I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 22 09:45:00 +14 2022 I: pbuilder-time-stamp: 1661111100 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 [bioperl-run_1.7.3-6.dsc] I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.kjmJFULO/trustedkeys.kbx': General error gpgv: Signature made Thu Jan 7 11:46:40 2021 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bioperl-run_1.7.3-6.dsc dpkg-source: info: extracting bioperl-run in bioperl-run-1.7.3 dpkg-source: info: unpacking bioperl-run_1.7.3.orig.tar.gz dpkg-source: info: unpacking bioperl-run_1.7.3-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Extract_version_from_BEDTools_properly.patch dpkg-source: info: applying skip_tests_for_RemoteBlast_rpsblast.patch dpkg-source: info: applying skip_tests_for_RemoteBlast.patch dpkg-source: info: applying kalign-input-via-piping.patch dpkg-source: info: applying kalign-version-regex.patch dpkg-source: info: applying skip_tests_for_wise.patch dpkg-source: info: applying skip_tests_for_phylip.patch dpkg-source: info: applying skip_tests_for_phyml.patch dpkg-source: info: applying skip_tests_for_infernal.patch dpkg-source: info: applying skip_tests_for_muscle.patch dpkg-source: info: applying skip_tests_for_ncbi-blast+.patch dpkg-source: info: applying hyphy.patch dpkg-source: info: applying remove_tests_for_ensembl.patch dpkg-source: info: applying skip_tests_for_soap.patch dpkg-source: info: applying get-overlap.patch dpkg-source: info: applying alternate-data.patch dpkg-source: info: applying skip-test-for-kalign.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26025/tmp/hooks/D01_modify_environment starting debug: Running on codethink9-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash 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/26025/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/26025/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]="aarch64-unknown-linux-gnu") 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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu 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=26025 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.ufesIY0dRc/pbuilderrc_yFPz --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ufesIY0dRc/b2 --logfile b2/build.log --extrapackages usrmerge bioperl-run_1.7.3-6.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 2021 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 2021 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 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 2021 more -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount -rwxr-xr-x 1 root root 14496 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 22 09:45 sh -> bash lrwxrwxrwx 1 root root 4 Aug 21 05:48 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/26025/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team 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: debhelper-compat (= 13), perl, libmodule-build-perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, clustalw, emboss, exonerate, hyphy-pt | hyphy-mpi, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, libwww-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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 debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl (>= 1.7.4); however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libalgorithm-diff-perl; however: Package libalgorithm-diff-perl is not installed. pbuilder-satisfydepends-dummy depends on libipc-run-perl; however: Package libipc-run-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libxml-twig-perl; however: Package libxml-twig-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-sort-perl; however: Package libfile-sort-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libarray-compare-perl; however: Package libarray-compare-perl is not installed. pbuilder-satisfydepends-dummy depends on libtree-dagnode-perl; however: Package libtree-dagnode-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-cluster-perl; however: Package libbio-cluster-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-featureio-perl; however: Package libbio-featureio-perl is not installed. pbuilder-satisfydepends-dummy depends on libconfig-any-perl; however: Package libconfig-any-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-tools-run-alignment-clustalw-perl; however: Package libbio-tools-run-alignment-clustalw-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-eutilities-perl; however: Package libbio-eutilities-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-tools-run-remoteblast-perl; however: Package libbio-tools-run-remoteblast-perl is not installed. pbuilder-satisfydepends-dummy depends on amap-align; however: Package amap-align is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on bedtools-test; however: Package bedtools-test is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+-legacy; however: Package ncbi-blast+-legacy is not installed. pbuilder-satisfydepends-dummy depends on clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on emboss; however: Package emboss is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on hyphy-pt | hyphy-mpi; however: Package hyphy-pt is not installed. Package hyphy-mpi is not installed. pbuilder-satisfydepends-dummy depends on kalign; however: Package kalign is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on muscle; however: Package muscle is not installed. pbuilder-satisfydepends-dummy depends on ncoils; however: Package ncoils is not installed. pbuilder-satisfydepends-dummy depends on phyml; however: Package phyml is not installed. pbuilder-satisfydepends-dummy depends on primer3; however: Package primer3 is not installed. pbuilder-satisfydepends-dummy depends on probcons; however: Package probcons is not installed. pbuilder-satisfydepends-dummy depends on python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on sim4; however: Package sim4 is not installed. pbuilder-satisfydepends-dummy depends on tigr-glimmer; however: Package tigr-glimmer is not installed. pbuilder-satisfydepends-dummy depends on wise; however: Package wise is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on lagan; however: Package lagan is not installed. pbuilder-satisfydepends-dummy depends on pal2nal; however: Package pal2nal is not installed. pbuilder-satisfydepends-dummy depends on libwww-perl; however: Package libwww-perl 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: amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} hyphy-common{a} hyphy-pt{a} ibverbs-providers{a} intltool-debian{a} kalign{a} lagan{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libarray-compare-perl{a} libb-hooks-op-check-perl{a} libbio-asn1-entrezgene-perl{a} libbio-cluster-perl{a} libbio-db-ncbihelper-perl{a} libbio-eutilities-perl{a} libbio-featureio-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbio-tools-run-remoteblast-perl{a} libbio-variation-perl{a} libbrotli1{a} libbsd0{a} libcache-cache-perl{a} libcapture-tiny-perl{a} libcbor0{a} libcgi-pm-perl{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libconfig-any-perl{a} libcurl3-gnutls{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libencode-locale-perl{a} liberror-perl{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfido2-1{a} libfile-listing-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgd3{a} libglib2.0-0{a} libhpdf-2.3.0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhts3{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu67{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libipc-run-perl{a} libipc-sharelite-perl{a} libjbig0{a} libjpeg62-turbo{a} libldap-2.4-2{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmariadb3{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmd0{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmpdec3{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenmpi3{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpng16-16{a} libpq5{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} librdmacm1{a} libreadline8{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libstrictures-perl{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-csv-perl{a} libtext-diff-perl{a} libtiff5{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} libucx0{a} liburi-perl{a} libwebp6{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml-dom-perl{a} libxml-dom-xpath-perl{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-parser-perl{a} libxml-perl{a} libxml-regexp-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml-twig-perl{a} libxml-writer-perl{a} libxml-xpathengine-perl{a} libxml2{a} libxnvctrl0{a} libxpm4{a} m4{a} mafft{a} man-db{a} mariadb-common{a} media-types{a} muscle{a} mysql-common{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncoils{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pal2nal{a} perl-openssl-defaults{a} phyml{a} po-debconf{a} primer3{a} probcons{a} python3{a} python3-minimal{a} python3-pybedtools{a} python3-pysam{a} python3-six{a} python3.9{a} python3.9-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} tigr-glimmer{a} ucf{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl dialign libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcgi-fast-perl libclass-xsaccessor-perl libclone-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtext-csv-xs-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-libxslt-perl libxml-sax-expat-perl libxml-sax-writer-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl lynx paml perl-doc perl-tk publicsuffix ruby shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 229 newly installed, 0 to remove and 0 not upgraded. Need to get 162 MB of archives. After unpacking 857 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libcbor0 arm64 0.5.0+dfsg-2 [20.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 libfido2-1 arm64 1.6.0-2 [50.2 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 openssh-client arm64 1:8.4p1-5 [892 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 amap-align arm64 2.2+git20080214.600fc29+dfsg-2 [125 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 bedtools arm64 2.30.0+dfsg-1 [579 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 bedtools-test all 2.30.0+dfsg-1 [10.8 MB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libdata-stag-perl all 0.14-2 [448 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libtest-deep-perl all 1.130-1 [49.3 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libtest-differences-perl all 0.67-1 [18.7 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libtest-most-perl all 0.37-1 [24.9 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 bioperl all 1.7.7-2 [246 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 clustalw arm64 2.1+lgpl-7 [248 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1 [276 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libgd3 arm64 2.3.0-2 [127 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1+b1 [346 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 mysql-common all 5.8+1.0.7 [7464 B] Get: 94 http://deb.debian.org/debian bullseye/main arm64 mariadb-common all 1:10.5.10-2 [36.0 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libmariadb3 arm64 1:10.5.10-2 [165 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libpq5 arm64 13.3-1 [171 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 emboss-lib arm64 6.6.0+dfsg-9 [2707 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 emboss-data all 6.6.0+dfsg-9 [61.1 MB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 emboss arm64 6.6.0+dfsg-9 [1017 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 exonerate arm64 2.4.0-5 [1439 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 fasttree arm64 2.1.11-2 [172 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 hyphy-common all 2.5.28+dfsg-3 [566 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 hyphy-pt arm64 2.5.28+dfsg-3 [784 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libnl-3-200 arm64 3.4.0-1+b1 [60.6 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libnl-route-3-200 arm64 3.4.0-1+b1 [149 