I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 26 06:49:33 +14 2021 I: pbuilder-time-stamp: 1627231774 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_2.23.0+dfsg-2.dsc] I: copying [./htsjdk_2.23.0+dfsg.orig.tar.xz] I: copying [./htsjdk_2.23.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.fyWbd0W5/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 23 03:31:19 2020 +14 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./htsjdk_2.23.0+dfsg-2.dsc dpkg-source: info: extracting htsjdk in htsjdk-2.23.0+dfsg dpkg-source: info: unpacking htsjdk_2.23.0+dfsg.orig.tar.xz dpkg-source: info: unpacking htsjdk_2.23.0+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 80-2to3.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8215/tmp/hooks/D01_modify_environment starting debug: Running on virt32b. 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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' 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/8215/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/8215/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=0b42cc21243143f4822e3b61ce65917e LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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 PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=8215 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 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/tmp.IaaQtPwj86/pbuilderrc_B3Cn --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.IaaQtPwj86/b2 --logfile b2/build.log --extrapackages usrmerge htsjdk_2.23.0+dfsg-2.dsc' SUDO_GID=112 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-2 (2021-07-20) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 26 06:50 sh -> bash lrwxrwxrwx 1 root root 4 Jul 25 23:26 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/8215/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: armhf Maintainer: Debian Pbuilder Team 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 (>= 2:1.9), javahelper, gradle-debian-helper, maven-repo-helper, debhelper-compat (= 13), libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-java, libsnappy-java, libcommons-compress-java, libxz-java, libngs-java, default-jdk-doc, testng (>= 6.9.9), junit4, 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 ... 19398 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 (>= 2:1.9); 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 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 libxz-java; however: Package libxz-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 testng (>= 6.9.9); however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on junit4; however: Package junit4 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: ant{a} ant-optional{a} antlr{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-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} 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} 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} libcdi-api-java{a} libclass-method-modifiers-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} libdbus-1-3{a} libdd-plist-java{a} libdebhelper-perl{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} 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} 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} 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} libicu67{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} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{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} 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-2.4-2{a} libllvm11{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} libmd0{a} libminlog-java{a} libmodule-runtime-perl{a} libmoo-perl{a} libmpdec3{a} libnative-platform-java{a} libnative-platform-jni{a} libncurses6{a} libnekohtml-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libngs-java{a} libngs-sdk-dev{a} libngs-sdk2{a} libnpth0{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libparams-classify-perl{a} libpcsclite1{a} libpipeline1{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} libpython3.9-minimal{a} libpython3.9-stdlib{a} libqdox-java{a} libreadline8{a} libreflectasm-java{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} libservlet3.1-java{a} libsigsegv2{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} libstrictures-perl{a} libsub-override-perl{a} libsub-quote-perl{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{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-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{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} netbase{a} openjdk-11-doc{a} openjdk-11-jdk{a} openjdk-11-jdk-headless{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} scala-library{a} sensible-utils{a} testng{a} ucf{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 libclass-xsaccessor-perl libclone-perl libdata-dump-perl libdistro-info-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpars-groovy-java libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libsub-name-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg shared-mime-info strace wget xdg-user-dirs 0 packages upgraded, 326 newly installed, 0 to remove and 0 not upgraded. Need to get 392 MB of archives. After unpacking 986 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf openssl armhf 1.1.1k-1 [826 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf ucf all 3.0043 [74.0 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libnspr4 armhf 2:4.29-1 [90.7 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libnss3 armhf 2:3.61-1 [1114 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf ca-certificates-java all 20190909 [15.7 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf java-common all 0.72 [14.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf libavahi-common-data armhf 0.8-5 [123 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libavahi-common3 armhf 0.8-5 [55.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libdbus-1-3 armhf 1.12.20-2 [196 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libavahi-client3 armhf 0.8-5 [58.5 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libcups2 armhf 2.3.3op2-3+deb11u1 [317 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf liblcms2-2 armhf 2.12~rc1-2 [123 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [123 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libpng16-16 armhf 1.6.37-3 [277 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [357 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf fonts-dejavu-core all 2.37-2 [1069 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf fontconfig-config all 2.13.1-4.2 [281 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libfontconfig1 armhf 2.13.1-4.2 [329 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libasound2 armhf 1.2.4-1.1 [310 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libharfbuzz0b armhf 2.7.4-1 [1427 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libpcsclite1 armhf 1.9.1-1 [57.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf openjdk-11-jre-headless armhf 11.0.11+9-1 [32.9 MB] Get: 51 http://deb.debian.org/debian bullseye/main armhf default-jre-headless armhf 2:1.11-72 [10.9 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf ant all 1.10.9-4 [2118 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf ant-optional all 1.10.9-4 [381 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libantlr-java all 2.7.7+dfsg-10 [458 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf antlr all 2.7.7+dfsg-10 [14.0 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf unzip armhf 6.0-26 [157 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf java-wrappers all 0.3 [10.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf libhamcrest-java all 1.3-9 [388 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf junit4 all 4.13.1-2 [347 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libosgi-annotation-java all 7.0.0-2 [10.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libosgi-core-java all 7.0.0-2 [157 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libhawtjni-runtime-java all 1.17-1 [35.3 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libjansi-native-java all 1.8-1 [26.0 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf libjansi-java all 1.18-1 [66.6 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf libjline2-java all 2.14.6-4 [151 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libslf4j-java all 1.7.30-1 [144 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libxz-java all 1.8-2 [141 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf libyaml-snake-java all 1.28-1 [313 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf bnd all 5.0.1-3 [9915 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf dctrl-tools armhf 2.24-3 [96.0 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 90 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 91 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 92 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 95 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 96 http://deb.debian.org/debian bullseye/main armhf libglvnd0 armhf 1.3.2-1 [51.8 kB] Get: 97 http://deb.debian.org/debian bullseye/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 98 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 99 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 100 http://deb.debian.org/debian bullseye/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 101 http://deb.debian.org/debian bullseye/main armhf libxcb1 armhf 1.14-3 [136 kB] Get: 102 http://deb.debian.org/debian bullseye/main armhf libx11-data all 2:1.7.1-1 [310 kB] Get: 103 http://deb.debian.org/debian bullseye/main armhf libx11-6 armhf 2:1.7.1-1 [712 kB] Get: 104 http://deb.debian.org/debian bullseye/main armhf libdrm-common all 2.4.104-1 [14.9 kB] Get: 105 