Tue Dec 24 23:10:56 UTC 2024 I: starting to build bioperl-run/trixie/arm64 on jenkins on '2024-12-24 23:10' Tue Dec 24 23:10:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/43300/console.log Tue Dec 24 23:10:56 UTC 2024 I: Downloading source for trixie/bioperl-run=1.7.3-13 --2024-12-24 23:10:56-- http://deb.debian.org/debian/pool/main/b/bioperl-run/bioperl-run_1.7.3-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3217 (3.1K) [text/prs.lines.tag] Saving to: ‘bioperl-run_1.7.3-13.dsc’ 0K ... 100% 386M=0s 2024-12-24 23:10:56 (386 MB/s) - ‘bioperl-run_1.7.3-13.dsc’ saved [3217/3217] Tue Dec 24 23:10:56 UTC 2024 I: bioperl-run_1.7.3-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bioperl-run Binary: bioperl-run, libbio-perl-run-perl Architecture: all Version: 1.7.3-13 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://metacpan.org/release/BioPerl-Run Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libmodule-build-perl Build-Depends-Indep: 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 [any-amd64], libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools [any-amd64], bedtools-test, ncbi-blast+-legacy, libbio-perl-perl, clustalw [any-amd64], emboss [any-amd64 arm64 mips64el ppc64el riscv64], exonerate, hmmer [any-amd64 any-i386 powerpc ppc64], hyphy-pt | hyphy-mpi [any-amd64], infernal [any-amd64 any-i386], kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools [any-amd64], raxml, samtools [any-amd64], sim4, tigr-glimmer [any-amd64 arm64 mips64el ppc64el riscv64], wise, fasttree, lagan, pal2nal, pftools [any-amd64], libwww-perl Package-List: bioperl-run deb science optional arch=all libbio-perl-run-perl deb perl optional arch=all Checksums-Sha1: 930b52695705a503be1583d42d637e84e0d71ee8 4872163 bioperl-run_1.7.3.orig.tar.gz a96257f30e707e7850a74a5e0843ca6ca8395e17 20124 bioperl-run_1.7.3-13.debian.tar.xz Checksums-Sha256: 04f11b3a931f625bf80770c3aec1b57658b41cde54573132b58b6179adda7c65 4872163 bioperl-run_1.7.3.orig.tar.gz 0f279704d404fce005f56feeeabbdc2f3dd91100b706f3c0c5b785b35a0654a7 20124 bioperl-run_1.7.3-13.debian.tar.xz Files: e582f2dc591b947348670ce1479da109 4872163 bioperl-run_1.7.3.orig.tar.gz 790859c2f0208080c74785584d58a8a2 20124 bioperl-run_1.7.3-13.debian.tar.xz Dgit: 0fbc132e7510c5bb9887adc365c51aa93f6489e9 debian archive/debian/1.7.3-13 https://git.dgit.debian.org/bioperl-run -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmdMOKcUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqw6w/8DLdedm6lwx4XuMfyb5iZZfi8yHSS 0VfHg1+HKaTqHrLN1hJO0oTDvheRDRFDriMdC3RyLH/RoqhPAO7QiHGOAsaD5t0l 4wVCn094ul2OulbX6Oerr5Vj7u/oX/GUF4AiWSnNTGEcjal5pyaI1V0IHie77dAH VXjqE6oPlbJR/MR2W51UU6edbV4UIj7oSGr15EfIF8jHbSzHtlP6v9tLTsrPxzdf gTdLWnDt5bmz9cnlP9oBveloP/jTEDtePSJqPP+xI5G1zjTiIV31AuiB+Mxd6tP2 cvKEO50yOAjjrfKO4cntFgYqGSqmNArOP4KJwP5Ya/sWyeR2kGvuXa6HQ2dqa0ss BzjF4sPFqctc83mGUfATHR38p8vqF6+bHEbUIgGM1fay4/Oh8pFtvruzBgFB6azc tCT23B1DNGzeT4cSG07+KIse4IRQK3prz1SOCMtWmcsySsvzn4Y5LNHhaAJUHLiu szb5JThF0HAYGgAmyk4+t1VXzLa9e3ckTF26gigx5S5FtLqUW/7tmkKzSFkeCfHX ZMxXFj5wT7R7vqzARXXQjxcuCd8OfzjkBYzF6WzYNmOhHEVjv7awVVztZnVHpfgW FGhpZtugQVJu0+RC/6StTF2HVwenmVStulhzF2B0ZsoEg7B7Q6qJwHP41eSNljRR x+erJaK8nvNse1I= =z32O -----END PGP SIGNATURE----- Tue Dec 24 23:10:56 UTC 2024 I: Checking whether the package is not for us Tue Dec 24 23:10:56 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Tue Dec 24 23:10:56 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Tue Dec 24 23:13:00 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 24 11:11:00 -12 2024 I: pbuilder-time-stamp: 1735081860 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bioperl-run_1.7.3-13.dsc] I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-13.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 1 10:21:27 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bioperl-run_1.7.3-13.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_1.7.3-13.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 dpkg-source: info: applying update-blastdbcmd-error-output.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3980862/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='462ef9e41dde49ef8f8aea4dbdfeb2a4' 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='3980862' 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.ta2MVVWb/pbuilderrc_7Ba9 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ta2MVVWb/b1 --logfile b1/build.log bioperl-run_1.7.3-13.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3980862/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools-test, ncbi-blast+-legacy, libbio-perl-perl, emboss, exonerate, hyphy-pt, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, raxml, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, libwww-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20082 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-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-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 libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on emboss; however: Package emboss is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on hyphy-pt; however: Package hyphy-pt 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 raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on sim4; however: Package sim4 is not installed. pbuilder-satisfydepends-dummy depends on tigr-glimmer; however: Package tigr-glimmer is not installed. pbuilder-satisfydepends-dummy depends on wise; however: Package wise is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on lagan; however: Package lagan is not installed. pbuilder-satisfydepends-dummy depends on pal2nal; however: Package pal2nal is not installed. pbuilder-satisfydepends-dummy depends on libwww-perl; however: Package libwww-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools-test{a} bioperl{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} hyphy-common{a} hyphy-pt{a} ibverbs-providers{a} intltool-debian{a} kalign{a} lagan{a} libabsl20230802{a} libalgorithm-diff-perl{a} libamd-comgr2{a} libamdhip64-5{a} libaom3{a} libarchive-zip-perl{a} libarray-compare-perl{a} libavif16{a} libb-hooks-op-check-perl{a} libbio-asn1-entrezgene-perl{a} libbio-cluster-perl{a} libbio-eutilities-perl{a} libbio-featureio-perl{a} libbio-perl-perl{a} libbio-tools-run-remoteblast-perl{a} libbio-variation-perl{a} libbrotli1{a} libcapture-tiny-perl{a} libcbor0.10{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libconfig-any-perl{a} libcurl3t64-gnutls{a} libdata-stag-perl{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-stacktrace-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfido2-1{a} libfile-listing-perl{a} libfile-slurp-tiny-perl{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhpdf-2.3.0{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs1{a} libicu72{a} libimagequant0{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblmdb0{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1t64{a} libmariadb3{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-build-perl{a} libmodule-pluggable-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libmunge2{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnl-3-200{a} libnl-route-3-200{a} libnsl2{a} libnuma1{a} libopenmpi40{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpmix2t64{a} libpng16-16t64{a} libpq5{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libsvtav1enc2{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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} libucx0{a} liburi-perl{a} libuv1t64{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml-dom-perl{a} libxml-dom-xpath-perl{a} libxml-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} libz3-4{a} m4{a} mafft{a} man-db{a} mariadb-common{a} media-types{a} mpi-default-bin{a} muscle{a} mysql-common{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncoils{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pal2nal{a} perl-openssl-defaults{a} phyml{a} po-debconf{a} primer3{a} probcons{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sim4{a} tigr-glimmer{a} tzdata{a} ucf{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl dialign krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libbio-perl-run-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 libgraph-perl libgraphviz-perl libheif-plugin-aomenc libheif-plugin-x265 libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl libio-compress-brotli-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libnamespace-clean-perl libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl libtext-csv-xs-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-libxslt-perl libxml-sax-expat-perl libxml-sax-writer-perl libxstring-perl libyaml-libyaml-perl libyaml-perl libyaml-syck-perl linux-sysctl-defaults lynx paml perl-doc perl-tk psmisc publicsuffix ruby shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 259 newly installed, 0 to remove and 0 not upgraded. Need to get 212 MB of archives. After unpacking 1170 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-3 [677 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0045 [45.2 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 amap-align arm64 2.2+git20080214.600fc29+dfsg-2+b1 [137 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-3 [723 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 