I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 23 09:11:21 -12 2024 I: pbuilder-time-stamp: 1719177081 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bioperl-run_1.7.3-9.dsc] I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-9.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 22 01:58:02 2023 -12 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_1.7.3-9.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_1.7.3-9.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/2181132/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='96c9abd396b94fabb91df3c5d1c93b1d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2181132' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.IOQfrG37/pbuilderrc_Z0x1 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IOQfrG37/b1 --logfile b1/build.log bioperl-run_1.7.3-9.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2181132/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 ... 19596 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} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} hyphy-common{a} hyphy-pt{a} ibverbs-providers{a} infernal{a} intltool-debian{a} kalign{a} lagan{a} libabsl20220623{a} libalgorithm-diff-perl{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif15{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} libbrotli1{a} libbsd0{a} libcapture-tiny-perl{a} libcbor0.8{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libconfig-any-perl{a} libcurl3-gnutls{a} libdata-stag-perl{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libencode-locale-perl{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfido2-1{a} libfile-listing-perl{a} libfile-slurp-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} libglib2.0-0{a} libheif1{a} libhpdf-2.3.0{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} libldap-2.5-0{a} liblerc4{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmariadb3{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{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} libpcre3{a} libpipeline1{a} libpmix2{a} libpng16-16{a} libpq5{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} librdmacm1{a} libreadline8{a} libregexp-ipv6-perl{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc1{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} libx265-199{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml-dom-perl{a} libxml-dom-xpath-perl{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-parser-perl{a} libxml-perl{a} libxml-regexp-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml-simple-perl{a} libxml-twig-perl{a} libxml-writer-perl{a} libxml-xpathengine-perl{a} libxml2{a} libxnvctrl0{a} libxpm4{a} libyuv0{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-pybedtools{a} python3-pysam{a} python3-six{a} python3.11{a} python3.11-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} tigr-glimmer{a} ucf{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl dialign libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl 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 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtext-csv-xs-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-libxslt-perl libxml-sax-expat-perl libxml-sax-writer-perl 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, 246 newly installed, 0 to remove and 0 not upgraded. Need to get 210 MB of archives. After unpacking 1043 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 bedtools amd64 2.30.0+dfsg-3 [665 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 bedtools-test all 2.30.0+dfsg-3 [10.8 MB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libtest-differences-perl all 0.69-1 [18.9 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libaom3 amd64 3.6.0-1 [1851 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libdav1d6 amd64 1.0.0-2 [495 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libabsl20220623 amd64 20220623.1-1 [391 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libgav1-1 amd64 0.18.0-1+b1 [332 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 librav1e0 amd64 0.5.1-6 [763 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libsvtav1enc1 amd64 1.4.1+dfsg-1 [2121 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libyuv0 amd64 0.0~git20230123.b2528b0-1 [168 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libavif15 amd64 0.11.1-1 [93.8 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libde265-0 amd64 1.0.11-1 [185 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libx265-199 amd64 3.5-2+b1 [1150 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libheif1 amd64 1.15.1-1 [215 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1 [48.4 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libgd3 amd64 2.3.3-9 [124 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1+b1 [349 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 mysql-common all 5.8+1.1.0 [6636 B] Get: 104 http://deb.debian.org/debian bookworm/main amd64 mariadb-common all 1:10.11.2-1 [22.4 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libmariadb3 amd64 1:10.11.2-1 [164 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libpq5 amd64 15.3-0+deb12u1 [185 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 emboss-lib amd64 6.6.0+dfsg-12 [2871 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 emboss-data all 6.6.0+dfsg-12 [61.1 MB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 emboss amd64 6.6.0+dfsg-12 [1069 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 exonerate amd64 2.4.0-5 [1616 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 hyphy-common all 2.5.47+dfsg-1 [586 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 hyphy-pt amd64 2.5.47+dfsg-1 [1487 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 infernal amd64 1.1.4-1 [5523 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 kalign amd64 1:3.3.5-1 [132 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 lagan amd64 2.0-9 [184 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libexporter-tiny-perl all 1.006000-1 [38.6 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libtype-tiny-perl all 2.002001-1 [377 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libarray-compare-perl all 3.0.8-1 [14.9 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 147 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libxml-parser-perl amd64 2.46-4 [201 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libxml-twig-perl all 1:3.52-2 [181 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libbio-variation-perl all 1.7.5-3 [72.6 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libbio-cluster-perl all 1.7.3-6 [53.3 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libbio-asn1-entrezgene-perl all 1.730-2 [48.6 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libtext-csv-perl all 2.02-2 [110 