http://deb.debian.org/debian bullseye/main armhf libdrm2 armhf 2.4.104-1 [37.7 kB] Get: 106 http://deb.debian.org/debian bullseye/main armhf libglapi-mesa armhf 20.3.5-1 [80.2 kB] Get: 107 http://deb.debian.org/debian bullseye/main armhf libx11-xcb1 armhf 2:1.7.1-1 [203 kB] Get: 108 http://deb.debian.org/debian bullseye/main armhf libxcb-dri2-0 armhf 1.14-3 [103 kB] Get: 109 http://deb.debian.org/debian bullseye/main armhf libxcb-dri3-0 armhf 1.14-3 [102 kB] Get: 110 http://deb.debian.org/debian bullseye/main armhf libxcb-glx0 armhf 1.14-3 [116 kB] Get: 111 http://deb.debian.org/debian bullseye/main armhf libxcb-present0 armhf 1.14-3 [101 kB] Get: 112 http://deb.debian.org/debian bullseye/main armhf libxcb-shm0 armhf 1.14-3 [101 kB] Get: 113 http://deb.debian.org/debian bullseye/main armhf libxcb-sync1 armhf 1.14-3 [104 kB] Get: 114 http://deb.debian.org/debian bullseye/main armhf libxcb-xfixes0 armhf 1.14-3 [105 kB] Get: 115 http://deb.debian.org/debian bullseye/main armhf libxdamage1 armhf 1:1.1.5-2 [15.1 kB] Get: 116 http://deb.debian.org/debian bullseye/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB] Get: 117 http://deb.debian.org/debian bullseye/main armhf libxfixes3 armhf 1:5.0.3-2 [20.6 kB] Get: 118 http://deb.debian.org/debian bullseye/main armhf libxshmfence1 armhf 1.3-1 [8592 B] Get: 119 http://deb.debian.org/debian bullseye/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.2 kB] Get: 120 http://deb.debian.org/debian bullseye/main armhf libdrm-amdgpu1 armhf 2.4.104-1 [27.1 kB] Get: 121 http://deb.debian.org/debian bullseye/main armhf libdrm-nouveau2 armhf 2.4.104-1 [24.6 kB] Get: 122 http://deb.debian.org/debian bullseye/main armhf libdrm-radeon1 armhf 2.4.104-1 [27.6 kB] Get: 123 http://deb.debian.org/debian bullseye/main armhf libedit2 armhf 3.1-20191231-2+b1 [81.1 kB] Get: 124 http://deb.debian.org/debian bullseye/main armhf libz3-4 armhf 4.8.10-1 [5959 kB] Get: 125 http://deb.debian.org/debian bullseye/main armhf libllvm11 armhf 1:11.0.1-2 [15.4 MB] Get: 126 http://deb.debian.org/debian bullseye/main armhf libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 127 http://deb.debian.org/debian bullseye/main armhf libsensors5 armhf 1:3.6.0-7 [49.6 kB] Get: 128 http://deb.debian.org/debian bullseye/main armhf libvulkan1 armhf 1.2.162.0-1 [84.3 kB] Get: 129 http://deb.debian.org/debian bullseye/main armhf libgl1-mesa-dri armhf 20.3.5-1 [6037 kB] Get: 130 http://deb.debian.org/debian bullseye/main armhf libglx-mesa0 armhf 20.3.5-1 [167 kB] Get: 131 http://deb.debian.org/debian bullseye/main armhf libglx0 armhf 1.3.2-1 [32.8 kB] Get: 132 http://deb.debian.org/debian bullseye/main armhf libgl1 armhf 1.3.2-1 [94.3 kB] Get: 133 http://deb.debian.org/debian bullseye/main armhf libgif7 armhf 5.1.9-2 [42.7 kB] Get: 134 http://deb.debian.org/debian bullseye/main armhf libxi6 armhf 2:1.7.10-1 [78.5 kB] Get: 135 http://deb.debian.org/debian bullseye/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 136 http://deb.debian.org/debian bullseye/main armhf x11-common all 1:7.7+22 [252 kB] Get: 137 http://deb.debian.org/debian bullseye/main armhf libxtst6 armhf 2:1.2.3-1 [26.3 kB] Get: 138 http://deb.debian.org/debian bullseye/main armhf openjdk-11-jre armhf 11.0.11+9-1 [151 kB] Get: 139 http://deb.debian.org/debian bullseye/main armhf default-jre armhf 2:1.11-72 [1044 B] Get: 140 http://deb.debian.org/debian bullseye/main armhf openjdk-11-jdk-headless armhf 11.0.11+9-1 [174 MB] Get: 141 http://deb.debian.org/debian bullseye/main armhf default-jdk-headless armhf 2:1.11-72 [1100 B] Get: 142 http://deb.debian.org/debian bullseye/main armhf openjdk-11-jdk armhf 11.0.11+9-1 [6937 kB] Get: 143 http://deb.debian.org/debian bullseye/main armhf default-jdk armhf 2:1.11-72 [1056 B] Get: 144 http://deb.debian.org/debian bullseye/main armhf openjdk-11-doc all 11.0.11+9-1 [13.5 MB] Get: 145 http://deb.debian.org/debian bullseye/main armhf default-jdk-doc armhf 2:1.11-72 [11.0 kB] Get: 146 http://deb.debian.org/debian bullseye/main armhf libassuan0 armhf 2.5.3-7.1 [44.2 kB] Get: 147 http://deb.debian.org/debian bullseye/main armhf gpgconf armhf 2.2.27-2 [532 kB] Get: 148 http://deb.debian.org/debian bullseye/main armhf libksba8 armhf 1.5.0-3 [105 kB] Get: 149 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 150 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 151 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 152 http://deb.debian.org/debian bullseye/main armhf libnpth0 armhf 1.6-3 [17.8 kB] Get: 153 http://deb.debian.org/debian bullseye/main armhf dirmngr armhf 2.2.27-2 [722 kB] Get: 154 http://deb.debian.org/debian bullseye/main armhf gnupg-l10n all 2.2.27-2 [1084 kB] Get: 155 http://deb.debian.org/debian bullseye/main armhf gnupg-utils armhf 2.2.27-2 [835 kB] Get: 156 http://deb.debian.org/debian bullseye/main armhf gpg armhf 2.2.27-2 [868 kB] Get: 157 http://deb.debian.org/debian bullseye/main armhf pinentry-curses armhf 1.1.0-4 [60.6 kB] Get: 158 http://deb.debian.org/debian bullseye/main armhf gpg-agent armhf 2.2.27-2 [630 kB] Get: 159 http://deb.debian.org/debian bullseye/main armhf gpg-wks-client armhf 2.2.27-2 [509 kB] Get: 160 http://deb.debian.org/debian bullseye/main armhf gpg-wks-server armhf 2.2.27-2 [503 kB] Get: 161 http://deb.debian.org/debian bullseye/main armhf gpgsm armhf 2.2.27-2 [618 kB] Get: 162 http://deb.debian.org/debian bullseye/main armhf gnupg all 2.2.27-2 [825 kB] Get: 163 http://deb.debian.org/debian bullseye/main armhf libfile-dirlist-perl all 0.05-2 [7444 B] Get: 164 http://deb.debian.org/debian bullseye/main armhf libfile-which-perl all 1.23-1 [16.6 kB] Get: 165 http://deb.debian.org/debian bullseye/main armhf libfile-homedir-perl all 1.006-1 [43.8 kB] Get: 166 http://deb.debian.org/debian bullseye/main armhf libfile-touch-perl all 0.11-1 [9254 B] Get: 167 http://deb.debian.org/debian bullseye/main armhf libio-pty-perl armhf 1:1.15-2 [36.2 kB] Get: 168 http://deb.debian.org/debian bullseye/main armhf libipc-run-perl all 20200505.0-1 [102 kB] Get: 169 http://deb.debian.org/debian bullseye/main armhf libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 170 http://deb.debian.org/debian bullseye/main armhf libb-hooks-op-check-perl armhf 0.22-1+b3 [11.0 kB] Get: 171 http://deb.debian.org/debian bullseye/main armhf libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 172 http://deb.debian.org/debian bullseye/main armhf libdevel-callchecker-perl armhf 0.008-1+b2 [15.7 kB] Get: 173 http://deb.debian.org/debian bullseye/main armhf libparams-classify-perl armhf 0.015-1+b3 [24.5 kB] Get: 174 http://deb.debian.org/debian bullseye/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 175 http://deb.debian.org/debian bullseye/main armhf libimport-into-perl all 1.002005-1 [11.6 kB] Get: 176 http://deb.debian.org/debian bullseye/main armhf librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 177 http://deb.debian.org/debian bullseye/main armhf libstrictures-perl all 2.000006-1 [18.6 kB] Get: 178 http://deb.debian.org/debian bullseye/main armhf libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 179 http://deb.debian.org/debian bullseye/main armhf libmoo-perl all 2.004004-1 [59.9 kB] Get: 180 http://deb.debian.org/debian bullseye/main armhf libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 181 http://deb.debian.org/debian bullseye/main armhf libtimedate-perl all 2.3300-2 [39.3 kB] Get: 182 http://deb.debian.org/debian bullseye/main armhf libhttp-date-perl all 6.05-1 [10.4 kB] Get: 183 http://deb.debian.org/debian bullseye/main armhf libfile-listing-perl all 6.14-1 [12.4 kB] Get: 184 http://deb.debian.org/debian bullseye/main armhf libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 185 http://deb.debian.org/debian bullseye/main armhf liburi-perl all 5.08-1 [90.6 kB] Get: 186 http://deb.debian.org/debian bullseye/main armhf libhtml-parser-perl armhf 3.75-1+b1 [102 kB] Get: 187 http://deb.debian.org/debian bullseye/main armhf libhtml-tree-perl all 5.07-2 [213 kB] Get: 188 http://deb.debian.org/debian bullseye/main armhf libio-html-perl all 1.004-2 [16.1 kB] Get: 189 http://deb.debian.org/debian bullseye/main armhf liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 190 http://deb.debian.org/debian bullseye/main armhf libhttp-message-perl all 6.28-1 [79.6 kB] Get: 191 http://deb.debian.org/debian bullseye/main armhf libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 192 http://deb.debian.org/debian bullseye/main armhf libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 193 http://deb.debian.org/debian bullseye/main armhf perl-openssl-defaults armhf 5 [7360 B] Get: 194 http://deb.debian.org/debian bullseye/main armhf libnet-ssleay-perl armhf 1.88-3+b1 [303 kB] Get: 195 http://deb.debian.org/debian bullseye/main armhf libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 196 http://deb.debian.org/debian bullseye/main armhf libnet-http-perl all 6.20-1 [25.1 kB] Get: 197 http://deb.debian.org/debian bullseye/main armhf liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 198 http://deb.debian.org/debian bullseye/main armhf libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 199 http://deb.debian.org/debian bullseye/main armhf libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 200 http://deb.debian.org/debian bullseye/main armhf libwww-perl all 6.52-1 [192 kB] Get: 201 http://deb.debian.org/debian bullseye/main armhf patchutils armhf 0.4.2-1 [72.5 kB] Get: 202 http://deb.debian.org/debian bullseye/main armhf wdiff armhf 1.2.2-2+b1 [121 kB] Get: 203 http://deb.debian.org/debian bullseye/main armhf devscripts armhf 2.21.3 [1092 kB] Get: 204 http://deb.debian.org/debian bullseye/main armhf ivy all 2.5.0-1 [1268 kB] Get: 205 http://deb.debian.org/debian bullseye/main armhf libasm-java all 9.1-1 [379 kB] Get: 206 http://deb.debian.org/debian bullseye/main armhf libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 207 http://deb.debian.org/debian bullseye/main