bedtools-test all 2.31.1+dfsg-2 [10.9 MB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 53 http://deb.debian.org/debian trixie/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 bioperl all 1.7.8-1 [246 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-3 [1532 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libaom3 arm64 3.11.0-1 [1690 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libgav1-1 arm64 0.19.0-2+b2 [493 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 librav1e0.7 arm64 0.7.1-7+b3 [655 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libsvtav1enc2 arm64 2.3.0+dfsg-1 [1558 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libyuv0 arm64 0.0.1898.20241125-1 [136 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.44-3 [273 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-dav1d arm64 1.19.3-1 [11.2 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libheif-plugin-libde265 arm64 1.19.3-1 [14.9 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libheif1 arm64 1.19.3-1 [419 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-1 [1411 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.1.0-1 [442 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.2-1 [13.6 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libxpm4 arm64 1:3.5.17-1+b2 [53.2 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1+b3 [347 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 mysql-common all 5.8+1.1.1 [6784 B] Get: 120 http://deb.debian.org/debian trixie/main arm64 mariadb-common all 1:11.4.3-1 [27.1 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libmariadb3 arm64 1:11.4.3-1 [170 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libpq5 arm64 17.2-1 [216 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 emboss-lib arm64 6.6.0+dfsg-15+b1 [2718 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 emboss-data all 6.6.0+dfsg-15 [61.1 MB] Get: 128 http://deb.debian.org/debian trixie/main arm64 emboss arm64 6.6.0+dfsg-15+b1 [1019 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 exonerate arm64 2.4.0-5+b2 [1730 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 fasttree arm64 2.1.11-2+b1 [175 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 hyphy-common all 2.5.63+dfsg-1 [607 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1 [332 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 hyphy-pt arm64 2.5.63+dfsg-1+b1 [799 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 52.0-2+b1 [58.8 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 52.0-2+b1 [321 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 kalign arm64 1:3.4.0-1+b2 [89.0 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 lagan arm64 2.0-10+b1 [177 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-18 [21.3 MB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 151 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-3 [278 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b4 [34.9 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libexporter-tiny-perl all 1.006002-1 [38.7 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libtype-tiny-perl all 2.004000-1 [357 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libarray-compare-perl all 3.0.8-1 [14.9 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 186 http://deb.debian.org/debian trixie/main arm64 libnet-ssleay-perl arm64 1.94-2 [323 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libwww-perl all 6.77-1 [183 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libxml-parser-perl arm64 2.47-1+b3 [197 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libxml-twig-perl all 1:3.52-3 [177 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libxml-writer-perl all 0.900-2 [26.8 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 libbio-variation-perl all 1.7.5-3 [72.6 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 libbio-cluster-perl all 1.7.3-6 [53.3 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 libtext-csv-perl all 2.04-1 [112 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-5+b1 [300 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 libbio-eutilities-perl all 1.77-2 [124 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 libfile-slurp-tiny-perl all 0.004-2 [7592 B] Get: 207 http://deb.debian.org/debian trixie/main arm64 libtree-dagnode-perl all 1.32-1 [61.7 kB] Get: 208 http://deb.debian.org/debian trixie/main arm64 libxml-perl all 0.08-4 [93.0 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 libxml-regexp-perl all 0.04-1.1 [7500 B] Get: 210 http://deb.debian.org/debian trixie/main arm64 libxml-dom-perl all 1.46-2 [152 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 libxml-dom-xpath-perl all 0.14-4 [9352 B] Get: 213 http://deb.debian.org/debian trixie/main arm64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 libmodule-pluggable-perl all 5.2-5 [23.0 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 libconfig-any-perl all 0.33-1 [31.0 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 52.0-2+b1 [67.4 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b2 [51.2 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1+b1 [14.1 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 227 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 libibumad3 arm64 52.0-2+b1 [27.1 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 libibmad5 arm64 52.0-2+b1 [41.5 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto16 arm64 3.6.2-3 [341 kB] Get: 234 http://deb.debian.org/debian trixie/main arm64 libmbedx509-7 arm64 3.6.2-3 [146 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 libmbedtls21 arm64 3.6.2-3 [222 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 libmodule-build-perl all 0.423400-2 [252 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.15-4+b1 [19.4 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.5-1 [576 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 240 http://deb.debian.org/debian trixie/main arm64 libopenmpi40 arm64 5.0.6-3 [2087 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 mafft arm64 7.505-1+b1 [960 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 5.0.6-3 [180 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 mpi-default-bin arm64 1.17 [2372 B] Get: 246 http://deb.debian.org/debian trixie/main arm64 muscle arm64 1:5.1.0-1+b1 [279 kB] Get: 247 http://deb.debian.org/debian trixie/main arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 ncbi-blast+ arm64 2.16.0+ds-6+b1 [13.8 MB] Get: 249 http://deb.debian.org/debian trixie/main arm64 ncbi-blast+-legacy all 2.16.0+ds-6 [10.4 kB] Get: 250 http://deb.debian.org/debian trixie/main arm64 ncoils arm64 2002-9+b1 [19.6 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 pal2nal all 14.1-3 [17.8 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 phyml arm64 3:3.3.20220408-4+b1 [1087 kB] Get: 253 http://deb.debian.org/debian trixie/main arm64 primer3 arm64 2.6.1-5 [187 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 probcons arm64 1.12-14+b1 [124 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 raxml arm64 8.2.13+dfsg-1+b2 [978 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 sim4 arm64 0.0.20121010-8+b1 [356 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 tigr-glimmer arm64 3.02b-6+b2 [274 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 wise-data all 2.4.1-25 [76.1 kB] Get: 259 http://deb.debian.org/debian trixie/main arm64 wise arm64 2.4.1-25 [1007 kB] Fetched 212 MB in 3s (70.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20082 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_arm64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:arm64 (3.12.8-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20402 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_arm64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21465 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../007-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.22.5-3_arm64.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../010-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.23.0-6_arm64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.40.2-12_arm64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../013-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../015-libedit2_3.1-20240808-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20240808-1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../016-libcbor0.10_0.10.2-2_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../017-libfido2-1_1.15.0-1+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.15.0-1+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../018-openssh-client_1%3a9.9p1-3_arm64.deb ... Unpacking openssh-client (1:9.9p1-3) ... Selecting previously unselected package ucf. Preparing to unpack .../019-ucf_3.0045_all.deb ... Moving old data out of the way Unpacking ucf (3.0045) ... Selecting previously unselected package amap-align. Preparing to unpack .../020-amap-align_2.2+git20080214.600fc29+dfsg-2+b1_arm64.deb ... Unpacking amap-align (2.2+git20080214.600fc29+dfsg-2+b1) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package bedtools-test. Preparing to unpack .../026-bedtools-test_2.31.1+dfsg-2_all.deb ... Unpacking bedtools-test (2.31.1+dfsg-2) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../027-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../028-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../029-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../030-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libdevel-stacktrace-perl. 