I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 3 14:20:54 +14 2025 I: pbuilder-time-stamp: 1748910054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bioperl-run_1.7.3-11.dsc] I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-11.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Apr 27 20:03:48 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bioperl-run_1.7.3-11.dsc: no acceptable signature found 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_1.7.3-11.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_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 dpkg-source: info: applying fix-whatis-entries.patch dpkg-source: info: applying unscramble-erpin.patch dpkg-source: info: applying fix-pod-conversion.patch dpkg-source: info: applying adjust-muscle-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/783320/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. 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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 3 00:21 /bin/sh -> /bin/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/783320/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/783320/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ea195305d0124837a94601a082cecb27 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=783320 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/r-b-build.P36OAyXm/pbuilderrc_0VjU --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P36OAyXm/b2 --logfile b2/build.log bioperl-run_1.7.3-11.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/783320/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: amd64 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), libmodule-build-perl, 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, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, 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 ... 19725 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 hmmer; however: Package hmmer 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 infernal; however: Package infernal 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 pftools; however: Package pftools 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} bioperl{a} bsdextrautils{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} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbio-perl-run-perl{a} libbio-tools-run-alignment-clustalw-perl{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-any-perl{a} libdata-stag-perl{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdynaloader-functions-perl{a} libelf1t64{a} libencode-locale-perl{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfile-slurp-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhttp-date-perl{a} libhttp-message-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblerc4{a} liblwp-mediatypes-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libparams-classify-perl{a} libpipeline1{a} libpng16-16t64{a} libpq5{a} librav1e0{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{a} m4{a} mafft{a} man-db{a} mariadb-common{a} muscle{a} mysql-common{a} ncoils{a} pal2nal{a} pftools{a} po-debconf{a} primer3{a} probcons{a} raxml{a} sensible-utils{a} sim4{a} tigr-glimmer{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl dialign krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcache-cache-perl libconfig-general-perl libconfig-tiny-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-parser-perl libhtml-tableextract-perl libio-compress-brotli-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-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 libsvg-graph-perl libsvg-perl libtype-tiny-xs-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-writer-perl libxstring-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl lynx paml perl-doc perl-tk ruby shared-mime-info wget xdg-user-dirs 0 packages upgraded, 155 newly installed, 0 to remove and 0 not upgraded. Need to get 147 MB of archives. After unpacking 801 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libxml-twig-perl but it is not installable Depends: libbio-cluster-perl but it is not installable Depends: libbio-featureio-perl but it is not installable Depends: libbio-eutilities-perl but it is not installable Depends: libbio-tools-run-remoteblast-perl but it is not installable Depends: bedtools-test but it is not installable Depends: ncbi-blast+-legacy but it is not installable Depends: hyphy-pt but it is not installable or hyphy-mpi but it is not installable Depends: phyml but it is not installable Depends: python3-pybedtools but it is not installable Depends: samtools but it is not installable Depends: libwww-perl but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) bedtools-test [2.31.1+dfsg-2 (testing)] 4) ca-certificates [20240203 (testing)] 5) hyphy-common [2.5.59+dfsg-1 (testing)] 6) hyphy-mpi [2.5.59+dfsg-1 (testing)] 7) ibverbs-providers [50.0-2+b1 (testing)] 8) libamd-comgr2 [6.0+git20231212.4510c28+dfsg-3+b1 (testing)] 9) libamdhip64-5 [5.7.1-3 (testing)] 10) libbio-asn1-entrezgene-perl [1.730-3 (testing)] 11) libbio-cluster-perl [1.7.3-6 (testing)] 12) libbio-eutilities-perl [1.77-2 (testing)] 13) libbio-featureio-perl [1.6.905-2 (testing)] 14) libbio-tools-run-remoteblast-perl [1.7.3-3 (testing)] 15) libbio-variation-perl [1.7.5-3 (testing)] 16) libblis4-serial [0.9.0-1+b2 (testing)] 17) libcbor0.10 [0.10.2-1.1 (testing)] 18) libcurl3t64-gnutls [8.7.1-3 (testing)] 19) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 20) libdrm-amdgpu1 [2.4.120-2 (testing)] 21) libdrm-common [2.4.120-2 (testing)] 22) libdrm2 [2.4.120-2 (testing)] 23) libedit2 [3.1-20230828-1+b1 (testing)] 24) libevent-core-2.1-7t64 [2.1.12-stable-8.1+b3 (testing)] 25) libevent-pthreads-2.1-7t64 [2.1.12-stable-8.1+b3 (testing)] 26) libfabric1 [1.17.0-3+b1 (testing)] 27) libfido2-1 [1.14.0-1+b2 (testing)] 28) libfile-listing-perl [6.16-1 (testing)] 29) libhsa-runtime64-1 [5.7.1-2 (testing)] 30) libhsakmt1 [5.7.0-1 (testing)] 31) libhtml-parser-perl [3.81-1+b1 (testing)] 32) libhtml-tagset-perl [3.24-1 (testing)] 33) libhtml-tree-perl [5.07-3 (testing)] 34) libhts3 [1.19+ds-1 (testing)] 35) libhtscodecs2 [1.6.0-1+b1 (testing)] 36) libhttp-cookies-perl [6.11-1 (testing)] 37) libhttp-negotiate-perl [6.01-2 (testing)] 38) libhwloc-plugins [2.10.0-1+b1 (testing)] 