armhf libcommons-cli-java all 1.4-2 [57.3 kB] Get: 208 http://deb.debian.org/debian bullseye/main armhf libapache-pom-java all 18-1 [4676 B] Get: 209 http://deb.debian.org/debian bullseye/main armhf libcommons-parent-java all 43-1 [10.8 kB] Get: 210 http://deb.debian.org/debian bullseye/main armhf libcommons-logging-java all 1.2-2 [62.2 kB] Get: 211 http://deb.debian.org/debian bullseye/main armhf libqdox-java all 1.12.1-3 [172 kB] Get: 212 http://deb.debian.org/debian bullseye/main armhf libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 213 http://deb.debian.org/debian bullseye/main armhf libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 214 http://deb.debian.org/debian bullseye/main armhf libel-api-java all 3.0.0-3 [64.9 kB] Get: 215 http://deb.debian.org/debian bullseye/main armhf libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 216 http://deb.debian.org/debian bullseye/main armhf libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 217 http://deb.debian.org/debian bullseye/main armhf libxpp3-java all 1.1.4c-3 [292 kB] Get: 218 http://deb.debian.org/debian bullseye/main armhf libxstream-java all 1.4.15-3 [546 kB] Get: 219 http://deb.debian.org/debian bullseye/main armhf groovy all 2.4.21-1 [12.9 MB] Get: 220 http://deb.debian.org/debian bullseye/main armhf libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 221 http://deb.debian.org/debian bullseye/main armhf libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 222 http://deb.debian.org/debian bullseye/main armhf libcommons-compress-java all 1.20-1 [574 kB] Get: 223 http://deb.debian.org/debian bullseye/main armhf libcommons-io-java all 2.8.0-1 [279 kB] Get: 224 http://deb.debian.org/debian bullseye/main armhf libcommons-lang-java all 2.6-9 [273 kB] Get: 225 http://deb.debian.org/debian bullseye/main armhf libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 226 http://deb.debian.org/debian bullseye/main armhf libguava-java all 29.0-6 [2419 kB] Get: 227 http://deb.debian.org/debian bullseye/main armhf libcommons-codec-java all 1.15-1 [292 kB] Get: 228 http://deb.debian.org/debian bullseye/main armhf libhttpcore-java all 4.4.14-1 [631 kB] Get: 229 http://deb.debian.org/debian bullseye/main armhf libhttpclient-java all 4.5.13-2 [1233 kB] Get: 230 http://deb.debian.org/debian bullseye/main armhf libjarjar-java all 1.4+svn142-10 [192 kB] Get: 231 http://deb.debian.org/debian bullseye/main armhf libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 232 http://deb.debian.org/debian bullseye/main armhf libjna-jni armhf 5.6.0-1 [57.5 kB] Get: 233 http://deb.debian.org/debian bullseye/main armhf libjna-java all 5.6.0-1 [223 kB] Get: 234 http://deb.debian.org/debian bullseye/main armhf libjzlib-java all 1.1.3-2 [80.0 kB] Get: 235 http://deb.debian.org/debian bullseye/main armhf libjsch-java all 0.1.55-1 [298 kB] Get: 236 http://deb.debian.org/debian bullseye/main armhf libminlog-java all 1.3.0-1.1 [7928 B] Get: 237 http://deb.debian.org/debian bullseye/main armhf libobjenesis-java all 3.1-1 [52.6 kB] Get: 238 http://deb.debian.org/debian bullseye/main armhf libreflectasm-java all 1.05-4.1 [18.4 kB] Get: 239 http://deb.debian.org/debian bullseye/main armhf libkryo-java all 2.20-6.2 [157 kB] Get: 240 http://deb.debian.org/debian bullseye/main armhf liblogback-java all 1:1.2.3-6 [763 kB] Get: 241 http://deb.debian.org/debian bullseye/main armhf libncurses6 armhf 6.2+20201114-2 [80.5 kB] Get: 242 http://deb.debian.org/debian bullseye/main armhf libnative-platform-jni armhf 0.14-5 [11.6 kB] Get: 243 http://deb.debian.org/debian bullseye/main armhf libnative-platform-java all 0.14-5 [71.0 kB] Get: 244 http://deb.debian.org/debian bullseye/main armhf libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 245 http://deb.debian.org/debian bullseye/main armhf libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 246 http://deb.debian.org/debian bullseye/main armhf libxerces2-java all 2.12.1-1 [1440 kB] Get: 247 http://deb.debian.org/debian bullseye/main armhf libnekohtml-java all 1.9.22-1.1 [124 kB] Get: 248 http://deb.debian.org/debian bullseye/main armhf libxbean-reflect-java all 4.5-8 [133 kB] Get: 249 http://deb.debian.org/debian bullseye/main armhf libgradle-core-java all 4.4.1-13 [4246 kB] Get: 250 http://deb.debian.org/debian bullseye/main armhf libbcprov-java all 1.68-2 [3512 kB] Get: 251 http://deb.debian.org/debian bullseye/main armhf libbcpg-java all 1.68-2 [323 kB] Get: 252 http://deb.debian.org/debian bullseye/main armhf libbsh-java all 2.0b4-20 [291 kB] Get: 253 http://deb.debian.org/debian bullseye/main armhf libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 254 http://deb.debian.org/debian bullseye/main armhf libjaxen-java all 1.1.6-4 [214 kB] Get: 255 http://deb.debian.org/debian bullseye/main armhf libdom4j-java all 2.1.3-1 [310 kB] Get: 256 http://deb.debian.org/debian bullseye/main armhf libbcel-java all 6.5.0-1 [636 kB] Get: 257 http://deb.debian.org/debian bullseye/main armhf libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 258 http://deb.debian.org/debian bullseye/main armhf libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 259 http://deb.debian.org/debian bullseye/main armhf libgoogle-gson-java all 2.8.6-1 [225 kB] Get: 260 http://deb.debian.org/debian bullseye/main armhf libaopalliance-java all 20070526-6 [9048 B] Get: 261 http://deb.debian.org/debian bullseye/main armhf libguice-java all 4.2.3-2 [1435 kB] Get: 262 http://deb.debian.org/debian bullseye/main armhf libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 263 http://deb.debian.org/debian bullseye/main armhf libjcifs-java all 1.3.19-2 [394 kB] Get: 264 http://deb.debian.org/debian bullseye/main armhf libeclipse-jdt-annotation-java all 2.2.600+eclipse4.18-1 [25.1 kB] Get: 265 http://deb.debian.org/debian bullseye/main armhf libjavaewah-java all 1.1.7-1 [156 kB] Get: 266 http://deb.debian.org/debian bullseye/main armhf libjetty9-java all 9.4.39-3 [2869 kB] Get: 267 http://deb.debian.org/debian bullseye/main armhf libjgit-java all 4.11.9-1 [2502 kB] Get: 268 http://deb.debian.org/debian bullseye/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 269 http://deb.debian.org/debian bullseye/main armhf libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 270 http://deb.debian.org/debian bullseye/main armhf libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 271 http://deb.debian.org/debian bullseye/main armhf libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 272 http://deb.debian.org/debian bullseye/main armhf libcommons-lang3-java all 3.11-1 [550 kB] Get: 273 http://deb.debian.org/debian bullseye/main armhf libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 274 http://deb.debian.org/debian bullseye/main armhf libmaven-parent-java all 31-2 [5100 B] Get: 275 http://deb.debian.org/debian bullseye/main armhf libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 276 http://deb.debian.org/debian bullseye/main armhf libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 277 http://deb.debian.org/debian bullseye/main armhf libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 278 http://deb.debian.org/debian bullseye/main armhf libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 279 http://deb.debian.org/debian bullseye/main armhf libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 280 http://deb.debian.org/debian bullseye/main armhf libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 281 http://deb.debian.org/debian bullseye/main armhf libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 282 http://deb.debian.org/debian bullseye/main armhf libcdi-api-java all 1.2-3 [54.3 kB] Get: 283 http://deb.debian.org/debian bullseye/main armhf libsisu-inject-java all 0.3.4-2 [347 kB] Get: 284 http://deb.debian.org/debian bullseye/main armhf libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 285 http://deb.debian.org/debian bullseye/main armhf libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 286 http://deb.debian.org/debian bullseye/main armhf libplexus-container-default-java all 2.1.0-1 [193 kB] Get: 287 http://deb.debian.org/debian bullseye/main armhf libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 288 http://deb.debian.org/debian bullseye/main armhf librhino-java all 1.7.7.2-3 [1200 kB] Get: 289 http://deb.debian.org/debian bullseye/main armhf libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 290 http://deb.debian.org/debian bullseye/main armhf libwagon-file-java all 3.3.4-1 [10.8 kB] Get: 291 http://deb.debian.org/debian bullseye/main armhf libjsoup-java all 1.10.2-2 [350 kB] Get: 292 http://deb.debian.org/debian bullseye/main armhf libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 293 http://deb.debian.org/debian bullseye/main armhf libjcommander-java all 1.71-3 [72.7 kB] Get: 294 http://deb.debian.org/debian bullseye/main armhf testng all 6.9.12-4 [795 kB] Get: 295 http://deb.debian.org/debian bullseye/main armhf libgradle-plugins-java all 4.4.1-13 [5158 kB] Get: 296 http://deb.debian.org/debian bullseye/main armhf gradle all 4.4.1-13 [401 kB] Get: 297 http://deb.debian.org/debian bullseye/main armhf maven-repo-helper all 1.10 [142 kB] Get: 298 http://deb.debian.org/debian bullseye/main armhf gradle-debian-helper all 2.1 [25.3 kB] Get: 299 http://deb.debian.org/debian bullseye/main armhf javahelper all 0.78 [97.2 kB] Get: 300 http://deb.debian.org/debian bullseye/main armhf libactivation-java all 1.2.0-2 [84.7 kB] Get: 301 http://deb.debian.org/debian bullseye/main armhf libargs4j-java all 2.33-1.1 [137 kB] Get: 302 http://deb.debian.org/debian bullseye/main armhf libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 303 http://deb.debian.org/debian bullseye/main armhf libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 304 http://deb.debian.org/debian bullseye/main armhf libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 305 http://deb.debian.org/debian bullseye/main armhf