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Unpacking liblmdb0:arm64 (0.9.31-1+b2) ... Selecting previously unselected package libmbedcrypto16:arm64. Preparing to unpack .../211-libmbedcrypto16_3.6.2-3_arm64.deb ... Unpacking libmbedcrypto16:arm64 (3.6.2-3) ... Selecting previously unselected package libmbedx509-7:arm64. Preparing to unpack .../212-libmbedx509-7_3.6.2-3_arm64.deb ... Unpacking libmbedx509-7:arm64 (3.6.2-3) ... Selecting previously unselected package libmbedtls21:arm64. Preparing to unpack .../213-libmbedtls21_3.6.2-3_arm64.deb ... Unpacking libmbedtls21:arm64 (3.6.2-3) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../214-libmodule-build-perl_0.423400-2_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 (0.423400-2) ... 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Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libaom3:arm64 (3.11.0-1) ... Setting up libpciaccess0:arm64 (0.17-3+b2) ... Setting up mysql-common (5.8+1.1.1) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-12) ... Setting up probcons (1.12-14+b1) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libxml-regexp-perl (0.04-1.1) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libcbor0.10:arm64 (0.10.2-2) ... Setting up mafft (7.505-1+b1) ... Setting up libclone-perl:arm64 (0.47-1+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libedit2:arm64 (3.1-20240808-1) ... Setting up libfile-slurp-tiny-perl (0.004-2) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:arm64 (1.48.0-7) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libibumad3:arm64 (52.0-2+b1) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up ncoils (2002-9+b1) ... Setting up libibmad5:arm64 (52.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2~rc1-2) ... Setting up hyphy-common (2.5.63+dfsg-1) ... Setting up file (1:5.45-3+b1) ... Setting up muscle (1:5.1.0-1+b1) ... Setting up emboss-data (6.6.0+dfsg-15) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Dec 24 23:11:42 UTC 2024. Universal Time is now: Tue Dec 24 23:11:42 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:11.4.3-1) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up primer3 (2.6.1-5) ... Setting up kalign (1:3.4.0-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.13.3-1) ... Setting up libglib2.0-0t64:arm64 (2.82.4-1) ... No schema files found: doing nothing. Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libmunge2:arm64 (0.5.15-4+b1) ... Setting up lagan (2.0-10+b1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:arm64 (2.3.0+dfsg-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxml-xpathengine-perl (0.14-2) ... Setting up sim4 (0.0.20121010-8+b1) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libfribidi0:arm64 (1.0.16-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-3) ... Setting up libhwloc15:arm64 (2.11.2-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.22.5-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up libmariadb3:arm64 (1:11.4.3-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up wise-data (2.4.1-25) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libnuma1:arm64 (2.0.18-1+b1) ... Setting up libtree-dagnode-perl (1.32-1) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libdav1d7:arm64 (1.5.0-1+b1) ... Setting up sensible-utils (0.0.24) ... 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Setting up libmbedcrypto16:arm64 (3.6.2-3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libexporter-tiny-perl (1.006002-1) ... Setting up libfido2-1:arm64 (1.15.0-1+b1) ... Setting up libde265-0:arm64 (1.0.15-1+b2) ... Setting up openssl (3.3.2-2) ... Setting up tigr-glimmer (3.02b-6+b2) ... Setting up libdrm-common (2.4.123-1) ... Setting up libyuv0:arm64 (0.0.1898.20241125-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up exonerate (2.4.0-5+b2) ... Setting up liburi-perl (5.30-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libfile-sort-perl (1.01-3) ... Setting up raxml (8.2.13+dfsg-1+b2) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libnet-ssleay-perl:arm64 (1.94-2) ... 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Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libmbedx509-7:arm64 (3.6.2-3) ... Setting up libllvm17t64:arm64 (1:17.0.6-18) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libgav1-1:arm64 (0.19.0-2+b2) ... Setting up ucf (3.0045) ... Setting up libmbedtls21:arm64 (3.6.2-3) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up groff-base (1.23.0-6) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b1) ... Setting up libharfbuzz0b:arm64 (10.1.0-1) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-4) ... 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 libmodule-runtime-perl (0.016-2) ... Setting up libraqm0:arm64 (0.10.2-1) ... Setting up libpmix2t64:arm64 (5.0.5-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+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 libnsl2:arm64 (1.3.0-3+b3) ... Setting up librdmacm1t64:arm64 (52.0-2+b1) ... Setting up libhsakmt1:arm64 (5.7.0-1) ... Setting up bioperl (1.7.8-1) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-3) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.20) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libhsa-runtime64-1:arm64 (5.7.1-3) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up bedtools-test (2.31.1+dfsg-2) ... Setting up ncbi-blast+-legacy (2.16.0+ds-6) ... Setting up libucx0:arm64 (1.17.0+ds-3) ... Setting up libopenmpi40:arm64 (5.0.6-3) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.17) ... Setting up phyml (3:3.3.20220408-4+b1) ... Setting up libheif-plugin-dav1d:arm64 (1.19.3-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libheif-plugin-libde265:arm64 (1.19.3-1) ... Setting up libwww-perl (6.77-1) ... Setting up libheif1:arm64 (1.19.3-1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up emboss-lib (6.6.0+dfsg-15+b1) ... Setting up libxml-parser-perl (2.47-1+b3) ... Setting up emboss (6.6.0+dfsg-15+b1) ... Setting up libxml-twig-perl (1:3.52-3) ... 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 (1.730-3) ... 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 (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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_1.7.3-13_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bioperl-run-1.7.3' dh_auto_configure -- --install_scripts /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro" --install_scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n ]n Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' make[1]: Leaving directory '/build/reproducible-path/bioperl-run-1.7.3' dh_auto_build /usr/bin/perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bioperl-run-1.7.3' mkdir t.skip for t in Blat Eponine Glimmer2 RepeatMasker Phyml Hyphy MCS ; do mv t/${t}.t t.skip ; done PATH=$PATH:/usr/lib/emboss:/usr/lib/phylip/bin/:/usr/lib/tigr-glimmer:debian/test_hack_bin \ PHYLIPDIR=/usr/lib/phylip/bin HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \ dh_auto_test --no-parallel /usr/bin/perl Build test --verbose 1 AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: t/data/cysprot.fa Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: /tmp/hjvom2XvTr 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 # Required executable for Bio::Tools::Run::BEDTools is not present t/BEDTools.t .................. 1..423 ok 1 - make a default factory ok 2 - default to command 'bam_to_bed' ok 3 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 4 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 5 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 6 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 7 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 8 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 9 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 10 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 11 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 12 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 13 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 14 # 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skip Required executable for Bio::Tools::Run::BEDTools is not present ok 106 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 107 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 108 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 109 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 110 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 111 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 112 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 113 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 114 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 115 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 116 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 117 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 118 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 119 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 120 