdk-3.0.4+dfsg'
	chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian
	gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian
	cd '/build/htsjdk-3.0.4+dfsg'
   dh_fixperms -O--buildsystem=gradle
	find debian/libhtsjdk-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/libhtsjdk-java-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
   dh_missing -O--buildsystem=gradle
   dh_installdeb -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java/DEBIAN
	install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN
   dh_gencontrol -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN
	echo misc:Depends= >> debian/libhtsjdk-java-doc.substvars
	echo misc:Pre-Depends= >> debian/libhtsjdk-java-doc.substvars
	dpkg-gencontrol -plibhtsjdk-java-doc -ldebian/changelog -Tdebian/libhtsjdk-java-doc.substvars -Pdebian/libhtsjdk-java-doc
	install -m0755 -d debian/libhtsjdk-java/DEBIAN
	echo misc:Depends= >> debian/libhtsjdk-java.substvars
	echo misc:Pre-Depends= >> debian/libhtsjdk-java.substvars
	dpkg-gencontrol -plibhtsjdk-java -ldebian/changelog -Tdebian/libhtsjdk-java.substvars -Pdebian/libhtsjdk-java
	chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control
	chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control
   dh_md5sums -O--buildsystem=gradle
	install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN
	install -m0755 -d debian/libhtsjdk-java/DEBIAN
	cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums
	chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums
   dh_builddeb -O--buildsystem=gradle
	dpkg-deb --root-owner-group --build debian/libhtsjdk-java ..
	dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc ..
dpkg-deb: pakket 'libhtsjdk-java' wordt gebouwd in '../libhtsjdk-java_3.0.4+dfsg-2_all.deb'.
dpkg-deb: pakket 'libhtsjdk-java-doc' wordt gebouwd in '../libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb'.
 dpkg-genbuildinfo --build=binary -O../htsjdk_3.0.4+dfsg-2_arm64.buildinfo
 dpkg-genchanges --build=binary -O../htsjdk_3.0.4+dfsg-2_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/6123/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/6123 and its subdirectories
I: Current time: Sat Apr 15 21:01:39 +14 2023
I: pbuilder-time-stamp: 1681542099