libsnappy1v5 armhf 1.1.8-1 [16.5 kB] Get: 306 http://deb.debian.org/debian bullseye/main armhf libsnappy-jni armhf 1.1.8.3-1 [6800 B] Get: 307 http://deb.debian.org/debian bullseye/main armhf libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 308 http://deb.debian.org/debian bullseye/main armhf libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 309 http://deb.debian.org/debian bullseye/main armhf libistack-commons-java all 3.0.6-5 [145 kB] Get: 310 http://deb.debian.org/debian bullseye/main armhf libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 311 http://deb.debian.org/debian bullseye/main armhf libcommons-jexl2-java all 2.1.1-5 [256 kB] Get: 312 http://deb.debian.org/debian bullseye/main armhf libdtd-parser-java all 1.2-1 [64.9 kB] Get: 313 http://deb.debian.org/debian bullseye/main armhf libjaxb-api-java all 2.3.1-1 [119 kB] Get: 314 http://deb.debian.org/debian bullseye/main armhf libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 315 http://deb.debian.org/debian bullseye/main armhf libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 316 http://deb.debian.org/debian bullseye/main armhf librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 317 http://deb.debian.org/debian bullseye/main armhf libxsom-java all 2.3.0.1-10 [396 kB] Get: 318 http://deb.debian.org/debian bullseye/main armhf libfastinfoset-java all 1.2.12-3 [343 kB] Get: 319 http://deb.debian.org/debian bullseye/main armhf librngom-java all 2.3.0.1-10 [288 kB] Get: 320 http://deb.debian.org/debian bullseye/main armhf libtxw2-java all 2.3.0.1-10 [134 kB] Get: 321 http://deb.debian.org/debian bullseye/main armhf libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 322 http://deb.debian.org/debian bullseye/main armhf libjimfs-java all 1.1-6 [191 kB] Get: 323 http://deb.debian.org/debian bullseye/main armhf libngs-sdk2 armhf 2.10.9-1 [46.1 kB] Get: 324 http://deb.debian.org/debian bullseye/main armhf libngs-sdk-dev armhf 2.10.9-1 [90.0 kB] Get: 325 http://deb.debian.org/debian bullseye/main armhf libngs-java armhf 2.10.9-1 [80.4 kB] Get: 326 http://deb.debian.org/debian bullseye/main armhf scala-library all 2.11.12-4 [9589 kB] Fetched 392 MB in 37s (10.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_armhf.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:armhf. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_armhf.deb ... Unpacking libpython3.9-minimal:armhf (3.9.2-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../6-libexpat1_2.2.10-2_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_armhf.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:armhf (3.9.2-1) ... Setting up libexpat1:armhf (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20265 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:armhf. Preparing to unpack .../2-libmpdec3_2.5.1-1_armhf.deb ... Unpacking libmpdec3:armhf (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../4-libreadline8_8.1-1_armhf.deb ... Unpacking libreadline8:armhf (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:armhf. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_armhf.deb ... Unpacking libpython3.9-stdlib:armhf (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_armhf.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20686 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_armhf.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... 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Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.1-1) ... Setting up libhawtjni-runtime-java (1.17-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up liburi-perl (5.08-1) ... Setting up libargs4j-java (2.33-1.1) ... Setting up libfile-touch-perl (0.11-1) ... Setting up dctrl-tools (2.24-3) ... Setting up libservlet3.1-java (1:4.0.1-2) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up pinentry-curses (1.1.0-4) ... Setting up libdom4j-java (2.1.3-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libwagon-provider-api-java (3.3.4-1) ... Setting up libnative-platform-java (0.14-5) ... Setting up libosgi-core-java (7.0.0-2) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libxstream-java (1.4.15-3) ... Setting up libnekohtml-java (1.9.22-1.1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libxcb1:armhf (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libjetty9-java (9.4.39-3) ... Setting up libxcb-xfixes0:armhf (1.14-3) ... Setting up java-wrappers (0.3) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libtool (2.4.6-15) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:armhf (1.14-3) ... Setting up libmaven-parent-java (31-2) ... Setting up libedit2:armhf (3.1-20191231-2+b1) ... Setting up libreadline8:armhf (8.1-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:armhf (0.8-5) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:armhf (2.4.57+dfsg-3) ... Setting up libnet-http-perl (6.20-1) ... Setting up m4 (1.4.18-5) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:armhf (2:3.61-1) ... Setting up libxcb-shm0:armhf (1.14-3) ... Setting up default-jdk-doc (2:1.11-72) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libcommons-lang-java (2.6-9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxcb-present0:armhf (1.14-3) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libmaven-resolver-java (1.4.2-3) ... Setting up libbcel-java (6.5.0-1) ... Setting up libllvm11:armhf (1:11.0.1-2) ... Setting up libfreetype6:armhf (2.10.4+dfsg-1) ... Setting up libguava-java (29.0-6) ... Setting up libxcb-sync1:armhf (1.14-3) ... Setting up testng (6.9.12-4) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up ucf (3.0043) ... Setting up libcommons-lang3-java (3.11-1) ... Setting up autoconf (2.69-14) ... Setting up libxcb-dri2-0:armhf (1.14-3) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... 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) ... Setting up libdrm2:armhf (2.4.104-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libjansi-native-java (1.8-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up gpgconf (2.2.27-2) ... Setting up libx11-6:armhf (2:1.7.1-1) ... Setting up libharfbuzz0b:armhf (2.7.4-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libwagon-file-java (3.3.4-1) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libavahi-client3:armhf (0.8-5) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libplexus-container-default-java (2.1.0-1) ... Setting up gpg (2.2.27-2) ... Setting up libpython3.9-stdlib:armhf (3.9.2-1) ... Setting up libpython3-stdlib:armhf (3.9.2-3) ... Setting up gnupg-utils (2.2.27-2) ... Setting up libhttp-message-perl (6.28-1) ... Setting up libdrm-amdgpu1:armhf (2.4.104-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:armhf (1.14-3) ... Setting up libx11-xcb1:armhf (2:1.7.1-1) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libdrm-nouveau2:armhf (2.4.104-1) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up libxdamage1:armhf (1:1.1.5-2) ... Setting up gpg-agent (2.2.27-2) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libcommons-compress-java (1.20-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.8.0-1) ... Setting up libdrm-radeon1:armhf (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up gpgsm (2.2.27-2) ... Setting up libgl1-mesa-dri:armhf (20.3.5-1) ... Setting up libxext6:armhf (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libguice-java (4.2.3-2) ... Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ... Setting up dh-autoreconf (20) ... Setting up dirmngr (2.2.27-2) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libxfixes3:armhf (1:5.0.3-2) ... Setting up libjansi-java (1.18-1) ... Setting up gpg-wks-server (2.2.27-2) ... Setting up libcups2:armhf (2.3.3op2-3+deb11u1) ... Setting up libhttpclient-java (4.5.13-2) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:armhf (2.13.1-4.2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libjline2-java (2.14.6-4) ... Setting up python3.9 (3.9.2-1) ... Setting up libjgit-java (4.11.9-1) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up libglx-mesa0:armhf (20.3.5-1) ... Setting up libxi6:armhf (2:1.7.10-1) ... Setting up gpg-wks-client (2.2.27-2) ... Setting up libglx0:armhf (1.3.2-1) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libxtst6:armhf (2:1.2.3-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libgl1:armhf (1.3.2-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up gnupg (2.2.27-2) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up libwww-perl (6.52-1) ... Setting up openjdk-11-jre-headless:armhf (11.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:armhf (11.0.11+9-1) ... Setting up maven-repo-helper (1.10) ... Setting up openjdk-11-jdk-headless:armhf (11.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre (2:1.11-72) ... Setting up antlr (2.7.7+dfsg-10) ... Setting up default-jdk-headless (2:1.11-72) ... Setting up devscripts (2.21.3) ... Setting up ivy (2.5.0-1) ... Setting up ant (1.10.9-4) ... Setting up openjdk-11-jdk:armhf (11.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up javahelper (0.78) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Certigna.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:SecureTrust_CA.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:ACCVRAIZ1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:GTS_Root_R2.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:ISRG_Root_X1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Izenpe.com.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:SecureSign_RootCA11.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Secure_Global_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:EC-ACC.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:GTS_Root_R1.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:GTS_Root_R3.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Entrust_Root_Certification_Authority.pem done. Setting up junit4 (4.13.1-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up groovy (2.4.21-1) ... 