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libibverbs1 arm64 33.2-1 [56.1 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 ibverbs-providers arm64 33.2-1 [235 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 kalign arm64 1:3.3-1+b3 [74.0 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 lagan arm64 2.0-6 [173 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b3 [11.2 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 libdevel-callchecker-perl arm64 0.008-1+b2 [15.8 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 libparams-classify-perl arm64 0.015-1+b3 [25.5 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get: 128 http://deb.debian.org/debian bullseye/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 libmoo-perl all 2.004004-1 [59.9 kB] Get: 130 http://deb.debian.org/debian bullseye/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get: 131 http://deb.debian.org/debian bullseye/main arm64 libtype-tiny-perl all 1.012001-2 [351 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 libarray-compare-perl all 3.0.8-1 [14.9 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 liberror-perl all 0.17029-1 [31.0 kB] Get: 134 http://deb.debian.org/debian bullseye/main arm64 libipc-sharelite-perl arm64 0.17-4+b5 [24.1 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 libcache-cache-perl all 1.08-2 [76.6 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 liburi-perl all 5.08-1 [90.6 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 libhtml-parser-perl arm64 3.75-1+b1 [103 kB] Get: 139 http://deb.debian.org/debian bullseye/main arm64 libcgi-pm-perl all 4.51-1 [224 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 142 http://deb.debian.org/debian bullseye/main arm64 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 libio-html-perl all 1.004-2 [16.1 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 145 http://deb.debian.org/debian bullseye/main arm64 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 libfile-listing-perl all 6.14-1 [12.4 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 149 http://deb.debian.org/debian bullseye/main arm64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 150 http://deb.debian.org/debian bullseye/main arm64 perl-openssl-defaults arm64 5 [7360 B] Get: 151 http://deb.debian.org/debian bullseye/main arm64 libnet-ssleay-perl arm64 1.88-3+b1 [316 kB] Get: 152 http://deb.debian.org/debian bullseye/main arm64 libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 libnet-http-perl all 6.20-1 [25.1 kB] Get: 154 http://deb.debian.org/debian bullseye/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 155 http://deb.debian.org/debian bullseye/main arm64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 libwww-perl all 6.52-1 [192 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 libxml-parser-perl arm64 2.46-2 [205 kB] Get: 159 http://deb.debian.org/debian bullseye/main arm64 libxml-twig-perl all 1:3.52-1 [181 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 libbio-db-ncbihelper-perl all 1.7.6-4 [58.1 kB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 libxml-writer-perl all 0.900-1 [29.9 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 libbio-variation-perl all 1.7.5-2 [72.5 kB] Get: 163 http://deb.debian.org/debian bullseye/main arm64 libbio-cluster-perl all 1.7.3-5 [53.2 kB] Get: 164 http://deb.debian.org/debian bullseye/main arm64 libbio-asn1-entrezgene-perl all 1.730-2 [48.6 kB] Get: 165 http://deb.debian.org/debian bullseye/main arm64 libtext-csv-perl all 2.00-1 [105 kB] Get: 166 http://deb.debian.org/debian bullseye/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get: 167 http://deb.debian.org/debian bullseye/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get: 168 http://deb.debian.org/debian bullseye/main arm64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get: 169 http://deb.debian.org/debian bullseye/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get: 170 http://deb.debian.org/debian bullseye/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get: 171 http://deb.debian.org/debian bullseye/main arm64 libbio-eutilities-perl all 1.77-1 [124 kB] Get: 172 http://deb.debian.org/debian bullseye/main arm64 libfile-slurp-tiny-perl all 0.004-1 [7288 B] Get: 173 http://deb.debian.org/debian bullseye/main arm64 libtree-dagnode-perl all 1.32-1 [61.7 kB] Get: 174 http://deb.debian.org/debian bullseye/main arm64 libxml-perl all 0.08-3.1 [93.9 kB] Get: 175 http://deb.debian.org/debian bullseye/main arm64 libxml-regexp-perl all 0.04-1.1 [7500 B] Get: 176 http://deb.debian.org/debian bullseye/main arm64 libxml-dom-perl all 1.46-1 [154 kB] Get: 177 http://deb.debian.org/debian bullseye/main arm64 libxml-xpathengine-perl all 0.14-1 [33.3 kB] Get: 178 http://deb.debian.org/debian bullseye/main arm64 libxml-dom-xpath-perl all 0.14-3 [9066 B] Get: 179 http://deb.debian.org/debian bullseye/main arm64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get: 180 http://deb.debian.org/debian bullseye/main arm64 libio-pty-perl arm64 1:1.15-2 [36.0 kB] Get: 181 http://deb.debian.org/debian bullseye/main arm64 libipc-run-perl all 20200505.0-1 [102 kB] Get: 182 http://deb.debian.org/debian bullseye/main arm64 libfile-sort-perl all 1.01-2 [21.2 kB] Get: 183 http://deb.debian.org/debian bullseye/main arm64 libbio-perl-run-perl all 1.7.3-6 [606 kB] Get: 184 http://deb.debian.org/debian bullseye/main arm64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-2 [24.5 kB] Get: 185 http://deb.debian.org/debian bullseye/main arm64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get: 186 http://deb.debian.org/debian bullseye/main arm64 libmodule-pluggable-perl all 5.2-1 [25.7 kB] Get: 187 http://deb.debian.org/debian bullseye/main arm64 libconfig-any-perl all 0.32-1 [32.2 kB] Get: 188 http://deb.debian.org/debian bullseye/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-1 [132 kB] Get: 189 http://deb.debian.org/debian bullseye/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-1 [57.2 kB] Get: 190 http://deb.debian.org/debian bullseye/main arm64 librdmacm1 arm64 33.2-1 [65.3 kB] Get: 191 http://deb.debian.org/debian bullseye/main arm64 libfabric1 arm64 1.11.0-2 [389 kB] Get: 192 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 193 http://deb.debian.org/debian bullseye/main arm64 libpciaccess0 arm64 0.16-1 [52.9 kB] Get: 194 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 195 http://deb.debian.org/debian bullseye/main arm64 libxnvctrl0 arm64 460.73.01-1 [26.7 kB] Get: 196 http://deb.debian.org/debian bullseye/main arm64 ocl-icd-libopencl1 arm64 2.2.14-2 [41.5 kB] Get: 197 http://deb.debian.org/debian bullseye/main arm64 libhwloc15 arm64 2.4.1+dfsg-1 [131 kB] Get: 198 http://deb.debian.org/debian bullseye/main arm64 libhwloc-plugins arm64 2.4.1+dfsg-1 [21.1 kB] Get: 199 http://deb.debian.org/debian bullseye/main arm64 liblmdb0 arm64 0.9.24-1 [43.7 kB] Get: 200 http://deb.debian.org/debian bullseye/main arm64 libmbedcrypto3 arm64 2.16.9-0.1 [211 kB] Get: 201 http://deb.debian.org/debian bullseye/main arm64 libmbedx509-0 arm64 2.16.9-0.1 [108 kB] Get: 202 http://deb.debian.org/debian bullseye/main arm64 libmbedtls12 arm64 2.16.9-0.1 [132 kB] Get: 203 http://deb.debian.org/debian bullseye/main arm64 libmodule-build-perl all 0.423100-1 [258 kB] Get: 204 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 205 http://deb.debian.org/debian bullseye/main arm64 libnuma1 arm64 2.0.12-1+b1 [25.8 kB] Get: 206 http://deb.debian.org/debian bullseye/main arm64 libpmix2 arm64 4.0.0-4 [513 kB] Get: 207 http://deb.debian.org/debian bullseye/main arm64 libucx0 arm64 1.10.1~rc1+really.1.10.0-1 [567 kB] Get: 208 http://deb.debian.org/debian bullseye/main arm64 libopenmpi3 arm64 4.1.0-10 [2152 kB] Get: 209 http://deb.debian.org/debian bullseye/main arm64 mafft arm64 7.475-1 [922 kB] Get: 210 http://deb.debian.org/debian bullseye/main arm64 muscle arm64 1:3.8.1551-2 [228 kB] Get: 211 http://deb.debian.org/debian bullseye/main arm64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 212 http://deb.debian.org/debian bullseye/main arm64 ncbi-blast+ arm64 2.11.0+ds-1 [10.2 MB] Get: 213 http://deb.debian.org/debian bullseye/main arm64 ncbi-blast+-legacy all 2.11.0+ds-1 [13.1 kB] Get: 214 http://deb.debian.org/debian bullseye/main arm64 ncoils arm64 2002-8 [21.8 kB] Get: 215 http://deb.debian.org/debian bullseye/main arm64 openmpi-common all 4.1.0-10 [179 kB] Get: 216 http://deb.debian.org/debian bullseye/main arm64 openmpi-bin arm64 4.1.0-10 [237 kB] Get: 217 http://deb.debian.org/debian bullseye/main arm64 pal2nal all 14.1-3 [17.8 kB] Get: 218 http://deb.debian.org/debian bullseye/main arm64 phyml arm64 3:3.3.20200621-1 [1723 kB] Get: 219 http://deb.debian.org/debian bullseye/main arm64 primer3 arm64 2.4.0-4 [165 kB] Get: 220 http://deb.debian.org/debian bullseye/main arm64 probcons arm64 1.12-13 [111 kB] Get: 221 http://deb.debian.org/debian bullseye/main arm64 python3-pysam arm64 0.15.4+ds-3+b2 [1386 kB] Get: 222 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-1 [17.1 kB] Get: 223 http://deb.debian.org/debian bullseye/main arm64 python3-pybedtools arm64 0.8.0-5+b2 [12.1 MB] Get: 224 http://deb.debian.org/debian bullseye/main arm64 raxml arm64 8.2.12+dfsg-6+b4 [953 kB] Get: 225 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 226 http://deb.debian.org/debian bullseye/main arm64 sim4 arm64 0.0.20121010-8 [355 kB] Get: 227 http://deb.debian.org/debian bullseye/main arm64 tigr-glimmer arm64 3.02b-5 [273 kB] Get: 228 http://deb.debian.org/debian bullseye/main arm64 wise-data all 2.4.1-23 [78.2 kB] Get: 229 http://deb.debian.org/debian bullseye/main arm64 wise arm64 2.4.1-23 [969 kB] Fetched 162 MB in 4s (41.1 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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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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 ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.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:arm64. 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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 ... 20934 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.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 ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../009-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../010-libbsd0_0.11.3-1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../011-libedit2_3.1-20191231-2+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:arm64. Preparing to unpack .../012-libcbor0_0.5.0+dfsg-2_arm64.deb ... Unpacking libcbor0:arm64 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../013-libfido2-1_1.6.0-2_arm64.deb ... Unpacking libfido2-1:arm64 (1.6.0-2) ... Selecting previously unselected package openssh-client. Preparing to unpack .../014-openssh-client_1%3a8.4p1-5_arm64.deb ... Unpacking openssh-client (1:8.4p1-5) ... Selecting previously unselected package ucf. Preparing to unpack .../015-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package amap-align. Preparing to unpack .../016-amap-align_2.2+git20080214.600fc29+dfsg-2_arm64.deb ... Unpacking amap-align (2.2+git20080214.600fc29+dfsg-2) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../017-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. 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Preparing to unpack .../027-libbio-perl-perl_1.7.7-2_all.deb ... Unpacking libbio-perl-perl (1.7.7-2) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../028-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../029-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../030-libexception-class-perl_1.44-1_all.deb ... Unpacking libexception-class-perl (1.44-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../031-libtest-deep-perl_1.130-1_all.deb ... Unpacking libtest-deep-perl (1.130-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../032-libcapture-tiny-perl_0.48-1_all.deb ... 