39) libhwloc15 [2.10.0-1+b1 (testing)] 40) libibverbs1 [50.0-2+b1 (testing)] 41) libio-socket-ssl-perl [2.085-1 (testing)] 42) liblapack3 [3.12.0-3 (testing)] 43) libllvm17t64 [1:17.0.6-11 (testing)] 44) liblmdb0 [0.9.31-1+b1 (testing)] 45) liblwp-protocol-https-perl [6.14-1 (testing)] 46) libmbedcrypto7t64 [2.28.8-1 (testing)] 47) libmbedtls14t64 [2.28.8-1 (testing)] 48) libmbedx509-1t64 [2.28.8-1 (testing)] 49) libmunge2 [0.5.15-4 (testing)] 50) libncurses6 [6.4+20240414-1 (testing)] 51) libnet-http-perl [6.23-1 (testing)] 52) libnet-ssleay-perl [1.94-1 (testing)] 53) libnghttp2-14 [1.59.0-1 (testing)] 54) libnl-3-200 [3.7.0-0.3 (testing)] 55) libnl-route-3-200 [3.7.0-0.3 (testing)] 56) libnuma1 [2.0.18-1 (testing)] 57) libopenmpi3 [4.1.6-5 (testing)] 58) libpciaccess0 [0.17-3+b1 (testing)] 59) libpmix2 [5.0.1-4+b1 (testing)] 60) libpsl5t64 [0.21.2-1.1 (testing)] 61) libpsm-infinipath1 [3.3+20.604758e7-6.3 (testing)] 62) libpsm2-2 [11.2.185-2 (testing)] 63) libpython3-stdlib [3.11.8-1 (testing)] 64) libpython3.11-minimal [3.11.9-1 (testing)] 65) libpython3.11-stdlib [3.11.9-1 (testing)] 66) libpython3.12-minimal [3.12.3-1 (testing)] 67) libpython3.12-stdlib [3.12.3-1 (testing)] 68) librdmacm1t64 [50.0-2+b1 (testing)] 69) libreadline8t64 [8.2-4 (testing)] 70) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 71) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 72) libssl3t64 [3.2.1-3 (testing)] 73) libtext-csv-perl [2.04-1 (testing)] 74) libtry-tiny-perl [0.31-2 (testing)] 75) libucx0 [1.16.0+ds-5 (testing)] 76) libwww-perl [6.77-1 (testing)] 77) libwww-robotrules-perl [6.02-1 (testing)] 78) libxext6 [2:1.3.4-1+b1 (testing)] 79) libxml-dom-perl [1.46-2 (testing)] 80) libxml-dom-xpath-perl [0.14-4 (testing)] 81) libxml-namespacesupport-perl [1.12-2 (testing)] 82) libxml-parser-perl [2.47-1+b1 (testing)] 83) libxml-perl [0.08-4 (testing)] 84) libxml-regexp-perl [0.04-1.1 (testing)] 85) libxml-sax-base-perl [1.09-3 (testing)] 86) libxml-sax-expat-perl [0.51-2 (testing)] 87) libxml-sax-perl [1.02+dfsg-3 (testing)] 88) libxml-simple-perl [2.25-2 (testing)] 89) libxml-twig-perl [1:3.52-3 (testing)] 90) libxml-writer-perl [0.900-2 (testing)] 91) libxml-xpathengine-perl [0.14-2 (testing)] 92) libxnvctrl0 [535.171.04-1 (testing)] 93) libz3-4 [4.8.12-3.1+b2 (testing)] 94) media-types [10.1.0 (testing)] 95) ncbi-blast+ [2.12.0+ds-4+b1 (testing)] 96) ncbi-blast+-legacy [2.12.0+ds-4 (testing)] 97) ncbi-data [6.1.20170106+dfsg1-10 (testing)] 98) netbase [6.4 (testing)] 99) ocl-icd-libopencl1 [2.3.2-1+b1 (testing)] 100) openmpi-bin [4.1.6-5 (testing)] 101) openmpi-common [4.1.6-5 (testing)] 102) openssh-client [1:9.6p1-4 (testing)] 103) openssl [3.2.1-3 (testing)] 104) perl-openssl-defaults [7+b2 (testing)] 105) phyml [3:3.3.20220408-3 (testing)] 106) python3 [3.11.8-1 (testing)] 107) python3-minimal [3.11.8-1 (testing)] 108) python3-numpy [1:1.24.2-2 (testing)] 109) python3-pkg-resources [68.1.2-2 (testing)] 110) python3-pybedtools [0.9.1-1+b1 (testing)] 111) python3-pysam [0.22.0+ds-1+b1 (testing)] 112) python3-six [1.16.0-6 (testing)] 113) python3.11 [3.11.9-1 (testing)] 114) python3.11-minimal [3.11.9-1 (testing)] 115) python3.12 [3.12.3-1 (testing)] 116) python3.12-minimal [3.12.3-1 (testing)] 117) readline-common [8.2-4 (testing)] 118) samtools [1.19.2-1 (testing)] 119) tzdata [2024a-3 (testing)] 120) ucf [3.0043+nmu1 (testing)] 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} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} hyphy-common{a} hyphy-mpi{a} ibverbs-providers{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-asn1-entrezgene-perl{a} libbio-cluster-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} libblis4-serial{a} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcbor0.10{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-any-perl{a} libcurl3t64-gnutls{a} libdata-stag-perl{a} libdav1d7{a} libdb5.3t64{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfido2-1{a} libfile-listing-perl{a} libfile-slurp-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgav1-1{a} libgd3{a} libgfortran5{a} libglib2.0-0t64{a} libgssapi-krb5-2{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhts3{a} libhtscodecs2{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{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} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmunge2{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} libpng16-16t64{a} libpq5{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} librav1e0{a} librdmacm1t64{a} libreadline8t64{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1d1{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} libtiff6{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} libwebp7{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-namespacesupport-perl{a} libxml-parser-perl{a} libxml-perl{a} libxml-regexp-perl{a} libxml-sax-base-perl{a} libxml-sax-expat-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} libyuv0{a} libz3-4{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} pftools{a} phyml{a} po-debconf{a} primer3{a} probcons{a} python3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-pybedtools{a} python3-pysam{a} python3-six{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} tigr-glimmer{a} tzdata{a} ucf{a} wise{a} wise-data{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl dialign krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libcache-cache-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 libheif-plugin-aomenc libheif-plugin-x265 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-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 libsvg-graph-perl libsvg-perl libtext-csv-xs-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-libxml-perl libxml-libxslt-perl libxml-sax-writer-perl libxstring-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, 273 newly installed, 2 to remove and 0 not upgraded. Need to get 290 MB of archives. After unpacking 1412 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.1-3 [2244 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-1.1 [27.8 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 38 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.6p1-4 [975 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 bedtools-test all 2.31.1+dfsg-2 [10.9 