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 default-jdk (2:1.11-72) ... Setting up ant-optional (1.10.9-4) ... Setting up bnd (5.0.1-3) ... Setting up libgradle-core-java (4.4.1-13) ... Setting up libgradle-plugins-java (4.4.1-13) ... Setting up gradle (4.4.1-13) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up gradle-debian-helper (2.1) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (633 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 41342 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Name or service not known I: Running cd /build/htsjdk-2.23.0+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_2.23.0+dfsg-2_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 2.23.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Olivier Sallou dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_auto_clean -O--buildsystem=gradle install -d /build/htsjdk-2.23.0\+dfsg/debian/.debhelper/generated/_source/home 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-2.23.0\+dfsg/.gradle /build/htsjdk-2.23.0\+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 mh_clean -O--buildsystem=gradle 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 install -d /build/htsjdk-2.23.0\+dfsg/debian/.debhelper/generated/_source/home jh_linkjars -O--buildsystem=gradle debian/rules override_dh_auto_build make[1]: ingresso nella directory «/build/htsjdk-2.23.0+dfsg» 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=4 jar javadoc Initialized native services in: /build/htsjdk-2.23.0+dfsg/.gradle/native Using 4 worker leases. Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@783f6c Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@783f6c Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@88660d WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access using Lookup on org.gradle.internal.reflect.JavaMethod (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class java.lang.ClassLoader WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Starting Build Compiling initialization script '/build/htsjdk-2.23.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c93d16 Compiling initialization script '/build/htsjdk-2.23.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/htsjdk-2.23.0+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-2.23.0+dfsg/build.gradle'. Compiling build file '/build/htsjdk-2.23.0+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/htsjdk-2.23.0+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/htsjdk-2.23.0+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.23.0 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-2.23.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@88d194 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-2.23.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@88660d Creating new cache for taskHistory, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@550d86 Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1b470df :compileJava (Thread[main,5,main]) started. :compileJava executing task ':compileJava' ... Putting task artifact state for task ':compileJava' into context took 0.031 secs. Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@ebd983 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:1.1.7.3 -> 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 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 8.976 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. 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. :compileJava (Thread[main,5,main]) completed. Took 1 mins 47.461 secs. :processResources (Thread[main,5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/htsjdk-2.23.0+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE :processResources (Thread[main,5,main]) completed. Took 0.085 secs. :classes (Thread[main,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes (Thread[main,5,main]) completed. Took 0.015 secs. :debianMavenPom (Thread[Task worker for ':' Thread 2,5,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 0.009 secs. It is not up-to-date because: No history is available. Generating pom file /build/htsjdk-2.23.0+dfsg/build/debian/htsjdk.pom :debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.162 secs. :jar (Thread[Task worker for ':' Thread 2,5,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 0.657 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 4.176 secs. :javadoc (Thread[Task worker for ':' Thread 2,5,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 1.796 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc''. Working directory: /build/htsjdk-2.23.0+dfsg Command: /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc @/build/htsjdk-2.23.0+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc'' /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java:54: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/filter/IntervalFilter.java:53: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java:59: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/index/DynamicIndexCreator.java:171: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:17: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/io/ITF8.java:31: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:165: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/index/linear/LinearIndex.java:166: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:75: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/readers/LongLineBufferedReader.java:453: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/readers/Positional.java:45: warning - invalid usage of tag > javadoc: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java:56: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java:464: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java:478: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/reference/FastaReferenceWriter.java:494: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/Bin.java:108: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/Bin.java:108: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/CoordinateSortedPairInfoMap.java:194: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:125: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/DuplicateScoringStrategy.java:150: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:106: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/GenomicIndexUtil.java:124: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/QueryInterval.java:18: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMFileWriterImpl.java:35: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMLineParser.java:221: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:53: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:159: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:159: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecord.java:770: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordComparator.java:37: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:39: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:40: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordCoordinateComparator.java:85: warning - invalid usage of tag < javadoc: warning - invalid usage of tag < javadoc: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java:77: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMSortOrderChecker.java:42: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:657: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:657: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:643: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:644: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:644: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:657: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:657: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:658: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:658: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:1127: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMUtils.java:1127: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMValidationError.java:84: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SAMValidationError.java:84: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:63: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:63: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:64: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/SQTagUtil.java:95: warning - invalid usage of tag > javadoc: warning - invalid usage of tag & /build/htsjdk-2.23.0+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. /build/htsjdk-2.23.0+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. /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/CRAMCompressionRecord.java:376: warning - Tag @link: reference not found: Slice#normalizeCRAMRecords(List, CRAMReferenceRegion, SubstitutionMatrix) /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java:70: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java:90: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java:114: warning - invalid usage of tag > /build/htsjdk-2.23.0+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. /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/FeatureCodecHeader.java:31: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/tribble/FeatureCodecHeader.java:71: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/AbstractLocusIterator.java:210: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:144: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:144: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:152: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:152: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:162: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:162: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:171: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:171: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java:64: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/BlockGunzipper.java:104: warning - Parameter "compressedBlock" is documented more than once. /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/CloserUtil.java:57: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/CloserUtil.java:57: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/CollectionUtil.java:108: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/CollectionUtil.java:108: warning - invalid usage of tag > /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/FormatUtil.java:97: warning - invalid usage of tag & /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:344: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/Histogram.java:520: warning - invalid usage of tag < /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning - invalid usage of tag {@link #uniqued()#getIntervals() /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning - invalid usage of tag {@link #uniqued(boolean)#getIntervals() /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:242: warning - invalid usage of tag {@link #uniqued()#getIntervals() /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning - invalid usage of tag {@link #uniqued(boolean)#getIntervals() /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:322: warning - invalid usage of tag > 100 warnings :javadoc (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1 mins 4.983 secs. BUILD SUCCESSFUL in 3m 27s 4 actionable tasks: 4 executed make[1]: uscita dalla directory «/build/htsjdk-2.23.0+dfsg» 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]: ingresso nella directory «/build/htsjdk-2.23.0+dfsg» # 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=4 test Initialized native services in: /build/htsjdk-2.23.0+dfsg/.gradle/native Using 4 worker leases. Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@e4ea87 Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@e4ea87 Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@19a65d3 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access using Lookup on org.gradle.internal.reflect.JavaMethod (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class java.lang.ClassLoader WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Starting Build Creating new cache for metadata-1.1/results, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@fbeb5 Settings evaluated using settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/htsjdk-2.23.0+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-2.23.0+dfsg/build.gradle'. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/htsjdk-2.23.0+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.23.0 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-2.23.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@13b1597 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-2.23.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@19a65d3 Creating new cache for taskHistory, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@ca9277 Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@842b8e :compileJava (Thread[main,5,main]) started. :compileJava executing task ':compileJava' ... Putting task artifact state for task ':compileJava' into context took 0.015 secs. Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@15a72cd 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:1.1.7.3 -> 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 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 3.653 secs). :compileJava UP-TO-DATE :compileJava (Thread[main,5,main]) completed. Took 3.846 secs. :processResources (Thread[main,5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/htsjdk-2.23.0+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE :processResources (Thread[main,5,main]) completed. Took 0.011 secs. :classes (Thread[main,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[main,5,main]) completed. Took 0.003 secs. :findScalaAndJavaTypes (Thread[main,5,main]) started. :findScalaAndJavaTypes executing task ':findScalaAndJavaTypes' ... Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.004 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-2.23.0+dfsg Command: ./scripts/checkScalaAndJavaFiles.sh Successfully started process 'command './scripts/checkScalaAndJavaFiles.sh'' :findScalaAndJavaTypes (Thread[main,5,main]) completed. Took 0.064 secs. :compileTestJava (Thread[main,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.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Passing through org.jsr-305:jsr305:jar:0.x Up-to-date check for task ':compileTestJava' took 13.857 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. 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. :compileTestJava (Thread[main,5,main]) completed. Took 1 mins 0.258 secs. :processTestResources (Thread[main,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 1.818 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[main,5,main]) completed. Took 4.686 secs. :testClasses (Thread[main,5,main]) started. :testClasses executing task ':testClasses' ... Skipping task ':testClasses' as it has no actions. :testClasses (Thread[main,5,main]) completed. Took 0.002 secs. :testWithDefaultReference (Thread[main,5,main]) started. :testWithDefaultReference executing task ':testWithDefaultReference' ... Putting task artifact state for task ':testWithDefaultReference' into context took 0.003 secs. Up-to-date check for task ':testWithDefaultReference' took 2.118 secs. It is not up-to-date because: Task.upToDateWhen is false. Finished generating test XML results (0.006 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... Finished generating test html results (0.06 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/testWithDefaultReference :testWithDefaultReference (Thread[main,5,main]) completed. Took 2.758 secs. :test (Thread[main,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 0.891 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/htsjdk-2.23.0+dfsg Command: /usr/lib/jvm/java-11-openjdk-armhf/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3242996417464042051txt -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.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters[0](ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf, variantFilter01.js, 61) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters[1](ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf, variantFilter02.js, 38) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR WARNING 2021-07-26 07:02:07 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 2021-07-26 07:02:07 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 2021-07-26 07:02:07 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:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_2 STANDARD_ERROR java.lang.RuntimeException: oops at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$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:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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.testFirstElementOfIterator[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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[3](/build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/htsjdk-2.23.0+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-2.23.0+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[2](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequenceExtended runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 18ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 18ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 19ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+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[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 19ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 19ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 17ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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[2](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/htsjdk-2.23.0+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[1](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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[1](/build/htsjdk-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 21ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 20ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 20ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 20ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 36ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 20ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 18ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 10ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 10ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR WARNING 2021-07-26 07:04:49 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@1cbbae3, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR WARNING 2021-07-26 07:04:49 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 2021-07-26 07:04:49 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 2021-07-26 07:04:49 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 2021-07-26 07:04:49 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.16960543688216336297.bai #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.16667814631212150471.bai #BAMIndexWriterTest diff /tmp/javaBai.16960543688216336297.bai /tmp/cBai.16667814631212150471.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.11248089402019277341.bai.txt #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.15528420282698297735java.bai #BAMIndexWriterTest diff /tmp/javaBai.15528420282698297735java.bai.txt /tmp/cBai.11248089402019277341.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 18ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT 6ms 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.4864242562824038291.