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Preparing to unpack .../038-libtest-warn-perl_0.36-1_all.deb ... Unpacking libtest-warn-perl (0.36-1) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../039-libtest-most-perl_0.37-1_all.deb ... Unpacking libtest-most-perl (0.37-1) ... Selecting previously unselected package bioperl. Preparing to unpack .../040-bioperl_1.7.7-2_all.deb ... Unpacking bioperl (1.7.7-2) ... Selecting previously unselected package clustalw. Preparing to unpack .../041-clustalw_2.1+lgpl-7_arm64.deb ... Unpacking clustalw (2.1+lgpl-7) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../046-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../047-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../048-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../049-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../050-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../051-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../052-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../053-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../054-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../055-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../056-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../057-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../058-libpng16-16_1.6.37-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../059-libfreetype6_2.10.4+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../060-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../061-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:arm64. 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Preparing to unpack .../186-libmodule-build-perl_0.423100-1_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423100-1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../187-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../188-libnuma1_2.0.12-1+b1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.12-1+b1) ... Selecting previously unselected package libpmix2:arm64. Preparing to unpack .../189-libpmix2_4.0.0-4_arm64.deb ... Unpacking libpmix2:arm64 (4.0.0-4) ... Selecting previously unselected package libucx0:arm64. Preparing to unpack .../190-libucx0_1.10.1~rc1+really.1.10.0-1_arm64.deb ... Unpacking libucx0:arm64 (1.10.1~rc1+really.1.10.0-1) ... Selecting previously unselected package libopenmpi3:arm64. Preparing to unpack .../191-libopenmpi3_4.1.0-10_arm64.deb ... Unpacking libopenmpi3:arm64 (4.1.0-10) ... Selecting previously unselected package mafft. Preparing to unpack .../192-mafft_7.475-1_arm64.deb ... Unpacking mafft (7.475-1) ... Selecting previously unselected package muscle. Preparing to unpack .../193-muscle_1%3a3.8.1551-2_arm64.deb ... Unpacking muscle (1:3.8.1551-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../194-ncbi-data_6.1.20170106+dfsg1-9_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-9) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../195-ncbi-blast+_2.11.0+ds-1_arm64.deb ... Unpacking ncbi-blast+ (2.11.0+ds-1) ... Selecting previously unselected package ncbi-blast+-legacy. Preparing to unpack .../196-ncbi-blast+-legacy_2.11.0+ds-1_all.deb ... 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Unpacking sim4 (0.0.20121010-8) ... Selecting previously unselected package tigr-glimmer. Preparing to unpack .../210-tigr-glimmer_3.02b-5_arm64.deb ... Unpacking tigr-glimmer (3.02b-5) ... Selecting previously unselected package wise-data. Preparing to unpack .../211-wise-data_2.4.1-23_all.deb ... Unpacking wise-data (2.4.1-23) ... Selecting previously unselected package wise. Preparing to unpack .../212-wise_2.4.1-23_arm64.deb ... Unpacking wise (2.4.1-23) ... Setting up media-types (4.0.0) ... Setting up libmodule-pluggable-perl (5.2-1) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up liblmdb0:arm64 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-9) ... Setting up libpciaccess0:arm64 (0.16-1) ... Setting up mysql-common (5.8+1.0.7) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up probcons (1.12-13) ... Setting up libicu67:arm64 (67.1-7) ... Setting up libdynaloader-functions-perl (0.003-1.1) ... Setting up libtest-deep-perl (1.130-1) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.15-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up mafft (7.475-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libfile-slurp-tiny-perl (0.004-1) ... Setting up libipc-sharelite-perl (0.17-4+b5) ... Setting up libcbor0:arm64 (0.5.0+dfsg-2) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up perl-openssl-defaults:arm64 (5) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4) ... Setting up libencode-locale-perl (1.05-1.1) ... Setting up ncoils (2002-8) ... Setting up hyphy-common (2.5.28+dfsg-3) ... Setting up file (1:5.39-3) ... Setting up muscle (1:3.8.1551-2) ... Setting up emboss-data (6.6.0+dfsg-9) ... Setting up libjbig0:arm64 (2.1-3.1+b2) ... Setting up libmodule-build-perl (0.423100-1) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up liberror-perl (0.17029-1) ... Setting up mariadb-common (1:10.5.10-2) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up primer3 (2.4.0-4) ... Setting up kalign (1:3.3-1+b3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up lagan (2.0-6) ... Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.1-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libxml-xpathengine-perl (0.14-1) ... Setting up sim4 (0.0.20121010-8) ... Setting up libxml-writer-perl (0.900-1) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up libhwloc15:arm64 (2.4.1+dfsg-1) ... Setting up libevent-core-2.1-7:arm64 (2.1.12-stable-1) ... Setting up libio-html-perl (1.004-2) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:arm64 (0.6.1-2.1) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up libmariadb3:arm64 (1:10.5.10-2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libipc-run-perl (20200505.0-1) ... Setting up wise-data (2.4.1-23) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libnuma1:arm64 (2.0.12-1+b1) ... Setting up libtree-dagnode-perl (1.32-1) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:arm64 (2.2.14-2) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up pal2nal (14.1-3) ... Setting up libnl-3-200:arm64 (3.4.0-1+b1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libconfig-any-perl (0.32-1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmbedcrypto3:arm64 (2.16.9-0.1) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libtiff5:arm64 (4.2.0-1) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up bedtools-test (2.30.0+dfsg-1) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libfido2-1:arm64 (1.6.0-2) ... Setting up openssl (1.1.1k-1) ... Setting up libbsd0:arm64 (0.11.3-1) ... Setting up tigr-glimmer (3.02b-5) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up exonerate (2.4.0-5) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up liburi-perl (5.08-1) ... Setting up libfile-sort-perl (1.01-2) ... Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-1) ... Setting up raxml (8.2.12+dfsg-6+b4) ... Setting up libtext-csv-perl (2.00-1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libbio-perl-run-perl (1.7.3-6) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libhpdf-2.3.0:arm64 (2.3.0+dfsg-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libxcb1:arm64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libcache-cache-perl (1.08-2) ... Setting up libtool (2.4.6-15) ... Setting up libmbedx509-0:arm64 (2.16.9-0.1) ... Setting up wise (2.4.1-23) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libedit2:arm64 (3.1-20191231-2+b1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libmbedtls12:arm64 (2.16.9-0.1) ... Setting up libtype-tiny-perl (1.012001-2) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up libnet-http-perl (6.20-1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libexception-class-perl (1.44-1) ... Setting up hyphy-pt (2.5.28+dfsg-3) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnl-route-3-200:arm64 (3.4.0-1+b1) ... Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-2) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up libx11-6:arm64 (2:1.7.1-1) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up libhttp-message-perl (6.28-1) ... 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 libhttp-negotiate-perl (6.01-1) ... Setting up libibverbs1:arm64 (33.2-1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up ibverbs-providers:arm64 (33.2-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libtest-most-perl (0.37-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up openssh-client (1:8.4p1-5) ... 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 libcgi-pm-perl (4.51-1) ... Setting up libpq5:arm64 (13.3-1) ... Setting up libxext6:arm64 (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 libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up samtools (1.11-1) ... Setting up libxnvctrl0:arm64 (460.73.01-1) ... Setting up dh-autoreconf (20) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up bioperl (1.7.7-2) ... Setting up librdmacm1:arm64 (33.2-1) ... Setting up libucx0:arm64 (1.10.1~rc1+really.1.10.0-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libhwloc-plugins:arm64 (2.4.1+dfsg-1) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up python3-six (1.16.0-1) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libgd3:arm64 (2.3.0-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up emboss-lib (6.6.0+dfsg-9) ... Setting up ncbi-blast+-legacy (2.11.0+ds-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up emboss (6.6.0+dfsg-9) ... Setting up libpmix2:arm64 (4.0.0-4) ... Setting up libopenmpi3:arm64 (4.1.0-10) ... Setting up openmpi-bin (4.1.0-10) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20200621-1) ... Setting up python3-pybedtools (0.8.0-5+b2) ... Setting up libbio-asn1-entrezgene-perl (1.730-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.52-1) ... Setting up libbio-eutilities-perl (1.77-1) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up libxml-parser-perl:arm64 (2.46-2) ... Setting up libxml-twig-perl (1:3.52-1) ... Setting up libbio-db-ncbihelper-perl (1.7.6-4) ... Setting up libxml-perl (0.08-3.1) ... Setting up libxml-dom-perl (1.46-1) ... Setting up libxml-dom-xpath-perl (0.14-3) ... Setting up libbio-variation-perl (1.7.5-2) ... Setting up libbio-featureio-perl (1.6.905-2) ... Setting up libbio-cluster-perl (1.7.3-5) ... Processing triggers for libc-bin (2.31-12) ... 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. 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 arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1867 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 ... 31737 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: Temporary failure in name resolution I: Running cd /build/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-6_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bioperl-run-1.7.3' dh_auto_configure -- --install_scripts perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/build/bioperl-run-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/bioperl-run-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n ]n Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' make[1]: Leaving directory '/build/bioperl-run-1.7.3' dh_auto_build perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/bioperl-run-1.7.3' mkdir t.skip for t in Blat Eponine Glimmer2 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t t.skip ; done PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \ PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \ dh_auto_test --no-parallel perl Build test --verbose 1 AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: t/data/cysprot.fa Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: /tmp/Q3btsTFAuP Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG t/Amap.t ...................... 1..18 ok 1 - use Bio::Tools::Run::Alignment::Amap; ok 2 - use Bio::SeqIO; ok 3 - use File::Spec; ok 4 - Found input file ok 5 - An object of class 'Bio::Tools::Run::Alignment::Amap' isa 'Bio::Tools::Run::Alignment::Amap' ok 6 - program_dir returned correct default ok 7 - error_string returned correct default ok 8 - aformat returned correct default ok 9 - outfile_name returned correct default ok 10 - Correct exe default name ok 11 - Correct minimum program version ok 12 - No error occured ok 13 - outfile_name returned something ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 15 - Correct number of seqs returned ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 17 - Correct number of seqs returned ok 18 - Got the correct ave % identity ok t/BEDTools.t .................. 