sbuild (Debian sbuild) 0.91.9 (05 May 2026) on carme.larted.org.uk +==============================================================================+ | bioperl-run 1.7.3-14 (amd64) Sat, 27 Jun 2026 22:56:24 +0000 | +==============================================================================+ Package: bioperl-run Version: 1.7.3-14 Source Version: 1.7.3-14 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sat, 27 Jun 2026 22:56:25 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.3-14 perl-5.44-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bioperl-run_1.7.3-14 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 27 Jun 2026 22:56:26 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:2 file:/srv/reprepro perl-5.44/main amd64 Packages [601 kB] Get:3 http://deb.debian.org/debian unstable InRelease [189 kB] Get:4 http://deb.debian.org/debian sid InRelease [189 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-06-27-2006.48-F-2026-06-27-2006.48.pdiff [51.6 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2026-06-27-2006.48-F-2026-06-27-2006.48.pdiff [31.5 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-06-27-2006.48-F-2026-06-27-2006.48.pdiff [51.6 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2026-06-27-2006.48-F-2026-06-27-2006.48.pdiff [31.5 kB] Fetched 589 kB in 8s (77.2 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sat, 27 Jun 2026 22:56:35 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bioperl-run_1.7.3-14.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 27 Jun 2026 22:56:36 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libmodule-build-perl, build-essential, perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, libbio-perl-perl, clustalw, emboss, exonerate, hmmer, hyphy-pt | hyphy-mpi, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl Filtered Build-Depends: debhelper-compat (= 13), libmodule-build-perl, build-essential, perl, bioperl (>= 1.7.4), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libfile-sort-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, libbio-cluster-perl, libbio-featureio-perl, libconfig-any-perl, libbio-tools-run-alignment-clustalw-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, amap-align, bedtools, bedtools-test, ncbi-blast+-legacy, libbio-perl-perl, clustalw, emboss, exonerate, hmmer, hyphy-pt, infernal, kalign, mafft, muscle, ncoils, phyml, primer3, probcons, python3-pybedtools, raxml, samtools, sim4, tigr-glimmer, wise, fasttree, lagan, pal2nal, pftools, libwww-perl dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive ./ InRelease Get:2 copy:/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive ./ Release [615 B] Ign:3 copy:/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive ./ Release.gpg Get:4 copy:/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive ./ Sources [1534 B] Get:5 copy:/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive ./ Packages [1313 B] Fetched 3462 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: amap-align autoconf automake autopoint autotools-dev bedtools bedtools-test bioperl bsdextrautils ca-certificates clustalw debhelper dh-autoreconf dh-strip-nondeterminism dwz emboss emboss-data emboss-lib exonerate fasttree file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base hmmer hyphy-common hyphy-pt ibverbs-providers infernal intltool-debian isa-support kalign lagan libabsl20260107 libalgorithm-diff-perl libamd-comgr3 libamdhip64-6 libaom3 libarchive-zip-perl libarray-compare-perl libavif16 libb-hooks-op-check-perl libbio-asn1-entrezgene-perl libbio-cluster-perl libbio-eutilities-perl libbio-featureio-perl libbio-perl-perl libbio-perl-run-perl libbio-tools-run-alignment-clustalw-perl libbio-tools-run-remoteblast-perl libbio-variation-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl libcbor0.10 libclang-common-21-dev libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-any-perl libcurl3t64-gnutls libcurl4-gnutls libdata-stag-perl libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm2 libdynaloader-functions-perl libedit2 libelf1t64 libencode-locale-perl libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfido2-1 libfile-listing-perl libfile-slurp-perl libfile-slurper-perl libfile-sort-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfuse3-4 libgav1-2 libgd3 libgfortran5 libglib2.0-0t64 libgssapi-krb5-2 libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libimagequant0 libimport-into-perl libio-html-perl libio-pty-perl libio-socket-ssl-perl libio-string-perl libipc-run-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblerc4 libllvm21 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmariadb3 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-build-perl libmodule-pluggable-perl libmodule-runtime-perl libmoo-perl libmunge2 libncbi-vdb3 libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi40 libparams-classify-perl libpciaccess0 libpipeline1 libpmix2t64 libpng16-16t64 libpq5 libproc2-0 libprrte-bin libprrte3 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librav1e0.8 librdmacm1t64 librole-tiny-perl libsharpyuv0 libssh2-1t64 libsub-quote-perl libsub-uplevel-perl libsvtav1enc4 libsystemd-shared libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-charwidth-perl libtext-csv-perl libtext-diff-perl libtext-wrapi18n-perl libtiff6 libtimedate-perl libtool libtree-dagnode-perl libtry-tiny-perl libtype-tiny-perl libucc1 libuchardet0 libucx0 liburi-perl libuv1t64 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml-dom-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpathengine-perl