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT Creating file /tmp/testCustomDeflater.6271485612348717737.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT Creating file /tmp/BCOST.17999024251458117106.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR WARNING 2021-07-26 07:08:30 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. WARNING 2021-07-26 07:08:30 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR WARNING 2021-07-26 07:08:45 ReferenceSource Sequence not found: chrSheila Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR WARNING 2021-07-26 07:08:46 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. WARNING 2021-07-26 07:08:46 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR WARNING 2021-07-26 07:08:46 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. WARNING 2021-07-26 07:08:46 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. Gradle is still running, please be patient... Gradle is still running, please be patient... Gradle is still running, please be patient... 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.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 Resetting tmpdir Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.11977248740310067094.tmp Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[0](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR WARNING 2021-07-26 07:35:05 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.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR WARNING 2021-07-26 07:35:05 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.testBuildFromFasta[2](src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta) STANDARD_ERROR WARNING 2021-07-26 07:35:05 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.testBuildFromFasta[3](src/test/resources/htsjdk/samtools/reference/crlf.fasta) STANDARD_ERROR WARNING 2021-07-26 07:35:05 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[0](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR WARNING 2021-07-26 07:35:06 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 2021-07-26 07:35:06 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[2](src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta) STANDARD_ERROR WARNING 2021-07-26 07:35:06 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[3](src/test/resources/htsjdk/samtools/reference/crlf.fasta) STANDARD_ERROR WARNING 2021-07-26 07:35:06 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 2021-07-26 07:35:13 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 2021-07-26 07:35:13 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 2021-07-26 07:35:14 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2021-07-26 07:35:14 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 2021-07-26 07:35:15 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2021-07-26 07:35:15 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 2021-07-26 07:35:16 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 WARNING 2021-07-26 07:35:16 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 2021-07-26 07:35:17 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 2021-07-26 07:35:17 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.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp Could not delete file file7758618483451857408.bad Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 1077 milliseconds Queried for the same 100-length mapping 52753798 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[0](unsorted.sam, samFilter01.js, 8) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[1](unsorted.sam, samFilter02.js, 10) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) INFO 2021-07-26 07:35:41 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 2021-07-26 07:35:41 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 2021-07-26 07:35:42 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.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 c b a Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR WARNING 2021-07-26 07:37:16 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 2021-07-26 07:37:16 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 2021-07-26 07:37:16 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 2021-07-26 07:37:16 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 2021-07-26 07:37:16 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR WARNING 2021-07-26 07:37:16 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null WARNING 2021-07-26 07:37:16 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 2021-07-26 07:37:16 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.8239380240928312678..cram INFO 2021-07-26 07:37:16 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2021-07-26 07:37:16 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2021-07-26 07:37:16 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR INFO 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension18247899185974824262.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.15694096978484727469.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 2021-07-26 07:37:16 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension6004022608792656798.cram INFO 2021-07-26 07:37:16 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: INFO 2021-07-26 07:37:16 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null INFO 2021-07-26 07:37:16 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR INFO 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension2213446337932331934 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR INFO 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension10531991986463680860.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR INFO 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://277a772f-ac23-42a2-b8c9-7cd559097f43/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 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://03a73a79-7c7b-47cc-99a8-de1933106333/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 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://951b047e-5ace-4814-a62c-dabdab4dc336/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 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://bcc064f9-de1c-4717-9e88-225049da08f0/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 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d38b6562-4510-428b-b81e-98d3ddf00087/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 2021-07-26 07:37:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://51a0ec28-e1d7-491c-b819-2ef3f84d8a7b/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), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null), false) STANDARD_ERROR ERROR 2021-07-26 07:37:18 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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR WARNING 2021-07-26 07:37:19 SamFiles The index file /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam WARNING 2021-07-26 07:37:19 SamFiles The index file /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR INFO 2021-07-26 07:37:25 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory INFO 2021-07-26 07:37:25 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory INFO 2021-07-26 07:37:25 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar INFO 2021-07-26 07:37:25 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 2021-07-26 07:37:25 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 2021-07-26 07:37:26 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 2021-07-26 07:37:27 SamReaderFactoryTest Finished queries in 100ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR WARNING 2021-07-26 07:37:27 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 2021-07-26 07:37:27 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 2021-07-26 07:37:27 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR WARNING 2021-07-26 07:37:29 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2021-07-26 07:37:29 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 2021-07-26 07:37:29 BAMRecordCodec Reference length is too large for BAM bin field. WARNING 2021-07-26 07:37:29 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 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:30 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 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 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 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:31 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 2021-07-26 07:37:31 Slice Slice mapped outside of reference: seqID=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 suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[0](A, 0, 0, 0, 0, 0, [B@a899a3) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[1](A, 0, 0, 0, 1, 0, [B@271363) STANDARD_OUT A:TCGN C:AGTN G:ACTN T:ACGN N:ACGT a:TCGN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[2](A, 0, 1, 2, 3, 4, [B@1a83f71) STANDARD_OUT A:NTGC C:AGTN G:ACTN T:ACGN N:ACGT a:NTGC c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[3](A, 0, 4, 3, 2, 1, [B@1fea2f4) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[4](C, 0, 0, 0, 0, 0, [B@7a6049) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[5](C, 0, 0, 0, 1, 0, [B@137253c) STANDARD_OUT A:CGTN C:TAGN G:ACTN T:ACGN N:ACGT a:CGTN c:TAGN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[6](C, 1, 0, 2, 3, 4, [B@a96115) STANDARD_OUT A:CGTN C:NTGA G:ACTN T:ACGN N:ACGT a:CGTN c:NTGA g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[7](C, 4, 0, 3, 2, 1, [B@1afb50f) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[8](G, 0, 0, 0, 0, 0, [B@69a049) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[9](G, 0, 0, 0, 1, 0, [B@932e95) STANDARD_OUT A:CGTN C:AGTN G:TACN T:ACGN N:ACGT a:CGTN c:AGTN g:TACN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[10](G, 1, 2, 0, 3, 4, [B@eaf463) STANDARD_OUT A:CGTN C:AGTN G:NTCA T:ACGN