1..423 ok 1 - make a default factory ok 2 - default to command 'bam_to_bed' ok 3 - make a factory using command 'annotate' ok 4 - factory command for 'annotate' is correct ok 5 - all available options for 'annotate' ok 6 - available parameters for 'annotate' ok 7 - available switches for 'annotate' ok 8 - get version for 'annotate' ok 9 - can run command 'annotate' ok 10 - result files exists for command 'annotate' ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' ok 14 - file format of '/tmp/tvgXrJ6T27/8zPt6BSbGk.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' ok 18 - can get the specific object result for command 'annotate' ok 19 - 'returned object is correct for command 'annotate'' isa 'Bio::SeqFeature::Collection' ok 20 - correct number of features for command 'annotate' # TODO maybe adapt reference results to Debian specific dataset ok 21 - make a factory using command 'fasta_from_bed' ok 22 - factory command for 'fasta_from_bed' is correct ok 23 - all available options for 'fasta_from_bed' ok 24 - available parameters for 'fasta_from_bed' ok 25 - available switches for 'fasta_from_bed' ok 26 - get version for 'fasta_from_bed' ok 27 - can run command 'fasta_from_bed' ok 28 - result files exists for command 'fasta_from_bed' ok 29 - can return output format for command 'fasta_from_bed' ok 30 - result claims to be in correct format for command 'fasta_from_bed' ok 31 - can return output file for command 'fasta_from_bed' ok 32 - file format consistent with claim for 'fasta_from_bed' ok 33 - can set want to IO object for command 'fasta_from_bed' ok 34 - can get the basic object result for command 'fasta_from_bed' ok 35 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::Root::IO' ok 36 - can get the specific object result for command 'fasta_from_bed' ok 37 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::SeqIO' ok 38 - correct number of sequences for command 'fasta_from_bed' ok 39 - make a factory using command 'overlap' ok 40 - factory command for 'overlap' is correct ok 41 - all available options for 'overlap' ok 42 - available parameters for 'overlap' ok 43 - available switches for 'overlap' ok 44 - get version for 'overlap' ok 45 - can set parameter -columns => '2,3,5,6' ok 46 - can run command 'overlap' ok 47 - result files exists for command 'overlap' ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' ok 51 - file format of '/tmp/GOcm6jmbop/cvPNRmvDnC.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' ok 55 - can get the specific object result for command 'overlap' ok 56 - 'returned object is correct for command 'overlap'' isa 'Bio::SeqFeature::Collection' ok 57 - correct number of features for command 'overlap' # TODO maybe adapt reference results to Debian specific dataset ok 58 - make a factory using command 'bam_to_bed' ok 59 - factory command for 'bam_to_bed' is correct ok 60 - all available options for 'bam_to_bed' ok 61 - available parameters for 'bam_to_bed' ok 62 - available switches for 'bam_to_bed' ok 63 - get version for 'bam_to_bed' ok 64 - can run command 'bam_to_bed' ok 65 - result files exists for command 'bam_to_bed' ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' ok 69 - file format of '/tmp/NDweTEU7GO/kqDLbho8bk.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' ok 73 - can get the specific object result for command 'bam_to_bed' ok 74 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::SeqFeature::Collection' ok 75 - correct number of features for command 'bam_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 76 - make a factory using command 'genome_coverage' ok 77 - factory command for 'genome_coverage' is correct ok 78 - all available options for 'genome_coverage' ok 79 - available parameters for 'genome_coverage' ok 80 - available switches for 'genome_coverage' ok 81 - get version for 'genome_coverage' ok 82 - can run command 'genome_coverage' ok 83 - result files exists for command 'genome_coverage' ok 84 - can return output format for command 'genome_coverage' ok 85 - result claims to be in correct format for command 'genome_coverage' ok 86 - can return output file for command 'genome_coverage' ok 87 - make readable output not ok 88 - - number of lines # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test ' - number of lines' # at t/BEDTools.t line 331. # got: '87' # expected: '38' ok 89 - can set want to IO object for command 'genome_coverage' ok 90 - can get the basic object result for command 'genome_coverage' ok 91 - 'returned object is correct for command 'genome_coverage'' isa 'Bio::Root::IO' ok 92 - make a factory using command 'pair_to_pair' ok 93 - factory command for 'pair_to_pair' is correct ok 94 - all available options for 'pair_to_pair' ok 95 - available parameters for 'pair_to_pair' ok 96 - available switches for 'pair_to_pair' ok 97 - get version for 'pair_to_pair' ok 98 - can set parameter -type => 'neither' ok 99 - can run command 'pair_to_pair' ok 100 - result files exists for command 'pair_to_pair' ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' ok 104 - file format of '/tmp/sziQWYkPe5/EoYqY2lAc8.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' ok 108 - can get the specific object result for command 'pair_to_pair' ok 109 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::SeqFeature::Collection' ok 110 - correct number of features for command 'pair_to_pair' # TODO maybe adapt reference results to Debian specific dataset ok 111 - make a factory using command 'bed_to_bam' ok 112 - factory command for 'bed_to_bam' is correct ok 113 - all available options for 'bed_to_bam' ok 114 - available parameters for 'bed_to_bam' ok 115 - available switches for 'bed_to_bam' ok 116 - get version for 'bed_to_bam' ok 117 - can run command 'bed_to_bam' ok 118 - result files exists for command 'bed_to_bam' ok 119 - can return output format for command 'bed_to_bam' ok 120 - result claims to be in correct format for command 'bed_to_bam' ok 121 - can return output file for command 'bed_to_bam' ok 122 - can set want to IO object for command 'bed_to_bam' ok 123 - can get the basic object result for command 'bed_to_bam' ok 124 - 'returned object is correct for command 'bed_to_bam'' isa 'Bio::Root::IO' ok 125 - make a factory using command 'graph_union' ok 126 - factory command for 'graph_union' is correct ok 127 - all available options for 'graph_union' ok 128 - available parameters for 'graph_union' ok 129 - available switches for 'graph_union' ok 130 - get version for 'graph_union' ok 131 - can run command 'graph_union' ok 132 - result files exists for command 'graph_union' ok 133 - can return output format for command 'graph_union' ok 134 - result claims to be in correct format for command 'graph_union' ok 135 - can return output file for command 'graph_union' ok 136 - can set want to IO object for command 'graph_union' ok 137 - can get the basic object result for command 'graph_union' ok 138 - 'returned object is correct for command 'graph_union'' isa 'Bio::Root::IO' ok 139 - make a factory using command 'pair_to_bed' ok 140 - factory command for 'pair_to_bed' is correct ok 141 - all available options for 'pair_to_bed' ok 142 - available parameters for 'pair_to_bed' ok 143 - available switches for 'pair_to_bed' ok 144 - get version for 'pair_to_bed' ok 145 - can run command 'pair_to_bed' ok 146 - result files exists for command 'pair_to_bed' ok 147 - can return output format for command 'pair_to_bed' ok 148 - result claims to be in correct format for command 'pair_to_bed' ok 149 - can return output file for command 'pair_to_bed' ok 150 - can set want to IO object for command 'pair_to_bed' ok 151 - can get the basic object result for command 'pair_to_bed' ok 152 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::Root::IO' ok 153 - can get the specific object result for command 'pair_to_bed' ok 154 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::SeqFeature::Collection' ok 155 - correct number of features for command 'pair_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 156 - make a factory using command 'bed_to_IGV' ok 157 - factory command for 'bed_to_IGV' is correct ok 158 - all available options for 'bed_to_IGV' ok 159 - available parameters for 'bed_to_IGV' ok 160 - available switches for 'bed_to_IGV' ok 161 - get version for 'bed_to_IGV' ok 162 - can run command 'bed_to_IGV' ok 163 - result files exists for command 'bed_to_IGV' ok 164 - can return output format for command 'bed_to_IGV' ok 165 - result claims to be in correct format for command 'bed_to_IGV' ok 166 - can return output file for command 'bed_to_IGV' ok 167 - can set want to IO object for command 'bed_to_IGV' ok 168 - can get the basic object result for command 'bed_to_IGV' ok 169 - 'returned object is correct for command 'bed_to_IGV'' isa 'Bio::Root::IO' ok 170 - make a factory using command 'group_by' ok 171 - factory command for 'group_by' is correct ok 172 - all available options for 'group_by' ok 173 - available parameters for 'group_by' ok 174 - available switches for 'group_by' ok 175 - get version for 'group_by' ok 176 - can set parameter -group => 1 ok 177 - can set parameter -columns => '2,2,3,3' ok 178 - can set parameter -operations => 'min,max,min,max' ok 179 - can run command 'group_by' ok 180 - result files exists for command 'group_by' ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' ok 184 - file format of '/tmp/e0tbWTi_nh/4t8LpUR1bS.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' ok 188 - can get the specific object result for command 'group_by' ok 189 - 'returned object is correct for command 'group_by'' isa 'Bio::SeqFeature::Collection' ok 190 - correct number of features for command 'group_by' # TODO maybe adapt reference results to Debian specific dataset ok 191 - make a factory using command 'shuffle' ok 192 - factory command for 'shuffle' is correct ok 193 - all available options for 'shuffle' ok 194 - available parameters for 'shuffle' ok 195 - available switches for 'shuffle' ok 196 - get version for 'shuffle' ok 197 - can run command 'shuffle' ok 198 - result files exists for command 'shuffle' ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' ok 202 - file format of '/tmp/z4UNm5mNMy/dx1GuXI4PL.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' ok 206 - can get the specific object result for command 'shuffle' ok 207 - 'returned object is correct for command 'shuffle'' isa 'Bio::SeqFeature::Collection' ok 208 - correct number of features for command 'shuffle' # TODO maybe adapt reference results to Debian specific dataset ok 209 - make a factory using command 'b12_to_b6' ok 210 - factory command for 'b12_to_b6' is correct ok 211 - all available options for 'b12_to_b6' ok 212 - available parameters for 'b12_to_b6' ok 213 - available switches for 'b12_to_b6' ok 214 - get version for 'b12_to_b6' ok 215 - can run command 'b12_to_b6' ok 216 - result files exists for command 'b12_to_b6' ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' ok 220 - file format of '/tmp/duCpxS3xBs/toWjKDAVow.