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 121 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 122 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 123 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 124 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 125 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 126 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 127 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 128 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 129 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 130 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 131 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 132 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 133 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 134 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 135 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 136 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 137 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 138 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 139 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 140 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 141 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 142 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 143 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 144 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 145 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 146 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 147 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 148 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 149 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 150 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 151 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 152 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 153 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 154 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 155 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 156 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 157 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 158 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 159 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 160 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 161 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 162 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 163 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 164 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 165 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 166 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 167 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 168 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 169 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 170 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 171 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 172 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 173 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 174 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 175 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 176 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 177 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 178 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 179 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 180 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 181 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 182 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 183 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 184 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 185 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 186 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 187 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 188 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 189 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 190 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 191 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 192 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 193 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 194 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 195 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 196 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 197 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 198 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 199 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 200 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 201 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 202 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 203 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 204 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 205 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 206 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 207 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 208 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 209 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 210 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 211 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 212 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 213 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 214 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 215 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 216 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 217 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 218 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 219 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 220 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 221 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 222 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 223 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 224 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 225 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 226 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 227 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 228 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 229 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 230 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 231 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 232 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 233 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 234 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 235 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 236 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 237 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 238 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 239 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 240 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 241 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 242 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 243 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 244 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 245 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 246 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 247 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 248 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 249 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 250 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 251 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 252 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 253 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 254 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 255 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 256 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 257 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 258 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 259 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 260 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 261 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 262 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 263 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 264 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 265 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 266 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 267 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 268 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 269 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 270 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 271 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 272 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 273 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 274 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 275 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 276 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 277 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 278 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 279 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 280 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 281 