MB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 54 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 74 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.8.2-2 [1869 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b1 [351 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 librav1e0 amd64 0.7.1-2 [900 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc1d1 amd64 1.7.0+dfsg-2+b1 [2169 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0~git202401110.af6ac82-1 [169 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.0.4-2 [106 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-9+b3 [125 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1+b2 [346 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 mysql-common all 5.8+1.1.0 [6636 B] Get: 117 http://deb.debian.org/debian trixie/main amd64 mariadb-common all 1:10.11.6-2 [25.2 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libmariadb3 amd64 1:10.11.6-2 [174 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libpq5 amd64 16.2-1 [216 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 emboss-lib amd64 6.6.0+dfsg-15 [2874 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 emboss-data all 6.6.0+dfsg-15 [61.1 MB] Get: 125 http://deb.debian.org/debian trixie/main amd64 emboss amd64 6.6.0+dfsg-15 [1072 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.78.4-7 [1455 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 hyphy-common all 2.5.59+dfsg-1 [602 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libpmix2 amd64 5.0.1-4+b1 [645 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-11 [23.7 MB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 160 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libopenmpi3 amd64 4.1.6-5 [2427 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 hyphy-mpi amd64 2.5.59+dfsg-1 [1607 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 infernal amd64 1.1.5-2 [5914 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 kalign amd64 1:3.4.0-1 [138 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 lagan amd64 2.0-10 [184 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b2 [36.3 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libarray-compare-perl all 3.0.8-1 [14.9 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 200 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 libxml-parser-perl amd64 2.47-1+b1 [199 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 libxml-twig-perl all 1:3.52-3 [177 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 libbio-variation-perl all 1.7.5-3 [72.6 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 libbio-cluster-perl all 1.7.3-6 [53.3 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 libxml-sax-expat-perl all 0.51-2 [11.1 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 libbio-eutilities-perl all 1.77-2 [124 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-tiny-perl all 0.004-2 [7592 B] Get: 221 http://deb.debian.org/debian trixie/main amd64 libtree-dagnode-perl all 1.32-1 [61.7 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 libxml-perl all 0.08-4 [93.0 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 libxml-regexp-perl all 0.04-1.1 [7500 B] Get: 224 http://deb.debian.org/debian trixie/main amd64 libxml-dom-perl all 1.46-2 [152 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] Get: 226 http://deb.debian.org/debian trixie/main amd64 libxml-dom-xpath-perl all 0.14-4 [9352 B] Get: 227 http://deb.debian.org/debian trixie/main amd64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1 [34.1 kB] Get: 229 http://deb.debian.org/debian trixie/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 230 http://deb.debian.org/debian trixie/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 231 http://deb.debian.org/debian trixie/main amd64 libbio-perl-run-perl all 1.7.3-11 [528 kB] Get: 232 http://deb.debian.org/debian trixie/main amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-4 [24.5 kB] Get: 233 http://deb.debian.org/debian trixie/main amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get: 234 http://deb.debian.org/debian trixie/main amd64 libblis4-serial amd64 0.9.0-1+b2 [5282 kB] Get: 235 http://deb.debian.org/debian trixie/main amd64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 236 http://deb.debian.org/debian trixie/main amd64 libconfig-any-perl all 0.33-1 [31.0 kB] Get: 237 http://deb.debian.org/debian trixie/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 238 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 239 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 240 http://deb.debian.org/debian trixie/main amd64 libhts3 amd64 1.19+ds-1 [447 kB] Get: 241 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 242 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get: 243 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 244 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 245 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 246 http://deb.debian.org/debian trixie/main amd64 libmodule-build-perl all 0.423400-2 [252 kB] Get: 247 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 248 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 249 http://deb.debian.org/debian trixie/main amd64 mafft amd64 7.505-1 [1078 kB] Get: 250 http://deb.debian.org/debian trixie/main amd64 muscle amd64 1:5.1.0-1 [297 kB] Get: 251 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 252 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.12.0+ds-4+b1 [12.5 MB] Get: 253 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B] Get: 254 http://deb.debian.org/debian trixie/main amd64 ncoils amd64 2002-9 [22.2 kB] Get: 255 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-5 [168 kB] Get: 256 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-5 [226 kB] Get: 257 http://deb.debian.org/debian trixie/main amd64 pal2nal all 14.1-3 [17.8 kB] Get: 258 http://deb.debian.org/debian trixie/main amd64 pftools amd64 3.2.12-1 [24.8 MB] Get: 259 http://deb.debian.org/debian trixie/main amd64 phyml amd64 3:3.3.20220408-3 [1103 kB] Get: 260 http://deb.debian.org/debian trixie/main amd64 primer3 amd64 2.6.1-4 [202 kB] Get: 261 http://deb.debian.org/debian trixie/main amd64 probcons amd64 1.12-14 [119 kB] Get: 262 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 