libxml2-16 libxnvctrl0 libxpm4 libyuv0 libz3-4 libze1 m4 mafft man-db mariadb-common media-types mount mpi-default-bin muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data ncbi-vdb-data ncoils netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl pal2nal perl-openssl-defaults pftools phyml po-debconf primer3 probcons procps python3 python3-minimal python3-numpy python3-numpy-dev python3-pybedtools python3-pysam python3.14 python3.14-minimal raxml samtools sensible-utils sim4 sse4.2-support systemd tigr-glimmer tzdata ucf wise wise-data Suggested packages: autoconf-archive gnu-standards autoconf-doc clustalx seaview dh-make emboss-doc emboss-test embassy gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff hmmer-doc libxml-sax-expatxs-perl libbio-alignio-stockholm-perl fuse3 libgd-tools low-memory-monitor krb5-doc krb5-user libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar libheif-plugin-rav1e libheif-plugin-svtenc libdata-dump-perl libhwloc-contrib-plugins libcrypt-ssleay-perl libscalar-number-perl pciutils libpq-oauth libarchive13t64 libcurl4t64 libdw1t64 libfdisk1 libmicrohttpd12t64 libpwquality1 libqrencode4 libtss2-esys-3.0.2-0t64 libtss2-mu-4.0.1-0t64 libtss2-rc0t64 libtss2-tcti-device0t64 libtool-doc gfortran | fortran95-compiler libsub-name-perl libdevel-lexalias-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools m4-doc apparmor less www-browser nfs-common gnuplot opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl ncbi-epcr probcons-extra python3-doc python3-tk python3-venv gfortran python-numpy-doc python3-dev python3-pytest python-pybedtools-doc python3.14-venv python3.14-doc binfmt-support cwltool systemd-container systemd-homed systemd-imds systemd-userdbd systemd-boot systemd-report systemd-resolved systemd-repart polkitd wise-doc Recommended packages: bioperl-run perl-doc libcache-cache-perl libdbi-perl libapache-dbi-perl libyaml-perl libace-perl liblist-moreutils-perl libset-scalar-perl dialign curl | wget | lynx libalgorithm-diff-xs-perl libalgorithm-munkres-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgraph-perl libgraphviz-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-sax-writer-perl libclang-rt-21-dev libconfig-general-perl libconfig-tiny-perl libyaml-libyaml-perl | libyaml-syck-perl | libyaml-perl libgd-perl libmldbm-perl libxml-libxslt-perl perl-tk libperlio-utf8-strict-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libheif-plugin-x265 libheif-plugin-aomenc libhtml-format-perl libio-compress-brotli-perl krb5-locales libmodule-signature-perl libpod-readme-perl libsoftware-license-perl libnamespace-clean-perl libgpm2 libpmix-dev publicsuffix libxstring-perl libapparmor1 libbpf1 libcryptsetup12 libkmod2 libtext-csv-xs-perl libltdl-dev libref-util-perl libtype-tiny-xs-perl libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl libtext-iconv-perl libtie-ixhash-perl lynx ruby xauth paml libmail-sendmail-perl psmisc linux-sysctl-defaults default-dbus-system-bus | dbus-system-bus login systemd-timesyncd | time-daemon systemd-cryptsetup systemd-tpm The following NEW packages will be installed: amap-align autoconf automake autopoint autotools-dev bedtools bedtools-test bioperl bsdextrautils ca-certificates clustalw debhelper dh-autoreconf dh-strip-nondeterminism dwz emboss emboss-data emboss-lib exonerate fasttree file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base hmmer hyphy-common hyphy-pt ibverbs-providers infernal intltool-debian isa-support kalign lagan libabsl20260107 libalgorithm-diff-perl libamd-comgr3 libamdhip64-6 libaom3 libarchive-zip-perl libarray-compare-perl libavif16 libb-hooks-op-check-perl libbio-asn1-entrezgene-perl libbio-cluster-perl libbio-eutilities-perl libbio-featureio-perl libbio-perl-perl libbio-perl-run-perl libbio-tools-run-alignment-clustalw-perl libbio-tools-run-remoteblast-perl libbio-variation-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl libcbor0.10 libclang-common-21-dev libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-any-perl libcurl3t64-gnutls libcurl4-gnutls libdata-stag-perl libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm2 libdynaloader-functions-perl libedit2 libelf1t64 libencode-locale-perl libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfido2-1 libfile-listing-perl libfile-slurp-perl libfile-slurper-perl libfile-sort-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfuse3-4 libgav1-2 libgd3 libgfortran5 libglib2.0-0t64 libgssapi-krb5-2 libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libimagequant0 libimport-into-perl libio-html-perl libio-pty-perl libio-socket-ssl-perl libio-string-perl libipc-run-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblerc4 libllvm21 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1t64 libmariadb3 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmodule-build-perl libmodule-pluggable-perl libmodule-runtime-perl libmoo-perl libmunge2 libncbi-vdb3 libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi40 libparams-classify-perl libpciaccess0 libpipeline1 libpmix2t64 libpng16-16t64 libpq5 libproc2-0 libprrte-bin libprrte3 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librav1e0.8 librdmacm1t64 librole-tiny-perl libsharpyuv0 libssh2-1t64 libsub-quote-perl libsub-uplevel-perl libsvtav1enc4 libsystemd-shared libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-charwidth-perl libtext-csv-perl libtext-diff-perl libtext-wrapi18n-perl libtiff6 libtimedate-perl libtool libtree-dagnode-perl libtry-tiny-perl libtype-tiny-perl libucc1 libuchardet0 libucx0 