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 282 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 283 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 284 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 285 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 286 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 287 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 288 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 289 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 290 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 291 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 292 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 293 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 294 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 295 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 296 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 297 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 298 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 299 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 300 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 301 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 302 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 303 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 304 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 305 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 306 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 307 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 308 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 309 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 310 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 311 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 312 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 313 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 314 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 315 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 316 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 317 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 318 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 319 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 320 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 321 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 322 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 323 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 324 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 325 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 326 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 327 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 328 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 329 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 330 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 331 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 332 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 333 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 334 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 335 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 336 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 337 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 338 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 339 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 340 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 341 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 342 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 343 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 344 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 345 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 346 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 347 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 348 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 349 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 350 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 351 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 352 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 353 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 354 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 355 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 356 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 357 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 358 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 359 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 360 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 361 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 362 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 363 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 364 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 365 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 366 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 367 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 368 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 369 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 370 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 371 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 372 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 373 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 374 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 375 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 376 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 377 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 378 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 379 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 380 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 381 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 382 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 383 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 384 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 385 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 386 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 387 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 388 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 389 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 390 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 391 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 392 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 393 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 394 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 395 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 396 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 397 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 398 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 399 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 400 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 401 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 402 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 403 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 404 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 405 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 406 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 407 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 408 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 409 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 410 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 411 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 412 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 413 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 414 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 415 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 416 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 417 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 418 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 419 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 420 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 421 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 422 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok 423 # skip Required executable for Bio::Tools::Run::BEDTools is not present ok # You named your test '71'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '91'. You shouldn't use numbers for your test names. # Very confusing. t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 ok 4 ok 5 - 71 ok 6 - 91 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [16%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [31%] 16000 Cells done [33%] 17000 Cells done [35%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [48%] 24000 Cells done [50%] 25000 Cells done [52%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [63%] 31000 Cells done [65%] 32000 Cells done [67%] 33000 Cells done [69%] 34000 Cells done [71%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [78%] 38000 Cells done [80%] 39000 Cells done [82%] 40000 Cells done [84%] 41000 Cells done [86%] 42000 Cells done [88%] 43000 Cells done [90%] 44000 Cells done [93%] 45000 Cells done [95%] 46000 Cells done [97%] 47000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [16%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [28%] 13000 Cells