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' ok 224 - can get the specific object result for command 'b12_to_b6' ok 225 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::SeqFeature::Collection' ok 226 - correct number of features for command 'b12_to_b6' # TODO maybe adapt reference results to Debian specific dataset ok 227 - make a factory using command 'intersect' ok 228 - factory command for 'intersect' is correct ok 229 - all available options for 'intersect' ok 230 - available parameters for 'intersect' ok 231 - available switches for 'intersect' ok 232 - get version for 'intersect' ok 233 - can run command 'intersect' ok 234 - result files exists for command 'intersect' ok 235 - can return output format for command 'intersect' ok 236 - result claims to be in correct format for command 'intersect' ok 237 - can return output file for command 'intersect' ok 238 - can set want to IO object for command 'intersect' ok 239 - can get the basic object result for command 'intersect' ok 240 - 'returned object is correct for command 'intersect'' isa 'Bio::Root::IO' ok 241 - can get the specific object result for command 'intersect' ok 242 - 'returned object is correct for command 'intersect'' isa 'Bio::SeqFeature::Collection' not ok 243 - correct number of features for command 'intersect' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'intersect'' # at t/BEDTools.t line 364. # got: '1305' # expected: '72534' ok 244 - make a factory using command 'slop' ok 245 - factory command for 'slop' is correct ok 246 - all available options for 'slop' ok 247 - available parameters for 'slop' ok 248 - available switches for 'slop' ok 249 - get version for 'slop' ok 250 - can set parameter -add_bidirectional => 100 ok 251 - can run command 'slop' ok 252 - result files exists for command 'slop' ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' ok 256 - file format of '/tmp/DFID73BRCL/9g1mYau0Ef.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' ok 260 - can get the specific object result for command 'slop' ok 261 - 'returned object is correct for command 'slop'' isa 'Bio::SeqFeature::Collection' ok 262 - correct number of features for command 'slop' # TODO maybe adapt reference results to Debian specific dataset ok 263 - make a factory using command 'closest' ok 264 - factory command for 'closest' is correct ok 265 - all available options for 'closest' ok 266 - available parameters for 'closest' ok 267 - available switches for 'closest' ok 268 - get version for 'closest' ok 269 - can run command 'closest' ok 270 - result files exists for command 'closest' ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' ok 274 - file format of '/tmp/WeqBgWX8HV/i2Sz1SkSqQ.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' ok 278 - can get the specific object result for command 'closest' ok 279 - 'returned object is correct for command 'closest'' isa 'Bio::SeqFeature::Collection' not ok 280 - correct number of features for command 'closest' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'closest'' # at t/BEDTools.t line 364. # got: '2121' # expected: '845' ok 281 - make a factory using command 'links' ok 282 - factory command for 'links' is correct ok 283 - all available options for 'links' ok 284 - available parameters for 'links' ok 285 - available switches for 'links' ok 286 - get version for 'links' ok 287 - can run command 'links' ok 288 - result files exists for command 'links' ok 289 - can return output format for command 'links' ok 290 - result claims to be in correct format for command 'links' ok 291 - can return output file for command 'links' ok 292 - make readable output ok 293 - - html tag line ok 294 - - number of lines ok 295 - can set want to IO object for command 'links' ok 296 - can get the basic object result for command 'links' ok 297 - 'returned object is correct for command 'links'' isa 'Bio::Root::IO' ok 298 - make a factory using command 'sort' ok 299 - factory command for 'sort' is correct ok 300 - all available options for 'sort' ok 301 - available parameters for 'sort' ok 302 - available switches for 'sort' ok 303 - get version for 'sort' ok 304 - can run command 'sort' ok 305 - result files exists for command 'sort' ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' ok 309 - file format of '/tmp/jYkDL6Rw4f/u2OUrYbOrJ.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' ok 313 - can get the specific object result for command 'sort' ok 314 - 'returned object is correct for command 'sort'' isa 'Bio::SeqFeature::Collection' ok 315 - correct number of features for command 'sort' # TODO maybe adapt reference results to Debian specific dataset ok 316 - make a factory using command 'complement' ok 317 - factory command for 'complement' is correct ok 318 - all available options for 'complement' ok 319 - available parameters for 'complement' ok 320 - available switches for 'complement' ok 321 - get version for 'complement' ok 322 - can run command 'complement' ok 323 - result files exists for command 'complement' ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' ok 327 - file format of '/tmp/_uVpGiGKDD/_ul5cHWNLB.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' ok 331 - can get the specific object result for command 'complement' ok 332 - 'returned object is correct for command 'complement'' isa 'Bio::SeqFeature::Collection' not ok 333 - correct number of features for command 'complement' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'complement'' # at t/BEDTools.t line 364. # got: '292' # expected: '291' ok 334 - make a factory using command 'mask_fasta_from_bed' ok 335 - factory command for 'mask_fasta_from_bed' is correct ok 336 - all available options for 'mask_fasta_from_bed' ok 337 - available parameters for 'mask_fasta_from_bed' ok 338 - available switches for 'mask_fasta_from_bed' ok 339 - get version for 'mask_fasta_from_bed' ok 340 - can run command 'mask_fasta_from_bed' ok 341 - result files exists for command 'mask_fasta_from_bed' ok 342 - can return output format for command 'mask_fasta_from_bed' ok 343 - result claims to be in correct format for command 'mask_fasta_from_bed' ok 344 - can return output file for command 'mask_fasta_from_bed' ok 345 - file format consistent with claim for 'mask_fasta_from_bed' ok 346 - can set want to IO object for command 'mask_fasta_from_bed' ok 347 - can get the basic object result for command 'mask_fasta_from_bed' ok 348 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::Root::IO' ok 349 - can get the specific object result for command 'mask_fasta_from_bed' ok 350 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::SeqIO' ok 351 - correct number of sequences for command 'mask_fasta_from_bed' ok 352 - make a factory using command 'subtract' ok 353 - factory command for 'subtract' is correct ok 354 - all available options for 'subtract' ok 355 - available parameters for 'subtract' ok 356 - available switches for 'subtract' ok 357 - get version for 'subtract' ok 358 - can run command 'subtract' ok 359 - result files exists for command 'subtract' ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' ok 363 - file format of '/tmp/uOtbtVa9oh/fe96qdcb0T.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' ok 367 - can get the specific object result for command 'subtract' ok 368 - 'returned object is correct for command 'subtract'' isa 'Bio::SeqFeature::Collection' not ok 369 - correct number of features for command 'subtract' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'subtract'' # at t/BEDTools.t line 364. # got: '1802' # expected: '57959' ok 370 - make a factory using command 'coverage' ok 371 - factory command for 'coverage' is correct ok 372 - all available options for 'coverage' ok 373 - available parameters for 'coverage' ok 374 - available switches for 'coverage' ok 375 - get version for 'coverage' ok 376 - can run command 'coverage' ok 377 - result files exists for command 'coverage' ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' ok 381 - file format of '/tmp/Nuu_nqu0yB/iZlVZSUWAT.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' ok 385 - can get the specific object result for command 'coverage' ok 386 - 'returned object is correct for command 'coverage'' isa 'Bio::SeqFeature::Collection' not ok 387 - correct number of features for command 'coverage' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'coverage'' # at t/BEDTools.t line 364. # got: '828' # expected: '57261' ok 388 - make a factory using command 'merge' ok 389 - factory command for 'merge' is correct ok 390 - all available options for 'merge' ok 391 - available parameters for 'merge' ok 392 - available switches for 'merge' ok 393 - get version for 'merge' ok 394 - can run command 'merge' ok 395 - result files exists for command 'merge' ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' ok 399 - file format of '/tmp/xXGVozYAOJ/B3V9Y_loT9.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' ok 403 - can get the specific object result for command 'merge' ok 404 - 'returned object is correct for command 'merge'' isa 'Bio::SeqFeature::Collection' ok 405 - correct number of features for command 'merge' # TODO maybe adapt reference results to Debian specific dataset ok 406 - make a factory using command 'window' ok 407 - factory command for 'window' is correct ok 408 - all available options for 'window' ok 409 - available parameters for 'window' ok 410 - available switches for 'window' ok 411 - get version for 'window' ok 412 - can run command 'window' ok 413 - result files exists for command 'window' ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' ok 417 - file format of '/tmp/xrulnuz63z/HEnOTxEBON.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' ok 421 - can get the specific object result for command 'window' ok 422 - 'returned object is correct for command 'window'' isa 'Bio::SeqFeature::Collection' not ok 423 - correct number of features for command 'window' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'window'' # at t/BEDTools.t line 364. # got: '1331' # expected: '74998' ok # You named your test '71'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '91'. You shouldn't use numbers for your test names. # Very confusing. t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 ok 4 ok 5 - 71 ok 6 - 91 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [16%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [31%] 16000 Cells done [33%] 17000 Cells done [35%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [48%] 24000 Cells done [50%] 25000 Cells done [52%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [63%] 31000 Cells done [65%] 32000 Cells done [67%] 33000 Cells done [69%] 34000 Cells done [71%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [78%] 38000 Cells done [80%] 39000 Cells done [82%] 40000 Cells done [84%] 41000 Cells done [86%] 42000 Cells done [88%] 43000 Cells done [90%] 44000 Cells done [93%] 45000 Cells done [95%] 46000 Cells done [97%] 47000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [16%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [28%] 13000 Cells done [31%] 14000 Cells done [33%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [40%] 18000 Cells done [43%] 19000 Cells done [45%] 20000 Cells done [48%] 21000 Cells done [50%] 22000 Cells done [52%] 23000 Cells done [55%] 24000 Cells done [57%] 25000 Cells done [60%] 26000 Cells done [62%] 27000 Cells done [64%] 28000 Cells done [67%] 29000 Cells done [69%] 30000 Cells done [72%] 31000 Cells done [74%] 32000 Cells done [76%] 33000 Cells done [79%] 34000 Cells done [81%] 35000 Cells done [84%] 36000 Cells done [86%] 37000 Cells done [89%] 38000 Cells done [91%] 39000 Cells done [93%] 40000 Cells done [96%] 41000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [16%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [31%] 16000 Cells done [33%] 17000 Cells done [35%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [48%] 24000 Cells done [50%] 25000 Cells done [52%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [63%] 31000 Cells done [65%] 32000 Cells done [67%] 33000 Cells done [69%] 34000 Cells done [71%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [78%] 38000 Cells done [80%] 39000 Cells done [82%] 40000 Cells done [84%] 41000 Cells done [86%] 42000 Cells done [88%] 43000 Cells done [90%] 44000 Cells done [93%] 45000 Cells done [95%] 46000 Cells done [97%] 47000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode t/DBA.t ....................... 1..5 ok 1 - use Bio::Tools::Run::Alignment::DBA; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::DBA' isa 'Bio::Tools::Run::Alignment::DBA' ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok -- namet is "-sequence" associated seqall qualifiers -- namet is "-outfile" associated outfile qualifiers t/EMBOSS.t .................... 1..31 ok 1 - use Bio::Root::IO; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - use Bio::Factory::EMBOSS; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok t/Exonerate.t ................. 