liburi-perl libuv1t64 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml-dom-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpathengine-perl libxml2-16 libxnvctrl0 libxpm4 libyuv0 libz3-4 libze1 m4 mafft man-db mariadb-common media-types mount mpi-default-bin muscle mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data ncbi-vdb-data ncoils netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssl pal2nal perl-openssl-defaults pftools phyml po-debconf primer3 probcons procps python3 python3-minimal python3-numpy python3-numpy-dev python3-pybedtools python3-pysam python3.14 python3.14-minimal raxml samtools sbuild-build-depends-main-dummy sensible-utils sim4 sse4.2-support systemd tigr-glimmer tzdata ucf wise wise-data 0 upgraded, 283 newly installed, 0 to remove and 0 not upgraded. Need to get 295 MB/297 MB of archives. After this operation, 1450 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libtext-charwidth-perl amd64 0.04-12+b1 [9324 B] Get:2 copy:/build/bioperl-run-sInbxY/resolver-kMtw6W/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1164 B] Get:3 file:/srv/reprepro perl-5.44/main amd64 libpq5 amd64 18.4-1+b1 [260 kB] Get:4 file:/srv/reprepro perl-5.44/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b6 [36.4 kB] Get:5 file:/srv/reprepro perl-5.44/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b5 [10.6 kB] Get:6 file:/srv/reprepro perl-5.44/main amd64 libdevel-callchecker-perl amd64 0.009-3+b1 [15.7 kB] Get:7 file:/srv/reprepro perl-5.44/main amd64 libparams-classify-perl amd64 0.015-2+b6 [22.5 kB] Get:8 file:/srv/reprepro perl-5.44/main amd64 libhtml-parser-perl amd64 3.83-2+b1 [99.4 kB] Get:9 file:/srv/reprepro perl-5.44/main amd64 libclone-perl amd64 0.50-1+b1 [21.8 kB] Get:10 file:/srv/reprepro perl-5.44/main amd64 libnet-ssleay-perl amd64 1.96-1+b1 [345 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.42.2-1 [165 kB] Get:12 file:/srv/reprepro perl-5.44/main amd64 libxml-parser-perl amd64 2.47-2+b1 [198 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 261.1-1 [2566 kB] Get:14 file:/srv/reprepro perl-5.44/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-8+b1 [314 kB] Get:15 file:/srv/reprepro perl-5.44/main amd64 libio-pty-perl amd64 1:1.31-1+b1 [38.4 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 systemd amd64 261.1-1 [3333 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.6-1 [896 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.6-1 [2416 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.6-1 [25.1 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.6-1 [2278 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.6-1 [846 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.6-1 [8108 B] Get:27 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.6-1 [25.1 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.4.6+ds-1 [136 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7+b2 [206 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7+b2 [2546 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.4.6+ds-1 [7333 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 isa-support amd64 27+b1 [15.5 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 sse4.2-support amd64 27+b1 [3692 B] Get:35 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b2 [63.8 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9+b2 [880 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.6.3-1 [1522 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20260601 [134 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-1 [332 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-3 [132 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1+b1 [28.6 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-1 [80.6 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:57 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.3p1-5 [1006 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-11 [7788 B] Get:61 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0056 [47.1 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-2 [132 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-1 [820 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-3 [698 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 bedtools-test all 2.31.1+dfsg-3 [10.8 MB] Get:70 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-4 [440 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-4 [2498 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:74 http://deb.debian.org/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.205-1 [52.3 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.50-1 [24.6 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.72-1 [17.7 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.42-1 [23.9 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 bioperl all 1.7.8-4 [231 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.2 [77.1 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:93 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-1 [2660 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.2 [933 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.13.1-2+b1 [1904 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.3-1+b2 [563 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libabsl20260107 amd64 20260107.0-5 [549 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libgav1-2 amd64 0.20.0-2+b1 [372 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 librav1e0.8 amd64 0.8.1-10 [973 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc4 amd64 4.1.0+dfsg-1 [2414 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:3.1.3-4 [213 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1922.20260106-1+b1 [175 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.4.1-1+b1 [147 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.58-1 [289 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.14.3+dfsg-1 [493 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-9 [488 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-9 [840 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1+b2 [115 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.18-1 [187 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.21.2-4 [16.9 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.21.2-4 [19.5 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.21.2-4 [649 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.1-1+b2 [255 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b3 [32.2 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.1.0+ds-1 [199 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1+b2 [335 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.1-3 [361 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.19-1 [58.9 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-13+b2 [126 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1.1+b1 [324 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 mysql-common all 5.8+1.1.1 [6784 B] Get:136 http://deb.debian.org/debian unstable/main amd64 mariadb-common all 1:11.8.8-1 [23.2 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libmariadb3 amd64 1:11.8.8-1 [176 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 emboss-lib amd64 6.6.0+dfsg-18 [2881 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 emboss-data all 6.6.0+dfsg-18 [61.1 MB] Get:140 http://deb.debian.org/debian unstable/main amd64 emboss amd64 6.6.0+dfsg-18 [1065 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.88.2-1 [1536 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-7+b1 [46.1 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 hmmer amd64 3.4+dfsg-3 [1079 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 hyphy-common all 2.5.69+dfsg-2 [612 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-1 [416 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-1 [16.9 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 hyphy-pt amd64 2.5.69+dfsg-2 [1592 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2+b1 [62.2 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2+b1 [200 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 63.0-1.1 [62.9 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 63.0-1.1 [382 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 infernal amd64 1.1.5-3 [5936 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 kalign amd64 1:3.5.1-1+b1 [201 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 lagan amd64 2.0-10 [184 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1.1 [8644 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7+b3 [28.2 MB] Get:165 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7+b3 [768 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Get:167 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-2 [7840 B] Get:168 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-2 [38.5 kB] Get:169 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-2 [23.3 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Get:173 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get:175 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get:176 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:177 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002005-1 [19.5 kB] Get:178 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get:179 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:180 http://deb.debian.org/debian unstable/main amd64 libexporter-tiny-perl all 1.006003-1 [37.5 kB] Get:181 http://deb.debian.org/debian unstable/main amd64 libtype-tiny-perl all 2.010001-1 [391 kB] Get:182 http://deb.debian.org/debian unstable/main amd64 libarray-compare-perl all 3.0.8-1 [14.9 kB] Get:183 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.35-1 [112 kB] Get:184 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:185 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3500-1 [64.2 kB] Get:186 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.07-1 [11.7 kB] Get:187 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:188 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:189 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:190 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:191 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:192 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 7.02-1 [79.5 kB] Get:193 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:194 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:195 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:196 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.098-1 [229 kB] Get:197 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.24-1 [23.2 kB] Get:198 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.15-1 [10.7 kB] Get:199 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:200 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.03-1 [15.8 kB] Get:201 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.83-1 [186 kB] Get:202 http://deb.debian.org/debian unstable/main amd64 libxml-twig-perl all 1:3.54-1 [177 kB] Get:203 http://deb.debian.org/debian unstable/main amd64 libxml-writer-perl all 0.900-2 [26.8 kB] Get:204 http://deb.debian.org/debian unstable/main amd64 