263 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 264 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get: 265 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] Get: 266 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 267 http://deb.debian.org/debian trixie/main amd64 python3-pybedtools amd64 0.9.1-1+b1 [12.3 MB] Get: 268 http://deb.debian.org/debian trixie/main amd64 raxml amd64 8.2.13+dfsg-1 [1480 kB] Get: 269 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1 [645 kB] Get: 270 http://deb.debian.org/debian trixie/main amd64 sim4 amd64 0.0.20121010-8 [359 kB] Get: 271 http://deb.debian.org/debian trixie/main amd64 tigr-glimmer amd64 3.02b-6+b1 [283 kB] Get: 272 http://deb.debian.org/debian trixie/main amd64 wise-data all 2.4.1-24 [76.0 kB] Get: 273 http://deb.debian.org/debian trixie/main amd64 wise amd64 2.4.1-24 [1041 kB] Fetched 290 MB in 37s (7761 kB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up probcons (1.12-14) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.20-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libcbor0.10:amd64 (0.10.2-1.1) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.46-1+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libfile-slurp-tiny-perl (0.004-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.59.0-1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libblis4-serial:amd64 (0.9.0-1+b2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/libblis.so.4 to provide /usr/lib/x86_64-linux-gnu/libblis.so.4 (libblis.so.4-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/blis-serial/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up ncoils (2002-9) ... Setting up libsvtav1enc1d1:amd64 (1.7.0+dfsg-2+b1) ... Setting up libcom-err2:amd64 (1.47.0-2.4) ... Setting up hyphy-common (2.5.59+dfsg-1) ... Setting up file (1:5.45-3) ... Setting up muscle (1:5.1.0-1) ... Setting up emboss-data (6.6.0+dfsg-15) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up librav1e0:amd64 (0.7.1-2) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libkrb5support0:amd64 (1.20.1-5+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jun 3 00:24:35 UTC 2025. Universal Time is now: Tue Jun 3 00:24:35 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:10.11.6-2) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up infernal (1.1.5-2) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up primer3 (2.6.1-4) ... Setting up kalign (1:3.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:amd64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libmunge2:amd64 (0.5.15-4) ... Setting up lagan (2.0-10) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libxml-xpathengine-perl (0.14-2) ... Setting up sim4 (0.0.20121010-8) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libncurses6:amd64 (6.4+20240414-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libhwloc15:amd64 (2.10.0-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b2) ... Setting up libmariadb3:amd64 (1:10.11.6-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up wise-data (2.4.1-24) ... Setting up libk5crypto3:amd64 (1.20.1-5+b1) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up libtree-dagnode-perl (1.32-1) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libdav1d7:amd64 (1.4.1-1) ... Setting up sensible-utils (0.0.22) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up pftools (3.2.12-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up pal2nal (14.1-3) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.6-5) ... Setting up libconfig-any-perl (0.33-1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libsub-override-perl (0.10-1) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b2) ... Setting up libkrb5-3:amd64 (1.20.1-5+b1) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up libde265-0:amd64 (1.0.15-1+b1) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up tigr-glimmer (3.02b-6+b1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libyuv0:amd64 (0.0~git202401110.af6ac82-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up exonerate (2.4.0-5+b1) ... Setting up bedtools (2.31.1+dfsg-2) ... Setting up liburi-perl (5.28-1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up raxml (8.2.13+dfsg-1) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libbio-perl-run-perl (1.7.3-11) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1+b2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-8.1+b3) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up wise (2.4.1-24) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libtype-tiny-perl (2.004000-1) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libllvm17t64:amd64 (1:17.0.6-11) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Setting up libgav1-1:amd64 (0.19.0-2+b1) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libhtml-parser-perl:amd64 (3.81-1+b1) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libibverbs1:amd64 (50.0-2+b1) ... Setting up libavif16:amd64 (1.0.4-2) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up openssh-client (1:9.6p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b2) ... Setting up libpq5:amd64 (16.2-1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-3) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... 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 libxnvctrl0:amd64 (535.171.04-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up bioperl (1.7.8-1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhts3:amd64 (1.19+ds-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up samtools (1.19.2-1) ... Setting up ncbi-blast+ (2.12.0+ds-4+b1) ... Setting up python3-six (1.16.0-6) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up bedtools-test (2.31.1+dfsg-2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up ncbi-blast+-legacy (2.12.0+ds-4) ... Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up libpmix2:amd64 (5.0.1-4+b1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... Setting up python3-pybedtools (0.9.1-1+b1) ... Setting up libopenmpi3:amd64 (4.1.6-5) ... Setting up hyphy-mpi (2.5.59+dfsg-1) ... Setting up openmpi-bin (4.1.6-5) ... 