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libbio-eutilities-perl all 1.77-2 [124 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libfile-slurp-tiny-perl all 0.004-2 [7592 B] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libtree-dagnode-perl all 1.32-1 [61.7 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libxml-perl all 0.08-4 [93.0 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libxml-regexp-perl all 0.04-1.1 [7500 B] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libxml-dom-perl all 1.46-2 [152 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libxml-dom-xpath-perl all 0.14-4 [9352 B] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-run-perl all 1.7.3-9 [605 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-3 [24.6 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libmodule-pluggable-perl all 5.2-4 [23.6 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libconfig-any-perl all 0.32-3 [29.9 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 205 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amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libmodule-build-perl all 0.423200-1 [253 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 mafft amd64 7.505-1 [1078 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 muscle amd64 1:5.1.0-1 [297 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+-legacy all 2.12.0+ds-3 [13.5 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 ncoils amd64 2002-9 [22.2 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 pal2nal all 14.1-3 [17.8 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 pftools amd64 3.2.12-1 [24.8 MB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 phyml amd64 3:3.3.20220408-3 [1103 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 primer3 amd64 2.6.1-4 [202 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 probcons amd64 1.12-14 [119 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 python3-pybedtools amd64 0.9.0-4+b1 [12.2 MB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 raxml amd64 8.2.12+dfsg-8+b2 [1481 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 sim4 amd64 0.0.20121010-8 [359 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 tigr-glimmer amd64 3.02b-6+b1 [283 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 wise-data all 2.4.1-23 [78.2 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 wise amd64 2.4.1-23 [994 kB] Fetched 210 MB in 3s (65.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20346 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Selecting previously unselected package liblmdb0:amd64. Preparing to unpack .../203-liblmdb0_0.9.24-1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.24-1) ... Selecting previously unselected package libmbedcrypto7:amd64. Preparing to unpack .../204-libmbedcrypto7_2.28.3-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../205-libmbedx509-1_2.28.3-1_amd64.deb ... Unpacking libmbedx509-1:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedtls14:amd64. Preparing to unpack .../206-libmbedtls14_2.28.3-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.3-1) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../207-libmodule-build-perl_0.423200-1_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423200-1) ... Selecting previously unselected package libmunge2. Preparing to unpack .../208-libmunge2_0.5.15-2_amd64.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../209-libncurses6_6.4-4_amd64.deb ... Unpacking libncurses6:amd64 (6.4-4) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../210-libpmix2_4.2.2-1+b1_amd64.deb ... Unpacking libpmix2:amd64 (4.2.2-1+b1) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../211-libucx0_1.13.1-1_amd64.deb ... Unpacking libucx0:amd64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:amd64. 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Setting up libpciaccess0:amd64 (0.17-2) ... Setting up mysql-common (5.8+1.1.0) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libabsl20220623:amd64 (20220623.1-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libfile-slurp-perl (9999.32-2) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up probcons (1.12-14) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libclass-method-modifiers-perl (2.14-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up mafft (7.505-1) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libhtml-tagset-perl (3.20-6) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libfile-slurp-tiny-perl (0.004-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libencode-locale-perl (1.05-3) ... Setting up ncoils (2002-9) ... Setting up hyphy-common (2.5.47+dfsg-1) ... Setting up file (1:5.44-3) ... Setting up libsvtav1enc1:amd64 (1.4.1+dfsg-1) ... Setting up muscle (1:5.1.0-1) ... Setting up emboss-data (6.6.0+dfsg-12) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up librav1e0:amd64 (0.5.1-6) ... Setting up libmodule-build-perl (0.423200-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up mariadb-common (1:10.11.2-1) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up infernal (1.1.4-1) ... 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 libpcre3:amd64 (2:8.39-15) ... Setting up kalign (1:3.3.5-1) ... Setting up autotools-dev (20220109.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libmunge2 (0.5.15-2) ... Setting up lagan (2.0-9) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... 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 (6.4-4) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-12) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libmariadb3:amd64 (1:10.11.2-1) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libgav1-1:amd64 (0.18.0-1+b1) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up wise-data (2.4.1-23) ... Setting up libdav1d6:amd64 (1.0.0-2) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up libtree-dagnode-perl (1.32-1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up pftools (3.2.12-1) ... Setting up libtiff6:amd64 (4.5.0-5) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up pal2nal (14.1-3) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up libconfig-any-perl (0.32-3) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up fasttree (2.1.11-2) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... 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 bedtools-test (2.30.0+dfsg-3) ... Setting up libexporter-tiny-perl (1.006000-1) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up libde265-0:amd64 (1.0.11-1) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up tigr-glimmer (3.02b-6+b1) ... Setting up libyuv0:amd64 (0.0~git20230123.b2528b0-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up exonerate (2.4.0-5) ... Setting up bedtools (2.30.0+dfsg-3) ... Setting up liburi-perl (5.17-1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up raxml (8.2.12+dfsg-8+b2) ... Setting up libtext-csv-perl (2.02-2) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libbio-perl-run-perl (1.7.3-9) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libavif15:amd64 (0.11.1-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up wise (2.4.1-23) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libtype-tiny-perl (2.002001-1) ... Setting up libtest-differences-perl (0.69-1) ... Setting up libnet-http-perl (6.22-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up dh-autoreconf (20) ... Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up ucf (3.0043+nmu1) ... Setting up libx265-199:amd64 (3.5-2+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up libxpm4:amd64 (1:3.5.12-1.1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libheif1:amd64 (1.15.1-1) ... Setting up libpq5:amd64 (15.3-0+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up hyphy-pt (2.5.47+dfsg-1) ... Setting up man-db (2.11.2-2) ... 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 (525.85.05-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libgd3:amd64 (2.3.3-9) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up emboss-lib (6.6.0+dfsg-12) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up bioperl (1.7.8-1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up emboss (6.6.0+dfsg-12) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up samtools (1.16.1-1) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up python3-six (1.16.0-4) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up ncbi-blast+-legacy (2.12.0+ds-3) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... 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 python3-pybedtools (0.9.0-4+b1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up libwww-perl (6.68-1) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up libxml-parser-perl (2.46-4) ... Setting up libxml-twig-perl (1:3.52-2) ... Setting up libbio-variation-perl (1.7.5-3) ... 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 (1.730-2) ... Setting up libxml-dom-xpath-perl (0.14-4) ... Setting up libbio-eutilities-perl (1.77-2) ... Setting up libbio-featureio-perl (1.6.905-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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: Running cd /build/bioperl-run-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bioperl-run_1.7.3-9_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-9 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/bioperl-run-1.7.3' dh_auto_configure -- --install_scripts /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -ffile-prefix-map=/build/bioperl-run-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/bioperl-run-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n ]n Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' make[1]: Leaving directory '/build/bioperl-run-1.7.3' dh_auto_build /usr/bin/perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/bioperl-run-1.7.3' mkdir t.skip for t in Blat Eponine Glimmer2 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t t.skip ; done PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \ PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \ dh_auto_test --no-parallel /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/L6L5JnSGOw 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/UVSbe27ST5/BqPfKgC_im.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/p4U1FkZnNT/yyRENcDyyR.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/6nLSCHH5Xt/HcvwK7ovSt.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/BeDIVB2T8E/YIomh5Vx5I.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/Ifp2bPsXMX/VIEMWg2buT.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/Ri2uEuXX10/DnGCPnnLhQ.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/iupKJyJXDj/1NZMzy80hz.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/_mxjBjP_Jg/jIst3EvYBj.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/MOKe7IBtGy/mvVjLyLeGa.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/7LmAFCtXdW/ABNgrkFHIL.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/lfRgDKuuNF/19oeZFUwTP.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/oXg6VCUcK3/3ozZ9lVgZ1.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/6MjBKtb3Et/bnLQpWDxyq.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/mkQ8CkSKmx/7lXyzjczSG.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/YJU5ZElmsN/h4gZi565LG.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 (3.3.5) Copyright (C) 2006,2019,2020,2021 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 [2024-06-23 09:17:01] : LOG : Detected protein sequences. [2024-06-23 09:17:01] : LOG : Read 7 sequences from standard input. [2024-06-23 09:17:01] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-06-23 09:17:01] : LOG : Calculating pairwise distances [2024-06-23 09:17:01] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-06-23 09:17:01] : LOG : Building guide tree. [2024-06-23 09:17:01] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-06-23 09:17:01] : LOG : Aligning [2024-06-23 09:17:01] : LOG : CPU Time: 0.09u 00:00:00.08 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.3.5) Copyright (C) 2006,2019,2020,2021 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 [2024-06-23 09:17:01] : LOG : Detected protein sequences. [2024-06-23 09:17:01] : LOG : Read 7 sequences from standard input. [2024-06-23 09:17:01] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-06-23 09:17:01] : LOG : Calculating pairwise distances [2024-06-23 09:17:01] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-06-23 09:17:01] : LOG : Building guide tree. [2024-06-23 09:17:01] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 [2024-06-23 09:17:01] : LOG : Aligning [2024-06-23 09:17:01] : LOG : CPU Time: 0.03u 00:00:00.03 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/sxXCoQX54p 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/RjEJhsUXid 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/lGXzhUyN2O 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, 333 wallclock secs ( 0.47 usr 0.20 sys + 280.32 cusr 28.94 csys = 309.93 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/bin/perl Build install --destdir /build/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing 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/build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl 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_1.7.3-9_all.deb'. dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-9_all.deb'. dpkg-genbuildinfo --build=binary -O../bioperl-run_1.7.3-9_amd64.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-9_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: 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/2181132 and its subdirectories I: Current time: Sun Jun 23 09:18:30 -12 2024 I: pbuilder-time-stamp: 1719177510