1..89 ok 1 - use Bio::Tools::Run::Alignment::Exonerate; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Exonerate' isa 'Bio::Tools::Run::Alignment::Exonerate' ok 3 ok 4 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok t/FastTree.t .................. 1..9 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::FastTree; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - Tree is defined ok 6 - Number of nodes is correct ok 7 - Tree is defined ok 8 - Tree is defined ok 9 - Tree is defined ok # Required executable for Bio::Tools::Run::FootPrinter is not present t/FootPrinter.t ............... 1..24 ok 1 - use Bio::Tools::Run::FootPrinter; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 4 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 5 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 6 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 7 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 8 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 9 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 10 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 11 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 12 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 13 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 14 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 15 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 16 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 17 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 18 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 19 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 20 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 21 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 22 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 23 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 24 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok # Required environment variable $GENEMARK_MODELS is not set t/Genemark.hmm.prokaryotic.t .. 1..99 ok 1 - use Bio::Tools::Run::Genemark; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 # skip Required environment variable $GENEMARK_MODELS is not set ok 5 # skip Required environment variable $GENEMARK_MODELS is not set ok 6 # skip Required environment variable $GENEMARK_MODELS is not set ok 7 # skip Required environment variable $GENEMARK_MODELS is not set ok 8 # skip Required environment variable $GENEMARK_MODELS is not set ok 9 # skip Required environment variable $GENEMARK_MODELS is not set ok 10 # skip Required environment variable $GENEMARK_MODELS is not set ok 11 # skip Required environment variable $GENEMARK_MODELS is not set ok 12 # skip Required environment variable $GENEMARK_MODELS is not set ok 13 # skip Required environment variable $GENEMARK_MODELS is not set ok 14 # skip Required environment variable $GENEMARK_MODELS is not set ok 15 # skip Required environment variable $GENEMARK_MODELS is not set ok 16 # skip Required environment variable $GENEMARK_MODELS is not set ok 17 # skip Required environment variable $GENEMARK_MODELS is not set ok 18 # skip Required environment variable $GENEMARK_MODELS is not set ok 19 # skip Required environment variable $GENEMARK_MODELS is not set ok 20 # skip Required environment variable $GENEMARK_MODELS is not set ok 21 # skip Required environment variable $GENEMARK_MODELS is not set ok 22 # skip Required environment variable $GENEMARK_MODELS is not set ok 23 # skip Required environment variable $GENEMARK_MODELS is not set ok 24 # skip Required environment variable $GENEMARK_MODELS is not set ok 25 # skip Required environment variable $GENEMARK_MODELS is not set ok 26 # skip Required environment variable $GENEMARK_MODELS is not set ok 27 # skip Required environment variable $GENEMARK_MODELS is not set ok 28 # skip Required environment variable $GENEMARK_MODELS is not set ok 29 # skip Required environment variable $GENEMARK_MODELS is not set ok 30 # skip Required environment variable $GENEMARK_MODELS is not set ok 31 # skip Required environment variable $GENEMARK_MODELS is not set ok 32 # skip Required environment variable $GENEMARK_MODELS is not set ok 33 # skip Required environment variable $GENEMARK_MODELS is not set ok 34 # skip Required environment variable $GENEMARK_MODELS is not set ok 35 # skip Required environment variable $GENEMARK_MODELS is not set ok 36 # skip Required environment variable $GENEMARK_MODELS is not set ok 37 # skip Required environment variable $GENEMARK_MODELS is not set ok 38 # skip Required environment variable $GENEMARK_MODELS is not set ok 39 # skip Required environment variable $GENEMARK_MODELS is not set ok 40 # skip Required environment variable $GENEMARK_MODELS is not set ok 41 # skip Required environment variable $GENEMARK_MODELS is not set ok 42 # skip Required environment variable $GENEMARK_MODELS is not set ok 43 # skip Required environment variable $GENEMARK_MODELS is not set ok 44 # skip Required environment variable $GENEMARK_MODELS is not set ok 45 # skip Required environment variable $GENEMARK_MODELS is not set ok 46 # skip Required environment variable $GENEMARK_MODELS is not set ok 47 # skip Required environment variable $GENEMARK_MODELS is not set ok 48 # skip Required environment variable $GENEMARK_MODELS is not set ok 49 # skip Required environment variable $GENEMARK_MODELS is not set ok 50 # skip Required environment variable $GENEMARK_MODELS is not set ok 51 # skip Required environment variable $GENEMARK_MODELS is not set ok 52 # skip Required environment variable $GENEMARK_MODELS is not set ok 53 # skip Required environment variable $GENEMARK_MODELS is not set ok 54 # skip Required environment variable $GENEMARK_MODELS is not set ok 55 # skip Required environment variable $GENEMARK_MODELS is not set ok 56 # skip Required environment variable $GENEMARK_MODELS is not set ok 57 # skip Required environment variable $GENEMARK_MODELS is not set ok 58 # skip Required environment variable $GENEMARK_MODELS is not set ok 59 # skip Required environment variable $GENEMARK_MODELS is not set ok 60 # skip Required environment variable $GENEMARK_MODELS is not set ok 61 # skip Required environment variable $GENEMARK_MODELS is not set ok 62 # skip Required environment variable $GENEMARK_MODELS is not set ok 63 # skip Required environment variable $GENEMARK_MODELS is not set ok 64 # skip Required environment variable $GENEMARK_MODELS is not set ok 65 # skip Required environment variable $GENEMARK_MODELS is not set ok 66 # skip Required environment variable $GENEMARK_MODELS is not set ok 67 # skip Required environment variable $GENEMARK_MODELS is not set ok 68 # skip Required environment variable $GENEMARK_MODELS is not set ok 69 # skip Required environment variable $GENEMARK_MODELS is not set ok 70 # skip Required environment variable $GENEMARK_MODELS is not set ok 71 # skip Required environment variable $GENEMARK_MODELS is not set ok 72 # skip Required environment variable $GENEMARK_MODELS is not set ok 73 # skip Required environment variable $GENEMARK_MODELS is not set ok 74 # skip Required environment variable $GENEMARK_MODELS is not set ok 75 # skip Required environment variable $GENEMARK_MODELS is not set ok 76 # skip Required environment variable $GENEMARK_MODELS is not set ok 77 # skip Required environment variable $GENEMARK_MODELS is not set ok 78 # skip Required environment variable $GENEMARK_MODELS is not set ok 79 # skip Required environment variable $GENEMARK_MODELS is not set ok 80 # skip Required environment variable $GENEMARK_MODELS is not set ok 81 # skip Required environment variable $GENEMARK_MODELS is not set ok 82 # skip Required environment variable $GENEMARK_MODELS is not set ok 83 # skip Required environment variable $GENEMARK_MODELS is not set ok 84 # skip Required environment variable $GENEMARK_MODELS is not set ok 85 # skip Required environment variable $GENEMARK_MODELS is not set ok 86 # skip Required environment variable $GENEMARK_MODELS is not set ok 87 # skip Required environment variable $GENEMARK_MODELS is not set ok 88 # skip Required environment variable $GENEMARK_MODELS is not set ok 89 # skip Required environment variable $GENEMARK_MODELS is not set ok 90 # skip Required environment variable $GENEMARK_MODELS is not set ok 91 # skip Required environment variable $GENEMARK_MODELS is not set ok 92 # skip Required environment variable $GENEMARK_MODELS is not set ok 93 # skip Required environment variable $GENEMARK_MODELS is not set ok 94 # skip Required environment variable $GENEMARK_MODELS is not set ok 95 # skip Required environment variable $GENEMARK_MODELS is not set ok 96 # skip Required environment variable $GENEMARK_MODELS is not set ok 97 # skip Required environment variable $GENEMARK_MODELS is not set ok 98 # skip Required environment variable $GENEMARK_MODELS is not set ok 99 # skip Required environment variable $GENEMARK_MODELS is not set ok These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values t/Genewise.t .................. 1..17 ok 1 - use Bio::Tools::Run::Genewise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Genewise' isa 'Bio::Tools::Run::Genewise' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok # Required environment variable $GENSCANDIR is not set t/Genscan.t ................... 1..6 ok 1 - use Bio::Tools::Run::Genscan; ok 2 - use Bio::Root::IO; ok 3 # skip Required environment variable $GENSCANDIR is not set ok 4 # skip Required environment variable $GENSCANDIR is not set ok 5 # skip Required environment variable $GENSCANDIR is not set ok 6 # skip Required environment variable $GENSCANDIR is not set ok # Required executable for Bio::Tools::Run::Phylo::Gerp is not present t/Gerp.t ...................... 1..33 ok 1 - use Bio::Tools::Run::Phylo::Gerp; ok 2 - use Bio::AlignIO; ok 3 - use Bio::TreeIO; ok 4 - use Bio::Root::Utilities; ok 5 - Found input alignment file ok 6 - Found input tree file ok 7 - An object of class 'Bio::Tools::Run::Phylo::Gerp' isa 'Bio::Tools::Run::Phylo::Gerp' ok 8 - has a created method not in args supplied to new ok 9 - quiet was set ok 10 - program_dir returned correct default ok 11 - Correct exe default name ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok t/Glimmer3.t .................. 1..111 ok 1 - use Bio::Tools::Run::Glimmer; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Glimmer' isa 'Bio::Tools::Run::Glimmer' ok 5 - An object of class 'Bio::Tools::Glimmer' isa 'Bio::Tools::Glimmer' ok 6 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 7 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 8 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 11 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 12 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 13 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 14 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 18 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 19 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 20 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 22 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 23 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 25 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 26 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 28 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 29 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 30 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 32 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 33 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 34 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 35 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 36 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 37 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 38 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 39 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 40 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 41 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 42 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 43 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 44 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 45 