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 (3:3.3.20220408-3) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1+b2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1+b2) ... Setting up libwww-perl (6.77-1) ... Setting up libheif1:amd64 (1.17.6-1+b2) ... Setting up libgd3:amd64 (2.3.3-9+b3) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up emboss-lib (6.6.0+dfsg-15) ... Setting up libxml-parser-perl (2.47-1+b1) ... Setting up emboss (6.6.0+dfsg-15) ... Setting up libxml-twig-perl (1:3.52-3) ... Setting up libbio-variation-perl (1.7.5-3) ... Setting up libxml-sax-expat-perl (0.51-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat 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 libxml-perl (0.08-4) ... Setting up libbio-cluster-perl (1.7.3-6) ... Setting up libxml-dom-perl (1.46-2) ... Setting up libbio-asn1-entrezgene-perl (1.730-3) ... Setting up libxml-dom-xpath-perl (0.14-4) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libbio-featureio-perl (1.6.905-2) ... Setting up libbio-eutilities-perl (1.77-2) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for ca-certificates (20240203) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/783320/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/783320/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/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_1.7.3-11_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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/reproducible-path/bioperl-run-1.7.3' dh_auto_configure -- --install_scripts /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/bioperl-run-1.7.3' dh_auto_build /usr/bin/perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/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 /usr/bin/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/OdI9uP3RqG 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/oIEqNRC3nh/4htOXbrP8g.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/pmm7mw0aMG/5UFb7xMXsx.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/aZgIkFQgDM/yLPGGN6t_T.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 ok 88 - - number of lines # TODO maybe adapt reference results to Debian specific dataset 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/_pmahjUp5s/Qqx2mDKtUT.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/6FdmP0WT_j/Wluj1B2lsr.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/qrHLS7OtB5/kRhui1Ye8K.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/2WagkZZVVY/BoOXF1bZiQ.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/OwU3epxWGK/trR5WvNcNd.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/juMMT0z84D/5_UFZ6YX6F.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' ok 280 - correct number of features for command 'closest' # TODO maybe adapt reference results to Debian specific dataset 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/_Aq_YoKMEQ/5Epn8ibmQk.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/omIG1sgUWx/coqri6yM0W.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' ok 333 - correct number of features for command 'complement' # TODO maybe adapt reference results to Debian specific dataset 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/l0yOWtsOkN/rN5p5CVkyq.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/zdyXxqFElB/8TYmSg0vmS.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/Gh8eCWH3w9/R6z9zCs3nU.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/IKJSOFBjYQ/87PnQEFugn.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 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 [17%] 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 [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 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 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 [17%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [29%] 13000 Cells done [31%] 14000 Cells done [34%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [41%] 18000 Cells done [43%] 19000 Cells done [46%] 20000 Cells done [48%] 21000 Cells done [51%] 22000 Cells done [53%] 23000 Cells done [55%] 24000 Cells done [58%] 25000 Cells done [60%] 26000 Cells done [63%] 27000 Cells done [65%] 28000 Cells done [68%] 29000 Cells done [70%] 30000 Cells done [72%] 31000 Cells done [75%] 32000 Cells done [77%] 33000 Cells done [80%] 34000 Cells done [82%] 35000 Cells done [85%] 36000 Cells done [87%] 37000 Cells done [89%] 38000 Cells done [92%] 39000 Cells done [94%] 40000 Cells done [97%] 41000 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 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 [17%] 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 [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 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 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 (3.4.0) Copyright (C) 2006,2019,2020,2021,2023 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 [2025-06-03 14:27:47] : LOG : Detected protein sequences. [2025-06-03 14:27:47] : LOG : Read 7 sequences from standard input. [2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2025-06-03 14:27:47] : LOG : Calculating pairwise distances [2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2025-06-03 14:27:47] : LOG : Building guide tree. [2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2025-06-03 14:27:47] : LOG : Aligning [2025-06-03 14:27:47] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.4.0) Copyright (C) 2006,2019,2020,2021,2023 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 [2025-06-03 14:27:47] : LOG : Detected protein sequences. [2025-06-03 14:27:47] : LOG : Read 7 sequences from standard input. [2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2025-06-03 14:27:47] : LOG : Calculating pairwise distances [2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2025-06-03 14:27:47] : LOG : Building guide tree. [2025-06-03 14:27:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2025-06-03 14:27:47] : LOG : Aligning [2025-06-03 14:27:47] : LOG : CPU Time: 0.01u 00:00:00.01 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..16 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 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 8 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 9 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 10 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 11 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 12 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 13 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 14 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 15 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests ok 16 # skip Only muscle version 3.6 or higher is supported by these tests. Skipping tests 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 # Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present t/PhastCons.t ................. 