N:ACGT a:CGTN c:AGTN g:NTCA t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[11](G, 4, 3, 0, 2, 1, [B@216f6f) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[12](T, 0, 0, 0, 0, 0, [B@1d22a30) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[13](T, 0, 0, 0, 0, 1, [B@1e34f66) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:NACG N:ACGT a:CGTN c:AGTN g:ACTN t:NACG n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[14](T, 1, 2, 3, 0, 4, [B@18778d9) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:NGCA N:ACGT a:CGTN c:AGTN g:ACTN t:NGCA n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[15](T, 4, 3, 2, 0, 1, [B@b4454d) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[16](N, 0, 0, 0, 0, 0, [B@179b844) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[17](N, 0, 0, 0, 1, 0, [B@7524f0) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:TACG a:CGTN c:AGTN g:ACTN t:ACGN n:TACG Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[18](N, 1, 2, 3, 4, 0, [B@1029a97) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:TGCA a:CGTN c:AGTN g:ACTN t:ACGN n:TGCA Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[19](N, 4, 3, 2, 1, 0, [B@1f93bb3) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[101](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. WARNING 2021-07-26 07:37:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle is still running, please be patient... Gradle Test Executor 1 finished executing tests. Finished generating test XML results (1.642 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (2.586 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/test :test (Thread[main,5,main]) completed. Took 41 mins 39.597 secs. BUILD SUCCESSFUL in 43m 9s 6 actionable tasks: 5 executed, 1 up-to-date make[1]: uscita dalla directory «/build/htsjdk-2.23.0+dfsg» 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 -d /build/htsjdk-2.23.0\+dfsg/debian/tmp dh_install -O--buildsystem=gradle install -d debian/libhtsjdk-java/usr/share/libhtsjdk-java cp --reflink=auto -a ./scripts/explain_sam_flags.py debian/libhtsjdk-java/usr/share/libhtsjdk-java/ install -d debian/.debhelper/generated/libhtsjdk-java install -d debian/.debhelper/generated/libhtsjdk-java-doc jh_installjavadoc -O--buildsystem=gradle Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc install -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc cp -r build/docs/javadoc debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/ cat > debian/libhtsjdk-java-doc.doc-base.javadoc dh_installdocs -O--buildsystem=gradle install -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 -p -m0644 debian/copyright debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/copyright install -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 dh_installchangelogs -O--buildsystem=gradle install -p -m0644 debian/changelog debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian install -p -m0644 debian/changelog debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian dh_installsystemduser -O--buildsystem=gradle 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]: ingresso nella directory «/build/htsjdk-2.23.0+dfsg» jh_installlibs --version-strip='[+]dfsg[.0-9]*' install -d debian/libhtsjdk-java/usr/share/java install -p -m0644 ./build/libs/htsjdk-2.23.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-2.23.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar make[1]: uscita dalla directory «/build/htsjdk-2.23.0+dfsg» jh_classpath -O--buildsystem=gradle jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar /usr/share/java/libjaxb-api.jar /usr/share/java/jaxb-impl.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar Updating symlinked /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar) Reading manifest from /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar Updating manifest in /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar jh_manifest -O--buildsystem=gradle find debian/libhtsjdk-java -name '*.jar' Found symlink usr/share/java/htsjdk.jar Found usr/share/java/htsjdk-2.23.0.jar Reading manifest from debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar No update of debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar required. find debian/libhtsjdk-java-doc -name '*.jar' jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle Searching /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java for libhtsjdk-java Searching /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar Found Jars: /usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/jaxb-impl.jar /usr/share/java/libjaxb-api.jar /usr/share/java/ngs-java.jar /usr/share/java/snappy-java.jar /usr/share/java/xz.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/commons-compress.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-compress.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/commons-jexl2.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-jexl2.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/commons-logging-1.2.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/commons-logging-1.2.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/jaxb-runtime.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/jaxb-runtime.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/libjaxb-api.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/libjaxb-api.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/ngs-java-2.10.9.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/ngs-java-2.10.9.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/snappy-java.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/snappy-java.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/xz-1.8.jar Checking: /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java-doc/usr/share/java/xz-1.8.jar Found Debs: libcommons-compress-java libcommons-jexl2-java libcommons-logging-java libjaxb-java libngs-java libsnappy-java libxz-java Adding substvars: java:Depends=libcommons-compress-java, libcommons-jexl2-java, libcommons-logging-java, libjaxb-java, libngs-java, libsnappy-java, libxz-java java:Recommends= Searching /build/htsjdk-2.23.0+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/.mh/pom.xml debian/.mh/pom.properties mv debian/.mh/pom.xml debian/.mh/htsjdk-debian.pom install -m 644 -D debian/.mh/htsjdk-2.14.3.pom debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.pom install -m 644 -D debian/.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/2.14.3/htsjdk-2.14.3.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-2.23.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.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-2.23.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/2.14.3/htsjdk-2.14.3.jar 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 1600780451 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar using File::StripNondeterminism::handlers::jar Using 1600780451 as canonical time Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ProcessExecutor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Locus.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.RevIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ProgressLogger.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Log.LogLevel.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamInputResource.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMValidationError.Severity.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexContent.BinList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/MergingSamRecordIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMValidationError.Type.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMIndexer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMStreamWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BamFileIoUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinaryTagCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/NotPrimarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DownsamplingIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMHeaderRecordComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DownsamplingIteratorFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing 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using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html ipNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/resources/x.png using File::StripNondeterminism::handlers::png Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/resources/glass.png using File::StripNondeterminism::handlers::png 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-2.23.0+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-2.23.0+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-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/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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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 -d debian/libhtsjdk-java/DEBIAN install -d debian/libhtsjdk-java-doc/DEBIAN dh_gencontrol -O--buildsystem=gradle 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 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 chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control dh_md5sums -O--buildsystem=gradle 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: generazione del pacchetto "libhtsjdk-java" in "../libhtsjdk-java_2.23.0+dfsg-2_all.deb". dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. dpkg-deb: generazione del pacchetto "libhtsjdk-java-doc" in "../libhtsjdk-java-doc_2.23.0+dfsg-2_all.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../htsjdk_2.23.0+dfsg-2_armhf.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/8215/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/8215/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/8215 and its subdirectories I: Current time: Mon Jul 26 07:44:44 +14 2021 I: pbuilder-time-stamp: 1627235084