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 46 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 47 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 48 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 49 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 50 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 51 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 52 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 53 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 54 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 55 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 56 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 57 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 58 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 59 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 60 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 61 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 62 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 63 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 64 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 66 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 67 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 68 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 69 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 72 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 73 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 74 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 75 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 76 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 77 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 78 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 79 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 80 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 81 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 82 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 83 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 84 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 85 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 86 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 87 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 88 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 89 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 90 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 91 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 92 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 93 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 94 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 95 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 96 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 98 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 99 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 100 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 101 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 102 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 103 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 104 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 105 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok # Required executable for Bio::Tools::Run::Hmmer is not present t/Hmmer.t ..................... 1..27 ok 1 - use Bio::Tools::Run::Hmmer; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer' ok 5 ok 6 ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok t/Infernal.t .................. 1..3 ok 1 - use Bio::Tools::Run::Infernal; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok t/Kalign.t .................... 1..7 ok 1 - use Bio::Tools::Run::Alignment::Kalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on kalign versions >= 2 Kalign (3.3) Copyright (C) 2006,2019,2020 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 WARNING: AVX2 instruction set not found! Kalign will not run optimally. [2022-08-22 09:52:29] : LOG : Detected protein sequences. [2022-08-22 09:52:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2022-08-22 09:52:29] : LOG : Detected: 7 sequences. [2022-08-22 09:52:29] : LOG : Calculating pairwise distances [2022-08-22 09:52:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2022-08-22 09:52:29] : LOG : 7 anchors [2022-08-22 09:52:29] : LOG : Building guide tree. [2022-08-22 09:52:29] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2022-08-22 09:52:29] : LOG : Aligning [2022-08-22 09:52:29] : LOG : CPU Time: 0.05u 00:00:00.04 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.3) Copyright (C) 2006,2019,2020 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 WARNING: AVX2 instruction set not found! Kalign will not run optimally. [2022-08-22 09:52:29] : LOG : Detected protein sequences. [2022-08-22 09:52:29] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2022-08-22 09:52:29] : LOG : Detected: 7 sequences. [2022-08-22 09:52:29] : LOG : Calculating pairwise distances [2022-08-22 09:52:29] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2022-08-22 09:52:29] : LOG : 7 anchors [2022-08-22 09:52:29] : LOG : Building guide tree. [2022-08-22 09:52:29] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2022-08-22 09:52:29] : LOG : Aligning [2022-08-22 09:52:29] : LOG : CPU Time: 0.05u 00:00:00.04 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present t/LVB.t ....................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::LVB; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::LVB' isa 'Bio::Tools::Run::Phylo::LVB' ok 4 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::LVB is not present ok # Required executable for Bio::Tools::Run::Alignment::Lagan is not present t/Lagan.t ..................... 1..12 ok 1 - use Bio::AlignIO; ok 2 - use Bio::Tools::Run::Alignment::Lagan; ok 3 - use Bio::Root::IO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Seq; ok 6 - use Bio::Matrix::Mlagan; ok 7 - An object of class 'Bio::Tools::Run::Alignment::Lagan' isa 'Bio::Tools::Run::Alignment::Lagan' ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Lagan is not present ok t/MAFFT.t ..................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::MAFFT; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - An object of class 'Bio::Tools::Run::Alignment::MAFFT' isa 'Bio::Tools::Run::Alignment::MAFFT' ok 5 ok 6 ok 7 ok 8 ok 9 - 42 or 43 expected ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 # skip Tests require version 6 of MAFFT ok 19 # skip Tests require version 6 of MAFFT ok 20 # skip Tests require version 6 of MAFFT ok 21 # skip Tests require version 6 of MAFFT ok 22 # skip Tests require version 6 of MAFFT ok 23 # skip Tests require version 6 of MAFFT ok # Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present t/MSAProbs.t .................. 1..19 ok 1 - use Bio::Tools::Run::Alignment::MSAProbs; ok 2 - use Bio::Tools::GuessSeqFormat; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - use Bio::Root::IO; ok 6 - use POSIX; ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 16 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 17 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 18 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok 19 # skip Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present ok # Required executable for Bio::Tools::Run::Match is not present t/Match.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Match; ok 2 - An object of class 'Bio::Tools::Run::Match' isa 'Bio::Tools::Run::Match' ok 3 - mxlib parameter was set ok 4 - program_dir returned correct default ok 5 - Correct exe default name ok 6 # skip Required executable for Bio::Tools::Run::Match is not present ok 7 # skip Required executable for Bio::Tools::Run::Match is not present ok # Required executable for Bio::Tools::Run::Mdust is not present t/Mdust.t ..................... 1..5 ok 1 - use Bio::Tools::Run::Mdust; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Mdust' isa 'Bio::Tools::Run::Mdust' ok 4 # skip Required executable for Bio::Tools::Run::Mdust is not present ok 5 # skip Required executable for Bio::Tools::Run::Mdust is not present ok # Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present t/Molphy.t .................... 1..10 ok 1 - use Bio::Tools::Phylo::Molphy; ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML; ok 3 - use Bio::AlignIO; ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok t/Muscle.t .................... 1..8 ok 1 - use Bio::Tools::Run::Alignment::Muscle; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Bio::Root::IO; ok 5 - use POSIX; ok 6 ok 7 - Code tested only on muscle versions > 3.6 ok 8 - log file ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present t/Neighbor.t .................. 1..19 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 - use Bio::Tools::Run::Phylo::Phylip::Neighbor; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present ok # Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present t/Njtree.t .................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Njtree::Best; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present ok --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- --------------------- WARNING --------------------- MSG: In sequence pseudogene residue count gives end value 183. Overriding value [178] with value 183 for Bio::LocatableSeq::end(). ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFSITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSSVYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKYKFEVYEKND --------------------------------------------------- t/Pal2Nal.t ................... 1..9 ok 1 - use Bio::Tools::Run::Alignment::Pal2Nal; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Pal2Nal' isa 'Bio::Tools::Run::Alignment::Pal2Nal' ok 3 - program_dir returned correct default ok 4 - Correct exe default name ok 5 ok 6 - use Bio::AlignIO; ok 7 - use Bio::SeqIO; ok 8 ok 9 ok t/PhastCons.t ................. skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Primate is not present t/Primate.t ................... 1..8 ok 1 - use Bio::Tools::Run::Primate; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::Primate is not present ok 4 # skip Required executable for Bio::Tools::Run::Primate is not present ok 5 # skip Required executable for Bio::Tools::Run::Primate is not present ok 6 # skip Required executable for Bio::Tools::Run::Primate is not present ok 7 # skip Required executable for Bio::Tools::Run::Primate is not present ok 8 # skip Required executable for Bio::Tools::Run::Primate is not present ok t/Primer3.t ................... skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Prints is not present t/Prints.t .................... 1..7 ok 1 - use Bio::Tools::Run::Prints; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints' ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present ok # Required executable for Bio::Tools::Run::Alignment::Probalign is not present t/Probalign.t ................. 1..13 ok 1 - use Bio::Tools::Run::Alignment::Probalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Cwd; ok 5 - use POSIX; ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: t/data/cysprot.fa Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/gDkKpn4cH3 Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/SxIe1ydEHI Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (6) CATL_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (4) CATH_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (6) CATL_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (4) CATH_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (4) CATH_RAT vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (4) CATH_RAT vs. (6) CATL_RAT -- done. Computing posterior matrix: (4) CATH_RAT vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (6) CATL_RAT vs. (7) PAPA_CARPA -- done. Trained parameter set: initDistrib[] = { 0.8318790197 5.246166256e-05 5.246166256e-05 0.08400797099 0.08400797099 } gapOpen[] = { 0.01386308484 0.01386308484 0.006556345616 0.006556345616 } gapExtend[] = { 0.3603379726 0.3603379726 0.7831884027 0.7831884027 } PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.8318790197 5.246169894e-05 5.246169894e-05 0.08400797099 0.08400797099 } gapOpen[] = { 0.01386308484 0.01386308484 0.006556345616 0.006556345616 } gapExtend[] = { 0.3603379726 0.3603379726 0.7831884027 0.7831884027 } Loading sequence file: /tmp/tDY1Q03nm4 Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # Required executable for Bio::Tools::Run::Profile is not present t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 # skip Required executable for Bio::Tools::Run::Profile is not present ok 6 # skip Required executable for Bio::Tools::Run::Profile is not present ok 7 # skip Required executable for Bio::Tools::Run::Profile is not present ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present t/ProtPars.t .................. 