libbio-variation-perl all 1.7.5-3 [72.6 kB] Get:205 http://deb.debian.org/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:206 http://deb.debian.org/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:207 http://deb.debian.org/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-5 [53.6 kB] Get:208 http://deb.debian.org/debian unstable/main amd64 libbio-cluster-perl all 1.7.3-6 [53.3 kB] Get:209 http://deb.debian.org/debian unstable/main amd64 libbio-asn1-entrezgene-perl all 1.730-3 [46.3 kB] Get:210 http://deb.debian.org/debian unstable/main amd64 libtext-csv-perl all 2.06-1 [116 kB] Get:211 http://deb.debian.org/debian unstable/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:212 http://deb.debian.org/debian unstable/main amd64 libbio-eutilities-perl all 1.77-3 [119 kB] Get:213 http://deb.debian.org/debian unstable/main amd64 libfile-slurper-perl all 0.014-1 [8560 B] Get:214 http://deb.debian.org/debian unstable/main amd64 libtree-dagnode-perl all 1.35-1 [62.4 kB] Get:215 http://deb.debian.org/debian unstable/main amd64 libxml-perl all 0.08-4 [93.0 kB] Get:216 http://deb.debian.org/debian unstable/main amd64 libxml-regexp-perl all 0.04-2 [6916 B] Get:217 http://deb.debian.org/debian unstable/main amd64 libxml-dom-perl all 1.46-2 [152 kB] Get:218 http://deb.debian.org/debian unstable/main amd64 libxml-xpathengine-perl all 0.14-2 [33.5 kB] Get:219 http://deb.debian.org/debian unstable/main amd64 libxml-dom-xpath-perl all 0.14-4 [9352 B] Get:220 http://deb.debian.org/debian unstable/main amd64 libbio-featureio-perl all 1.6.905-2 [53.2 kB] Get:221 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20260402.0-1 [112 kB] Get:222 http://deb.debian.org/debian unstable/main amd64 libfile-sort-perl all 1.01-4 [21.1 kB] Get:223 http://deb.debian.org/debian unstable/main amd64 libbio-perl-run-perl all 1.7.3-14 [527 kB] Get:224 http://deb.debian.org/debian unstable/main amd64 libbio-tools-run-alignment-clustalw-perl all 1.7.4-4 [24.5 kB] Get:225 http://deb.debian.org/debian unstable/main amd64 libbio-tools-run-remoteblast-perl all 1.7.3-3 [17.5 kB] Get:226 http://deb.debian.org/debian unstable/main amd64 libmodule-pluggable-perl all 6.3-1 [24.1 kB] Get:227 http://deb.debian.org/debian unstable/main amd64 libconfig-any-perl all 0.33-1 [31.0 kB] Get:228 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Get:229 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b2 [54.3 kB] Get:230 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:231 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 63.0-1.1 [71.7 kB] Get:232 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b2 [716 kB] Get:233 http://deb.debian.org/debian unstable/main amd64 libfile-slurp-perl all 9999.32-2.1 [26.5 kB] Get:234 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.2-2 [103 kB] Get:235 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:236 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:237 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Get:238 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:239 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Get:240 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.28.2-2 [795 kB] Get:241 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1+b1 [42.8 kB] Get:242 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.14.0-2 [166 kB] Get:243 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.14.0-2 [21.7 kB] Get:244 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 63.0-1.1 [28.5 kB] Get:245 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 63.0-1.1 [43.1 kB] Get:246 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b3 [46.1 kB] Get:247 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.6-0.1 [365 kB] Get:248 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.6-0.1 [154 kB] Get:249 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.6-0.1 [248 kB] Get:250 http://deb.debian.org/debian unstable/main amd64 libmodule-build-perl all 0.423400-3 [234 kB] Get:251 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Get:252 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:253 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2+b1 [1180 kB] Get:254 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20251231-1+b1 [107 kB] Get:255 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3+b1 [670 kB] Get:256 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.21.0-1 [977 kB] Get:257 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.8.0-2 [345 kB] Get:258 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Get:259 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-3 [451 kB] Get:260 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 3.0.13-3 [51.9 kB] Get:261 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.52.1-4 [158 kB] Get:262 http://deb.debian.org/debian unstable/main amd64 mafft amd64 7.525-1 [1186 kB] Get:263 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Get:264 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Get:265 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.20 [2720 B] Get:266 http://deb.debian.org/debian unstable/main amd64 muscle amd64 1:5.1.0-1 [297 kB] Get:267 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-7 [3540 kB] Get:268 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.17.0+ds-7 [17.0 MB] Get:269 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+-legacy all 2.17.0+ds-7 [10.4 kB] Get:270 http://deb.debian.org/debian unstable/main amd64 ncoils amd64 2002-10 [19.4 kB] Get:271 http://deb.debian.org/debian unstable/main amd64 pal2nal all 14.1-3 [17.8 