1..181 ok 1 - use Bio::AlignIO; ok 2 - use Bio::TreeIO; ok 3 - use Bio::DB::Taxonomy; ok 4 - Found input alignment file ok 5 - Found input tree file ok 6 - use Bio::Tools::Run::Phylo::Phast::PhastCons; ok 7 - An object of class 'Bio::Tools::Run::Phylo::Phast::PhastCons' isa 'Bio::Tools::Run::Phylo::Phast::PhastCons' ok 8 - has a created method not in args ok 9 - dashed parameter with internal dash was set ok 10 - wrong-case method wasn't created ok 11 - dashless wrong-case parameter was set ok 12 - synonym installed and accessed primary value ok 13 - double-dashed parameter was set ok 14 - program_dir returned correct default ok 15 - Correct exe default name ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 34 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 35 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 36 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 37 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 38 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 39 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 40 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 41 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 42 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 43 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 44 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 45 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 46 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 47 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 48 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 49 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 50 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 51 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 52 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 53 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 54 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 55 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 56 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 57 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 58 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 59 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 60 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 61 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 62 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 63 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 64 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 65 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 66 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 67 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 68 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 69 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 70 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 71 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 72 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 73 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 74 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 75 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 76 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 77 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 78 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 79 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 80 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 81 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 82 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 83 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 84 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 85 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 86 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 87 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 88 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 89 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 90 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 91 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 92 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 93 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 94 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 95 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 96 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 97 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 98 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 99 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 100 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 101 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 102 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 103 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 104 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 105 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 106 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 107 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 108 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 109 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 110 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 111 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 112 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 113 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 114 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 115 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 116 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 117 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 118 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 119 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 120 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 121 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 122 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 123 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 124 