done [31%] 14000 Cells done [33%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [40%] 18000 Cells done [43%] 19000 Cells done [45%] 20000 Cells done [48%] 21000 Cells done [50%] 22000 Cells done [52%] 23000 Cells done [55%] 24000 Cells done [57%] 25000 Cells done [60%] 26000 Cells done [62%] 27000 Cells done [64%] 28000 Cells done [67%] 29000 Cells done [69%] 30000 Cells done [72%] 31000 Cells done [74%] 32000 Cells done [76%] 33000 Cells done [79%] 34000 Cells done [81%] 35000 Cells done [84%] 36000 Cells done [86%] 37000 Cells done [89%] 38000 Cells done [91%] 39000 Cells done [93%] 40000 Cells done [96%] 41000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Warning Error Strangely truncated line in fasta file Warning Error Strangely truncated line in fasta file Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [16%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [31%] 16000 Cells done [33%] 17000 Cells done [35%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [48%] 24000 Cells done [50%] 25000 Cells done [52%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [63%] 31000 Cells done [65%] 32000 Cells done [67%] 33000 Cells done [69%] 34000 Cells done [71%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [78%] 38000 Cells done [80%] 39000 Cells done [82%] 40000 Cells done [84%] 41000 Cells done [86%] 42000 Cells done [88%] 43000 Cells done [90%] 44000 Cells done [93%] 45000 Cells done [95%] 46000 Cells done [97%] 47000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode t/DBA.t ....................... 1..5 ok 1 - use Bio::Tools::Run::Alignment::DBA; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::DBA' isa 'Bio::Tools::Run::Alignment::DBA' ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok -- namet is "-sequence" associated seqall qualifiers -- namet is "-outfile" associated outfile qualifiers t/EMBOSS.t .................... 1..31 ok 1 - use Bio::Root::IO; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - use Bio::Factory::EMBOSS; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok t/Exonerate.t ................. 1..89 ok 1 - use Bio::Tools::Run::Alignment::Exonerate; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Exonerate' isa 'Bio::Tools::Run::Alignment::Exonerate' ok 3 ok 4 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok t/FastTree.t .................. 1..9 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::FastTree; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - Tree is defined ok 6 - Number of nodes is correct ok 7 - Tree is defined ok 8 - Tree is defined ok 9 - Tree is defined ok # Required executable for Bio::Tools::Run::FootPrinter is not present t/FootPrinter.t ............... 1..24 ok 1 - use Bio::Tools::Run::FootPrinter; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 4 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 5 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 6 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 7 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 8 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 9 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 10 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 11 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 12 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 13 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 14 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 15 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 16 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 17 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 18 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 19 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 20 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 21 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 22 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 23 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 24 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok # Required environment variable $GENEMARK_MODELS is not set t/Genemark.hmm.prokaryotic.t .. 1..99 ok 1 - use Bio::Tools::Run::Genemark; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 # skip Required environment variable $GENEMARK_MODELS is not set ok 5 # skip Required environment variable $GENEMARK_MODELS is not set ok 6 # skip Required environment variable $GENEMARK_MODELS is not set ok 7 # skip Required environment variable $GENEMARK_MODELS is not set ok 8 # skip Required environment variable $GENEMARK_MODELS is not set ok 9 # skip Required environment variable $GENEMARK_MODELS is not set ok 10 # skip Required environment variable $GENEMARK_MODELS is not set ok 11 # skip Required environment variable $GENEMARK_MODELS is not set ok 12 # skip Required environment variable $GENEMARK_MODELS is not set ok 13 # skip Required environment variable $GENEMARK_MODELS is not set ok 14 # skip Required environment variable $GENEMARK_MODELS is not set ok 15 # skip Required environment variable $GENEMARK_MODELS is not set ok 16 # skip Required environment variable $GENEMARK_MODELS is not set ok 17 # skip Required environment variable $GENEMARK_MODELS is not set ok 18 # skip Required environment variable $GENEMARK_MODELS is not set ok 19 # skip Required environment variable $GENEMARK_MODELS is not set ok 20 # skip Required environment variable $GENEMARK_MODELS is not set ok 21 # skip Required environment variable $GENEMARK_MODELS is not set ok 22 # skip Required environment variable $GENEMARK_MODELS is not set ok 23 # skip Required environment variable $GENEMARK_MODELS is not set ok 24 # skip Required environment variable $GENEMARK_MODELS is not set ok 25 # skip Required environment variable $GENEMARK_MODELS is not set ok 26 # skip Required environment variable $GENEMARK_MODELS is not set ok 27 # skip Required environment variable $GENEMARK_MODELS is not set ok 28 # skip Required environment variable $GENEMARK_MODELS is not set ok 29 # skip Required environment variable $GENEMARK_MODELS is not set ok 30 # skip Required environment variable $GENEMARK_MODELS is not set ok 31 # skip Required environment variable $GENEMARK_MODELS is not set ok 32 # skip Required environment variable $GENEMARK_MODELS is not set ok 33 # skip Required environment variable $GENEMARK_MODELS is not set ok 34 # skip Required environment variable $GENEMARK_MODELS is not set ok 35 # skip Required environment variable $GENEMARK_MODELS is not set ok 36 # skip Required environment variable $GENEMARK_MODELS is not set ok 37 # skip Required environment variable $GENEMARK_MODELS is not set ok 38 # skip Required environment variable $GENEMARK_MODELS is not set ok 39 # skip Required environment variable $GENEMARK_MODELS is not set ok 40 # skip Required environment variable $GENEMARK_MODELS is not set ok 41 # skip Required environment variable $GENEMARK_MODELS is not set ok 42 # skip Required environment variable $GENEMARK_MODELS is not set ok 43 # skip Required environment variable $GENEMARK_MODELS is not set ok 44 # skip Required environment variable $GENEMARK_MODELS is not set ok 45 # skip Required environment variable $GENEMARK_MODELS is not set ok 46 # skip Required environment variable $GENEMARK_MODELS is not set ok 47 # skip Required environment variable $GENEMARK_MODELS is not set ok 48 # skip Required environment variable $GENEMARK_MODELS is not set ok 49 # skip Required environment variable $GENEMARK_MODELS is not set ok 50 # skip Required environment variable $GENEMARK_MODELS is not set ok 51 # skip Required environment variable $GENEMARK_MODELS is not set ok 52 # skip Required environment variable $GENEMARK_MODELS is not set ok 53 # skip Required environment variable $GENEMARK_MODELS is not set ok 54 # skip Required environment variable $GENEMARK_MODELS is not set ok 55 # skip Required environment variable $GENEMARK_MODELS is not set ok 56 # skip Required environment variable $GENEMARK_MODELS is not set ok 57 # skip Required environment variable $GENEMARK_MODELS is not set ok 58 # skip Required environment variable $GENEMARK_MODELS is not set ok 59 # skip Required environment variable $GENEMARK_MODELS is not set ok 60 # skip Required environment variable $GENEMARK_MODELS is not set ok 61 # skip Required environment variable $GENEMARK_MODELS is not set ok 62 # skip Required environment variable $GENEMARK_MODELS is not set ok 63 # skip Required environment variable $GENEMARK_MODELS is not set ok 64 # skip Required environment variable $GENEMARK_MODELS is not set ok 65 # skip Required environment variable $GENEMARK_MODELS is not set ok 66 # skip Required environment variable $GENEMARK_MODELS is not set ok 67 # skip Required environment variable $GENEMARK_MODELS is not set ok 68 # skip Required environment variable $GENEMARK_MODELS is not set ok 69 # skip Required environment variable $GENEMARK_MODELS is not set ok 70 # skip Required environment variable $GENEMARK_MODELS is not set ok 71 # skip Required environment variable $GENEMARK_MODELS is not set ok 72 # skip Required environment variable $GENEMARK_MODELS is not set ok 73 # skip Required environment variable $GENEMARK_MODELS is not set ok 74 # skip Required environment variable $GENEMARK_MODELS is not set ok 75 # skip Required environment variable $GENEMARK_MODELS is not set ok 76 # skip Required environment variable $GENEMARK_MODELS is not set ok 77 # skip Required environment variable $GENEMARK_MODELS is not set ok 78 # skip Required environment variable $GENEMARK_MODELS is not set ok 79 # skip Required environment variable $GENEMARK_MODELS is not set ok 80 # skip Required environment variable $GENEMARK_MODELS is not set ok 81 # skip Required environment variable $GENEMARK_MODELS is not set ok 82 # skip Required environment variable $GENEMARK_MODELS is not set ok 83 # skip Required environment variable $GENEMARK_MODELS is not set ok 84 # skip Required environment variable $GENEMARK_MODELS is not set ok 85 # skip Required environment variable $GENEMARK_MODELS is not set ok 86 # skip Required environment variable $GENEMARK_MODELS is not set ok 87 # skip Required environment variable $GENEMARK_MODELS is not set ok 88 # skip Required environment variable $GENEMARK_MODELS is not set ok 89 # skip Required environment variable $GENEMARK_MODELS is not set ok 90 # skip Required environment variable $GENEMARK_MODELS is not set ok 91 # skip Required environment variable $GENEMARK_MODELS is not set ok 92 # skip Required environment variable $GENEMARK_MODELS is not set ok 93 # skip Required environment variable $GENEMARK_MODELS is not set ok 94 # skip Required environment variable $GENEMARK_MODELS is not set ok 95 # skip Required environment variable $GENEMARK_MODELS is not set ok 96 # skip Required environment variable $GENEMARK_MODELS is not set ok 97 # skip Required environment variable $GENEMARK_MODELS is not set ok 98 # skip Required environment variable $GENEMARK_MODELS is not set ok 99 # skip Required environment variable $GENEMARK_MODELS is not set ok These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values t/Genewise.t .................. 1..17 ok 1 - use Bio::Tools::Run::Genewise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Genewise' isa 'Bio::Tools::Run::Genewise' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok # Required environment variable $GENSCANDIR is not set t/Genscan.t ................... 1..6 ok 1 - use Bio::Tools::Run::Genscan; ok 2 - use Bio::Root::IO; ok 3 # skip Required environment variable $GENSCANDIR is not set ok 4 # skip Required environment variable $GENSCANDIR is not set ok 5 # skip Required environment variable $GENSCANDIR is not set ok 6 # skip Required environment variable $GENSCANDIR is not set ok # Required executable for Bio::Tools::Run::Phylo::Gerp is not present t/Gerp.t ...................... 1..33 ok 1 - use Bio::Tools::Run::Phylo::Gerp; ok 2 - use Bio::AlignIO; ok 3 - use Bio::TreeIO; ok 4 - use Bio::Root::Utilities; ok 5 - Found input alignment file ok 6 - Found input tree file ok 7 - An object of class 'Bio::Tools::Run::Phylo::Gerp' isa 'Bio::Tools::Run::Phylo::Gerp' ok 8 - has a created method not in args supplied to new ok 9 - quiet was set ok 10 - program_dir returned correct default ok 11 - Correct exe default name ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok t/Glimmer3.t .................. 1..111 ok 1 - use Bio::Tools::Run::Glimmer; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Glimmer' isa 'Bio::Tools::Run::Glimmer' ok 5 - An object of class 'Bio::Tools::Glimmer' isa 'Bio::Tools::Glimmer' ok 6 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 7 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 8 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 11 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 12 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 13 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 14 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 18 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 19 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 20 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 22 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 23 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 25 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 26 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 28 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 29 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 30 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 32 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 33 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 34 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 35 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 36 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 37 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 38 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 39 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 40 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 41 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 42 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 43 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 44 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 45 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 46 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 47 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 48 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 49 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 50 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 51 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 52 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 53 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 54 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 55 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 56 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 57 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 58 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 59 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 60 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 61 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 62 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 63 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 64 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 66 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 67 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 68 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 69 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 72 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 73 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 74 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 75 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 76 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 77 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 78 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 79 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 80 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 81 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 82 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 83 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 84 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 85 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 86 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 87 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 88 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 89 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 90 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 91 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 92 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 93 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 94 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 95 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 96 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 98 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 99 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 100 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 101 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 102 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 103 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 104 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 105 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok # Required executable for Bio::Tools::Run::Hmmer is not present t/Hmmer.t ..................... 1..27 ok 1 - use Bio::Tools::Run::Hmmer; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer' ok 5 ok 6 ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok t/Infernal.t .................. 1..3 ok 1 - use Bio::Tools::Run::Infernal; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok t/Kalign.t .................... 1..7 ok 1 - use Bio::Tools::Run::Alignment::Kalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on kalign versions >= 2 Kalign (3.4.0) Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 [2024-12-24 11:12:17] : LOG : Detected protein sequences. [2024-12-24 11:12:17] : LOG : Read 7 sequences from standard input. [2024-12-24 11:12:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-12-24 11:12:17] : LOG : Calculating pairwise distances [2024-12-24 11:12:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-12-24 11:12:17] : LOG : Building guide tree. [2024-12-24 11:12:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-12-24 11:12:17] : LOG : Aligning [2024-12-24 11:12:17] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 ok 5 ok 6 Kalign (3.4.0) Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann This program comes with ABSOLUTELY NO WARRANTY; for details type: `kalign -showw'. This is free software, and you are welcome to redistribute it under certain conditions; consult the COPYING file for details. Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 [2024-12-24 11:12:17] : LOG : Detected protein sequences. [2024-12-24 11:12:17] : LOG : Read 7 sequences from standard input. [2024-12-24 11:12:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-12-24 11:12:17] : LOG : Calculating pairwise distances [2024-12-24 11:12:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-12-24 11:12:17] : LOG : Building guide tree. [2024-12-24 11:12:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2024-12-24 11:12:17] : LOG : Aligning [2024-12-24 11:12:17] : LOG : CPU Time: 0.01u 00:00:00.00 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/Ej8jmgsgVT 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/6jhmzjHhTx Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (6) CATL_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (4) CATH_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (6) CATL_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (4) CATH_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (4) CATH_RAT vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (4) CATH_RAT vs. (6) CATL_RAT -- done. Computing posterior matrix: (4) CATH_RAT vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (6) CATL_RAT vs. (7) PAPA_CARPA -- done. Trained parameter set: initDistrib[] = { 0.8318790197 5.246166256e-05 5.246166256e-05 0.08400797099 0.08400797099 } gapOpen[] = { 0.01386308484 0.01386308484 0.006556345616 0.006556345616 } gapExtend[] = { 0.3603379726 0.3603379726 0.7831884027 0.7831884027 } PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.8318790197 5.246169894e-05 5.246169894e-05 0.08400797099 0.08400797099 } gapOpen[] = { 0.01386308484 0.01386308484 0.006556345616 0.006556345616 } gapExtend[] = { 0.3603379726 0.3603379726 0.7831884027 0.7831884027 } Loading sequence file: /tmp/pfroLeJ0gY Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # Required executable for Bio::Tools::Run::Profile is not present t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 # skip Required executable for Bio::Tools::Run::Profile is not present ok 6 # skip Required executable for Bio::Tools::Run::Profile is not present ok 7 # skip Required executable for Bio::Tools::Run::Profile is not present ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 12 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 13 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 14 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 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 The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed 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 # Required executable for Bio::Tools::Run::Samtools is not present 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 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 27 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 28 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 29 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 30 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 31 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 32 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 33 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 34 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 35 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 36 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 37 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 38 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 39 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 40 # skip Required executable for Bio::Tools::Run::Samtools is not present ok 41 # skip Required executable for Bio::Tools::Run::Samtools is not present 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. Files=60, Tests=1652, 58 wallclock secs ( 0.35 usr 0.13 sys + 48.51 cusr 5.06 csys = 54.05 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/reproducible-path/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/bin/perl Build install --destdir /build/reproducible-path/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Muscle.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/MAFFT.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Gmap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Exonerate.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/DBA.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Amap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Vista.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::TribeMCL.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Tmhmm.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlast.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Simprot.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools::Config.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Samtools.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RepeatMasker.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::RNAMotif.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Pseudowise.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Promoterwise.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Profile.3pm Installing 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/build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.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_1.7.3-13_all.deb'. dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-13_all.deb'. dpkg-genbuildinfo --build=binary -O../bioperl-run_1.7.3-13_arm64.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-13_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/3980862 and its subdirectories I: Current time: Tue Dec 24 11:12:58 -12 2024 I: pbuilder-time-stamp: 1735081978 Tue Dec 24 23:13:00 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue Dec 24 23:13:00 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue Dec 24 23:16:23 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue Dec 24 23:16:24 UTC 2024 I: bioperl-run_1.7.3-13_arm64.changes: Format: 1.8 Date: Sun, 01 Dec 2024 10:57:53 +0100 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: all Version: 1.7.3-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bioperl-run - BioPerl wrappers: scripts libbio-perl-run-perl - BioPerl wrappers: modules Closes: 1077454 Changes: bioperl-run (1.7.3-13) unstable; urgency=medium . * Revert "skip_tests_for_ncbi-blast+.patch: remove." * Revert "d/control: remove build dependency on ncbi-blast+-legacy." * update-blastdbcmd-error-output.patch: fix test regression. This patch updates the expected blastdbcmd error output parsed by the StandAloneBlastPlus.pm runner, fixing the corresponding test item in the maneuver. Thanks to Aaron M. Ucko (Closes: #1077454) Checksums-Sha1: 1f4b0f16bfc6bae7900157b8e04c898c8de93b72 36432 bioperl-run_1.7.3-13_all.deb 11e5efdd3d7b3e829c5df23fa045dcdf3d970202 12718 bioperl-run_1.7.3-13_arm64.buildinfo 5a609a99bb16b128958997f13fd063bbea46f1d4 528204 libbio-perl-run-perl_1.7.3-13_all.deb Checksums-Sha256: 18fdd1bace57347f20349fae3b8524e28971c4297c7552aaf0120df04cf1b8e0 36432 bioperl-run_1.7.3-13_all.deb a33dbbb99b37c9ae5961b33557ad874bae1085dfc6bf7fb3be84c5d9426421b0 12718 bioperl-run_1.7.3-13_arm64.buildinfo 18e76f8e8bc62e13564623e01781a4a5445a3c832a42af59878c728e96b16587 528204 libbio-perl-run-perl_1.7.3-13_all.deb Files: 7396c72f750bef0ae2fe55333295eee0 36432 science optional bioperl-run_1.7.3-13_all.deb 69d2c76929af62a34f32a72a10d6051d 12718 science optional bioperl-run_1.7.3-13_arm64.buildinfo e8b79990b69d2d1782db99595f69bb02 528204 perl optional libbio-perl-run-perl_1.7.3-13_all.deb Tue Dec 24 23:16:25 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_8-43300.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ta2MVVWb/bioperl-run_1.7.3-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ta2MVVWb/bioperl-run_1.7.3-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ta2MVVWb/bioperl-run_1.7.3-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ta2MVVWb/b1/bioperl-run_1.7.3-13_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ta2MVVWb/b2/bioperl-run_1.7.3-13_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.404s) 0.404s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.024s) 0.024s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 751ms CPU time consumed: 752ms Tue Dec 24 23:16:30 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Tue Dec 24 23:16:30 UTC 2024 I: bioperl-run from trixie built successfully and reproducibly on arm64. Tue Dec 24 23:16:32 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 24 23:16:32 UTC 2024 I: Submitting 16K b1/bioperl-run_1.7.3-13_arm64.buildinfo.asc Tue Dec 24 23:16:34 UTC 2024 I: Submitting 16K b2/bioperl-run_1.7.3-13_arm64.buildinfo.asc Tue Dec 24 23:16:34 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 24 23:16:34 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 24 23:16:34 UTC 2024 I: Removing signed bioperl-run_1.7.3-13_arm64.buildinfo.asc files: removed './b1/bioperl-run_1.7.3-13_arm64.buildinfo.asc' removed './b2/bioperl-run_1.7.3-13_arm64.buildinfo.asc'