kB] Get:272 http://deb.debian.org/debian unstable/main amd64 pftools amd64 3.2.12-3 [24.8 MB] Get:273 http://deb.debian.org/debian unstable/main amd64 phyml amd64 3:3.3.20250515-2 [1238 kB] Get:274 http://deb.debian.org/debian unstable/main amd64 primer3 amd64 2.6.1-6 [207 kB] Get:275 http://deb.debian.org/debian unstable/main amd64 probcons amd64 1.12-15 [142 kB] Get:276 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.23.3+ds-2+b1 [4456 kB] Get:277 http://deb.debian.org/debian unstable/main amd64 python3-pybedtools amd64 0.10.0-6 [12.3 MB] Get:278 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.13+dfsg-3+b1 [1545 kB] Get:279 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Get:280 http://deb.debian.org/debian unstable/main amd64 sim4 amd64 0.0.20121010-9 [362 kB] Get:281 http://deb.debian.org/debian unstable/main amd64 tigr-glimmer amd64 3.02b-6+b1 [283 kB] Get:282 http://deb.debian.org/debian unstable/main amd64 wise-data all 2.4.1-28 [76.4 kB] Get:283 http://deb.debian.org/debian unstable/main amd64 wise amd64 2.4.1-28 [1065 kB] Preconfiguring packages ... Fetched 295 MB in 7s (43.7 MB/s) Selecting previously unselected package mount. (Reading database ... 14526 files and directories currently installed.) Preparing to unpack .../mount_2.42.2-1_amd64.deb ... Unpacking mount (2.42.2-1) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_261.1-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (261.1-1) ... Setting up libsystemd-shared:amd64 (261.1-1) ... Selecting previously unselected package systemd. (Reading database ... 14561 files and directories currently installed.) Preparing to unpack .../systemd_261.1-1_amd64.deb ... Unpacking systemd (261.1-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.8.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.2-1) ... Selecting previously unselected package libpython3.14-minimal:amd64. Preparing to unpack .../libpython3.14-minimal_3.14.6-1_amd64.deb ... 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Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../217-libxnvctrl0_535.171.04-1+b3_amd64.deb ... Unpacking libxnvctrl0:amd64 (535.171.04-1+b3) ... Selecting previously unselected package libze1:amd64. Preparing to unpack .../218-libze1_1.28.2-2_amd64.deb ... Unpacking libze1:amd64 (1.28.2-2) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../219-ocl-icd-libopencl1_2.3.4-1+b1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.4-1+b1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../220-libhwloc15_2.14.0-2_amd64.deb ... Unpacking libhwloc15:amd64 (2.14.0-2) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../221-libhwloc-plugins_2.14.0-2_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.14.0-2) ... Selecting previously unselected package libibumad3:amd64. Preparing to unpack .../222-libibumad3_63.0-1.1_amd64.deb ... 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Preparing to unpack .../228-libmodule-build-perl_0.423400-3_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 (0.423400-3) ... Selecting previously unselected package libmunge2:amd64. Preparing to unpack .../229-libmunge2_0.5.18-1_amd64.deb ... Unpacking libmunge2:amd64 (0.5.18-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../230-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:amd64. Preparing to unpack .../231-libncbi-vdb3_3.2.1+dfsg-2+b1_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2+b1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../232-libncurses6_6.6+20251231-1+b1_amd64.deb ... 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Setting up liblmdb0:amd64 (0.9.31-1+b3) ... Setting up ncbi-data (6.1.20170106+dfsg2-7) ... Setting up libtext-charwidth-perl:amd64 (0.04-12+b1) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1+b2) ... Setting up libaom3:amd64 (3.13.1-2+b1) ... Setting up libpciaccess0:amd64 (0.17-3+b4) ... Setting up libfile-slurper-perl (0.014-1) ... 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:amd64 (1:1.0.11-1+b2) ... Setting up libxdmcp6:amd64 (1:1.1.5-2+b1) ... Setting up libkeyutils1:amd64 (1.6.3-6+b2) ... Setting up libfile-slurp-perl (9999.32-2.1) ... Setting up libxcb1:amd64 (1.17.0-2+b2) ... Setting up liblerc4:amd64 (4.1.0+ds-1) ... Setting up bsdextrautils (2.42.2-1) ... Setting up probcons (1.12-15) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libtest-deep-perl (1.205-1) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libxml-regexp-perl (0.04-2) ... Setting up libio-pty-perl (1:1.31-1+b1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libcbor0.10:amd64 (0.10.2-2.1+b1) ... Setting up mafft (7.525-1) ... Setting up libclone-perl:amd64 (0.50-1+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (14.2) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libuv1t64:amd64 (1.52.1-4) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libpsl5t64:amd64 (0.22.0-1) ... Setting up libnghttp2-14:amd64 (1.69.0-1) ... Setting up libibumad3:amd64 (63.0-1.1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (1.0-1) ... Setting up m4 (1.4.21-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up ncoils (2002-10) ... Setting up libibmad5:amd64 (63.0-1.1) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up hyphy-common (2.5.69+dfsg-2) ... Setting up file (1:5.47-4) ... Setting up muscle (1:5.1.0-1) ... Setting up emboss-data (6.6.0+dfsg-18) ... Setting up libtext-wrapi18n-perl (0.06-11) ... Setting up libjbig0:amd64 (2.1-6.1+b3) ... Setting up libze1:amd64 (1.28.2-2) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up libmodule-build-perl (0.423400-3) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up librav1e0.8:amd64 (0.8.1-10) ... Setting up tzdata (2026b-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jun 27 22:57:24 UTC 2026. Universal Time is now: Sat Jun 27 22:57:24 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:11.8.8-1) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up infernal (1.1.5-3) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up primer3 (2.6.1-6) ... Setting up kalign (1:3.5.1-1+b1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libz3-4:amd64 (4.13.3-1.1) ... Setting up libglib2.0-0t64:amd64 (2.88.2-1) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.1-7+b2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libmunge2:amd64 (0.5.18-1) ... Setting up lagan (2.0-10) ... Setting up libjpeg62-turbo:amd64 (1:3.1.3-4) ... Setting up libx11-data (2:1.8.13-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up libxml-xpathengine-perl (0.14-2) ... Setting up sim4 (0.0.20121010-9) ... Setting up libxml-writer-perl (0.900-2) ... Setting up libncurses6:amd64 (6.6+20251231-1+b1) ... Setting up libimagequant0:amd64 (4.4.1-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-9+b2) ... Setting up fonts-dejavu-mono (2.37-9) ... Setting up libpng16-16t64:amd64 (1.6.58-1) ... Setting up libhwloc15:amd64 (2.14.0-2) ... Setting up python3-numpy-dev:amd64 (1:2.4.6+ds-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (1.0-1) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b5) ... Setting up libmariadb3:amd64 (1:11.8.8-1) ... Setting up fonts-dejavu-core (2.37-9) ... Setting up libipc-run-perl (20260402.0-1) ... Setting up wise-data (2.4.1-28) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up amap-align (2.2+git20080214.600fc29+dfsg-2) ... Setting up libsvtav1enc4:amd64 (4.1.0+dfsg-1) ... Setting up libgfortran5:amd64 (16.1.0-2) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libwebp7:amd64 (1.5.0-0.1+b2) ... Setting up libcapture-tiny-perl (0.50-1) ... Setting up libtimedate-perl (2.3500-1) ... Setting up libnuma1:amd64 (2.0.19-1+b2) ... Setting up libtree-dagnode-perl (1.35-1) ... Setting up dwz (0.16-4) ... Setting up libdata-stag-perl (0.14-4) ... Setting up libdav1d7:amd64 (1.5.3-1+b2) ... Setting up mount (2.42.2-1) ... Setting up sensible-utils (0.0.26) ... Setting up ocl-icd-libopencl1:amd64 (2.3.4-1+b1) ... Setting up pftools (3.2.12-3) ... Setting up libtiff6:amd64 (4.7.1-3) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up pal2nal (14.1-3) ... Setting up procps (2:4.0.4-9+b2) ... Setting up sse4.2-support (27+b1) ... Setting up libnl-3-200:amd64 (3.12.0-2+b1) ... Setting up librole-tiny-perl (2.002005-1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.10-1) ... Setting up libconfig-any-perl (0.33-1) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libx11-6:amd64 (2:1.8.13-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up fasttree (2.1.11-2) ... Setting up libabsl20260107:amd64 (20260107.0-5) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libsub-quote-perl (2.006009-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b6) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libbio-perl-perl (1.7.8-4) ... Setting up libmbedcrypto16:amd64 (3.6.6-0.1) ... Setting up libclang-common-21-dev:amd64 (1:21.1.8-7+b3) ... Setting up libssh2-1t64:amd64 (1.11.1-4) ... Setting up libfuse3-4:amd64 (3.18.2-2) ... Setting up libexporter-tiny-perl (1.006003-1) ... Setting up libfido2-1:amd64 (1.17.0-1) ... Setting up libde265-0:amd64 (1.0.18-1) ... Setting up libdivsufsort3:amd64 (2.0.1-7+b1) ... Setting up openssl (3.6.3-1) ... Setting up libbsd0:amd64 (0.12.2-3) ... Setting up tigr-glimmer (3.02b-6+b1) ... Setting up libdrm-common (2.4.134-2) ... Setting up libyuv0:amd64 (0.0.1922.20260106-1+b1) ... Setting up exonerate (2.4.0-5+b1) ... Setting up bedtools (2.31.1+dfsg-3) ... Setting up liburi-perl (5.35-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libfile-sort-perl (1.01-4) ... Setting up raxml (8.2.13+dfsg-3+b1) ... Setting up libtext-csv-perl (2.06-1) ... Setting up libnet-ssleay-perl:amd64 (1.96-1+b1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up libbio-perl-run-perl (1.7.3-14) ... Setting up libhttp-date-perl (6.07-1) ... Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1.1+b1) ... Setting up liblapack3:amd64 (3.12.1-7+b2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (1.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libxpm4:amd64 (1:3.5.19-1) ... Setting up libtool (2.5.4-11) ... Setting up libpython3.14-stdlib:amd64 (3.14.6-1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up fontconfig-config (2.17.1-5) ... Setting up wise (2.4.1-28) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libedit2:amd64 (3.1-20260512-1) ... Setting up libtype-tiny-perl (2.010001-1) ... Setting up libtest-differences-perl (0.72-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up libnet-http-perl (6.24-1) ... Setting up systemd (261.1-1) ... Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Created symlink '/etc/systemd/system/autovt@.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Initializing machine ID from random generator. Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:amd64 (3.12.0-2+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b3) ... Setting up dh-autoreconf (22) ... Setting up libbio-tools-run-alignment-clustalw-perl (1.7.4-4) ... Setting up ca-certificates (20260601) ... Updating certificates in /etc/ssl/certs... 