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 125 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 126 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 127 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 128 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 129 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 130 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 131 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 132 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 133 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 134 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 135 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 136 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 137 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 138 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 139 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 140 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 141 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 142 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 143 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 144 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 145 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 146 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 147 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 148 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 149 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 150 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 151 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 152 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 153 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 154 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 155 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 156 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 157 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 158 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 159 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 160 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 161 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 162 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 163 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 164 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 165 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 166 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 167 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 168 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 169 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 170 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 171 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 172 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 173 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 174 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 175 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 176 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 177 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 178 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 179 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 180 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok 181 # skip Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present ok # 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 ................... 1..9 ok 1 - use Bio::Tools::Run::Primer3; ok 2 - use Bio::SeqIO; ok 3 ok 4 # skip Primer3 wrapper only supports Primer3 v1 ok 5 # skip Primer3 wrapper only supports Primer3 v1 ok 6 # skip Primer3 wrapper only supports Primer3 v1 ok 7 # skip Primer3 wrapper only supports Primer3 v1 ok 8 # skip Primer3 wrapper only supports Primer3 v1 ok 9 # skip Primer3 wrapper only supports Primer3 v1 ok # 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/KslrF_BtZE 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/TQWW4w8Mu8 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[] = { 0.8318762183 5.24617426e-05 5.24617426e-05 0.08400939405 0.08400939405 } gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.8318762183 5.246169894e-05 5.246169894e-05 0.08400939405 0.08400939405 } gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } Loading sequence file: /tmp/aIVzuXDWBZ 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 # You named your test '15'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '340'. You shouldn't use numbers for your test names. # Very confusing. 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 - An object of class 'Bio::SeqFeature::FeaturePair' isa 'Bio::SeqFeatureI' ok 6 - 15 ok 7 - 340 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, 88, 110, 155, 190, 208, 226 262, 280, 315, 333, 405 Files=60, Tests=1652, 192 wallclock secs ( 0.37 usr 0.08 sys + 179.66 cusr 10.80 csys = 190.91 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/reproducible-path/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/bin/perl Build install --destdir /build/reproducible-path/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Primer3.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::SLR.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Exonerate.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Semphy.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Muscle.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Ensembl.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Probalign.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genemark.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm Installing 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/build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.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 'bioperl-run' in '../bioperl-run_1.7.3-11_all.deb'. dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-11_all.deb'. dpkg-genbuildinfo --build=binary -O../bioperl-run_1.7.3-11_amd64.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-11_amd64.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/783320/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/783320/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/783320 and its subdirectories I: Current time: Tue Jun 3 14:28:18 +14 2025 I: pbuilder-time-stamp: 1748910498