1..11 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars' ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok # Required executable for Bio::Tools::Run::Pseudowise is not present t/Pseudowise.t ................ 1..18 ok 1 - use Bio::Tools::Run::Pseudowise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 ok 5 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 6 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 7 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 8 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 9 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 10 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 11 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 12 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 13 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 14 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 15 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 16 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 17 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 18 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok # Required executable for Bio::Tools::Run::Phylo::QuickTree is not present t/QuickTree.t ................. 1..13 ok 1 - use Bio::Tools::Run::Phylo::QuickTree; ok 2 - use Bio::AlignIO; ok 3 - Found input file ok 4 - An object of class 'Bio::Tools::Run::Phylo::QuickTree' isa 'Bio::Tools::Run::Phylo::QuickTree' ok 5 - program_dir returned correct default ok 6 - Correct exe default name ok 7 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok t/Raxml.t ..................... 1..12 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Raxml; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - An object of class 'Bio::Tools::Run::Phylo::Raxml' isa 'Bio::Tools::Run::Phylo::Raxml' ok 6 - Tree is defined ok 7 - Tree is defined ok 8 - File containing best tree exists in tempdir ok 9 - Tree is defined ok 10 - Tree is defined ok 11 - Number of nodes is correct ok 12 - Tree is defined ok # DB and mask make tests # run BLAST methods t/SABlastPlus.t ............... 1..71 ok 1 - use Bio::Tools::Run::StandAloneBlastPlus; ok 2 - use Bio::Tools::Run::WrapperBase; ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts; ok 4 - BlastPlus factory ok 5 - make factory ok 6 - test db made with fasta ok 7 - temp db ok 8 - right type ok 9 ok 10 - named db made ok 11 - check_db ok 12 - correct name ok 13 - dbinfo hash returned ok 14 - correct type ok 15 - windowmasker mask made ok 16 - dustmasker mask made ok 17 - check_db with arg ok 18 - db_info with arg ok 19 - protein db made ok 20 - correct type ok 21 - segmasker mask made ok 22 - segmasker mask made; blastdb as data ok 23 ok 24 - protein db made with pre-built mask ok 25 - db_info records mask info ok 26 ok 27 - mask built and db made on construction (windowmasker) ok 28 ok 29 - mask built and db made on construction (segmasker) ok 30 ok 31 - mask built and db made on construction (dustmasker) ok 32 ok 33 ok 34 ok 35 - make db from Bio::SeqIO ok 36 ok 37 - make db from Bio::AlignIO ok 38 ok 39 - make db from \@seqs ok 40 - dbdir : ./a/b; dbname : test; create ok 41 - make db ok 42 ok 43 ok 44 ok 45 ok 46 - run blastn ok 47 - default hit limit ok 48 - return more alignments (arg spec) ok 49 - got more hits ok 50 - run blastn with Bio::Seq query ok 51 - run tblastn ok 52 - tblastn hits ok 53 - run tblastx ok 54 - tblastx hits ok 55 ok 56 - run blastp ok 57 - blastp hits ok 58 - bl2seq (blastn) ok 59 - got hit ok 60 - bl2seq (tblastx) ok 61 - got hit ok 62 - bl2seq (blastx) ok 63 - got hit ok 64 - bl2seq (blastp) ok 65 - no hit ok 66 - bl2seq (blastp) ok 67 - got hit ok 68 - bl2seq (tblastx) - multiple outfmt options ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg) ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should also work) ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in quotes ok # Required executable for Bio::Tools::Run::Phylo::SLR is not present t/SLR.t ....................... 1..7 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::SLR; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok t/Samtools.t .................. 1..41 ok 1 - make a factory using command 'pileup' ok 2 - parameters changed on construction ok 3 - access parameter ok 4 - parameters_changed cleared on read ok 5 - set a param not set in constructor ok 6 - parameters_changed set ok 7 - parameter really set ok 8 - original parameter unchanged ok 9 - parameters_changed cleared on read ok 10 - change an original parameter ok 11 - parameter really changed ok 12 - reset parameters with arg ok 13 - original parameters undefined ok 14 - parameter really reset via arg ok 15 - parameters changed ok 16 - all available options ok 17 - available parameters ok 18 - available switches ok 19 - get_parameters correct ok 20 - command attribute set ok 21 - internal command array set ok 22 - internal prefix hash set ok 23 - commands filtered by prefix ok 24 - translate_params: command correct ok 25 - translate_params: options correct ok 26 - merge bam factory instantiated ok 27 - merged bam file created ok 28 - fasta index factory ok 29 - make fasta index ok 30 - fai file present ok 31 - bam -> sam cvt factory ok 32 - convert bam -> sam ok 33 - sam file present and text ok 34 - sam -> bam cvt factory ok 35 - convert sam -> bam ok 36 - bam file present and binary ok 37 - bam sort factory ok 38 - sort bam file ok 39 - bam index factory ok 40 - make bam index ok 41 - bai file present and binary ok # Required executable for Bio::Tools::Run::Seg is not present t/Seg.t ....................... 1..8 ok 1 - use Bio::Tools::Run::Seg; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Seg' isa 'Bio::Tools::Run::Seg' ok 5 # skip Required executable for Bio::Tools::Run::Seg is not present ok 6 # skip Required executable for Bio::Tools::Run::Seg is not present ok 7 # skip Required executable for Bio::Tools::Run::Seg is not present ok 8 # skip Required executable for Bio::Tools::Run::Seg is not present ok # Required executable for Bio::Tools::Run::Phylo::Semphy is not present t/Semphy.t .................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::Semphy; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Semphy' isa 'Bio::Tools::Run::Phylo::Semphy' ok 3 - has a created method not in args ok 4 - ratio param was set via -z ok 5 - jtt switch was set ok 6 - program_dir returned correct default ok 7 - Correct exe default name ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present t/SeqBoot.t ................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok # Required executable for Bio::Tools::Run::Signalp is not present t/Signalp.t ................... 1..7 ok 1 - use Bio::Tools::Run::Signalp; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Signalp' isa 'Bio::Tools::Run::Signalp' ok 5 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 6 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 7 # skip Required executable for Bio::Tools::Run::Signalp is not present ok t/Sim4.t ...................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::Sim4; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::Sim4' isa 'Bio::Tools::Run::Alignment::Sim4' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok # Required executable for Bio::Tools::Run::Simprot is not present t/Simprot.t ................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Simprot; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Simprot is not present ok t/SoapEU-function.t ........... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present t/StandAloneFasta.t ........... 1..15 ok 1 - use Bio::Tools::Run::Alignment::StandAloneFasta; ok 2 - use Bio::SeqIO; ok 3 ok 4 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok # Required executable for Bio::Tools::Run::Tmhmm is not present t/Tmhmm.t ..................... 1..9 ok 1 - use Bio::Tools::Run::Tmhmm; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm' ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok t/TribeMCL.t .................. 1..24 ok 1 - use Bio::Tools::Run::TribeMCL; ok 2 - use Bio::SearchIO; ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa 'Bio::Tools::Run::TribeMCL' ok 4 # skip Tribe Matrix program not found. Skipping tests... ok 5 # skip Tribe Matrix program not found. Skipping tests... ok 6 # skip Tribe Matrix program not found. Skipping tests... ok 7 # skip Tribe Matrix program not found. Skipping tests... ok 8 # skip Tribe Matrix program not found. Skipping tests... ok 9 # skip Tribe Matrix program not found. Skipping tests... ok 10 # skip Tribe Matrix program not found. Skipping tests... ok 11 # skip Tribe Matrix program not found. Skipping tests... ok 12 # skip Tribe Matrix program not found. Skipping tests... ok 13 # skip Tribe Matrix program not found. Skipping tests... ok 14 # skip Tribe Matrix program not found. Skipping tests... ok 15 # skip Tribe Matrix program not found. Skipping tests... ok 16 # skip Tribe Matrix program not found. Skipping tests... ok 17 # skip Tribe Matrix program not found. Skipping tests... ok 18 # skip Tribe Matrix program not found. Skipping tests... ok 19 # skip Tribe Matrix program not found. Skipping tests... ok 20 # skip Tribe Matrix program not found. Skipping tests... ok 21 # skip Tribe Matrix program not found. Skipping tests... ok 22 # skip Tribe Matrix program not found. Skipping tests... ok 23 # skip Tribe Matrix program not found. Skipping tests... ok 24 # skip Tribe Matrix program not found. Skipping tests... ok t/Vista.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Vista; ok 2 - use Bio::AlignIO; ok 3 # skip Skipping due to old java version ok 4 # skip Skipping due to old java version ok 5 # skip Skipping due to old java version ok 6 # skip Skipping due to old java version ok 7 # skip Skipping due to old java version ok # Required executable for Bio::Tools::Run::Alignment::Gmap is not present t/gmap-run.t .................. 1..8 ok 1 - use Bio::Tools::Run::Alignment::Gmap; ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok # Required executable for Bio::Tools::Run::tRNAscanSE is not present t/tRNAscanSE.t ................ 1..12 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa 'Bio::Tools::Run::tRNAscanSE' ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok All tests successful. Test Summary Report ------------------- t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 110, 155, 190, 208, 226, 262 315, 405 Files=60, Tests=1454, 450 wallclock secs ( 0.59 usr 0.19 sys + 430.63 cusr 19.86 csys = 451.27 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install perl Build install --destdir /build/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primate.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Raxml.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::QuickTree.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm Installing 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/build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-6_all.deb'. dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-6_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bioperl-run_1.7.3-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/26025/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/26025/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/26025 and its subdirectories I: Current time: Mon Aug 22 09:53:49 +14 2022 I: pbuilder-time-stamp: 1661111629