121 added, 0 removed; done. Setting up libmbedx509-7:amd64 (3.6.6-0.1) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libfreetype6:amd64 (2.14.3+dfsg-1) ... Setting up libllvm21:amd64 (1:21.1.8-7+b3) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up ucf (3.0056) ... Setting up libmbedtls21:amd64 (3.6.6-0.1) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up libwww-robotrules-perl (6.03-1) ... Setting up libgav1-2:amd64 (0.20.0-2+b1) ... Setting up libdrm2:amd64 (2.4.134-2) ... Setting up groff-base (1.24.1-1) ... Setting up libamd-comgr3:amd64 (7.0.2+dfsg-3) ... Setting up libhtml-parser-perl:amd64 (3.83-2+b1) ... Setting up hmmer (3.4+dfsg-3) ... Setting up libfontconfig1:amd64 (2.17.1-5) ... Setting up python3.14 (3.14.6-1) ... Setting up libio-socket-ssl-perl (2.098-1) ... Setting up libpython3-stdlib:amd64 (3.14.6-1) ... Setting up libhttp-message-perl (7.02-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.134-2) ... Setting up libcurl4-gnutls:amd64 (8.21.0-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libibverbs1:amd64 (63.0-1.1) ... Creating group 'rdma' with GID 993. Setting up libavif16:amd64 (1.4.1-1+b1) ... Setting up ibverbs-providers:amd64 (63.0-1.1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libtest-most-perl (0.42-1) ... Setting up openssh-client (1:10.3p1-5) ... Created symlink '/etc/systemd/user/sockets.target.wants/ssh-agent.socket' → '/usr/lib/systemd/user/ssh-agent.socket'. Setting up po-debconf (1.0.22) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b6) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2+b1) ... Setting up libpq5:amd64 (18.4-1+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-1) ... Setting up python3 (3.14.6-1) ... Setting up hyphy-pt (2.5.69+dfsg-2) ... Setting up libhwloc-plugins:amd64 (2.14.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libxml-sax-perl (1.02+dfsg-5) ... 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 ncbi-blast+ (2.17.0+ds-7) ... Setting up libmodule-runtime-perl (0.018-1) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.9-3+b1) ... Setting up python3-numpy (1:2.4.6+ds-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-8+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... Setting up libhsa-runtime64-1:amd64 (6.4.3+dfsg-5) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up librdmacm1t64:amd64 (63.0-1.1) ... Setting up bedtools-test (2.31.1+dfsg-3) ... Setting up bioperl (1.7.8-4) ... Setting up ncbi-blast+-legacy (2.17.0+ds-7) ... Setting up libfabric1:amd64 (2.1.0-1.1+b2) ... Setting up python3-pysam (0.23.3+ds-2+b1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up debhelper (14.2) ... Setting up samtools (1.22.1-1) ... Setting up libarray-compare-perl (3.0.8-1) ... Setting up libamdhip64-6:amd64 (6.4.3-5) ... Setting up libprrte3:amd64 (3.0.13-3) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libprrte-bin (3.0.13-3) ... Setting up libucx0:amd64 (1.21.0-1) ... Setting up python3-pybedtools (0.10.0-6) ... Setting up libucc1:amd64 (1.8.0-2) ... Setting up libopenmpi40:amd64 (5.0.10-1) ... Setting up openmpi-bin (5.0.10-1) ... 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) does not exist update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.20) ... Setting up phyml (3:3.3.20250515-2) ... Setting up libheif-plugin-dav1d:amd64 (1.21.2-4) ... Setting up liblwp-protocol-https-perl (6.15-1) ... Setting up libwww-perl (6.83-1) ... Setting up libheif1:amd64 (1.21.2-4) ... Setting up libgd3:amd64 (2.3.3-13+b2) ... Setting up libbio-tools-run-remoteblast-perl (1.7.3-3) ... Setting up emboss-lib (6.6.0+dfsg-18) ... Setting up libheif-plugin-libde265:amd64 (1.21.2-4) ... Setting up libxml-parser-perl (2.47-2+b1) ... Setting up emboss (6.6.0+dfsg-18) ... Setting up libxml-twig-perl (1:3.54-1) ... 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 (1.77-3) ... Setting up libbio-featureio-perl (1.6.905-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... Processing triggers for ca-certificates (20260601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures Sat, 27 Jun 2026 22:57:38 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Sat, 27 Jun 2026 22:57:39 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.0.13-1 Package versions: amap-align_2.2+git20080214.600fc29+dfsg-2 apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-1 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 bedtools_2.31.1+dfsg-3 bedtools-test_2.31.1+dfsg-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bioperl_1.7.8-4 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 ca-certificates_20260601 clustalw_2.1+lgpl-7 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.2 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 emboss_6.6.0+dfsg-18 emboss-data_6.6.0+dfsg-18 emboss-lib_6.6.0+dfsg-18 exonerate_2.4.0-5+b1 fasttree_2.1.11-2 file_1:5.47-4 findutils_4.10.0-4 fontconfig-config_2.17.1-5 fonts-dejavu-core_2.37-9 fonts-dejavu-mono_2.37-9 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-1 gettext-base_1.0-1 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hmmer_3.4+dfsg-3 hostname_3.25 hyphy-common_2.5.69+dfsg-2 hyphy-pt_2.5.69+dfsg-2 ibverbs-providers_63.0-1.1 infernal_1.1.5-3 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 isa-support_27+b1 kalign_1:3.5.1-1+b1 lagan_2.0-10 libabsl20260107_20260107.0-5 libacl1_2.3.2-3 libalgorithm-diff-perl_1.201-1 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libaom3_3.13.1-2+b1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libarray-compare-perl_3.0.8-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libavif16_1.4.1-1+b1 libb-hooks-op-check-perl_0.22-3+b5 libbinutils_2.46.50.20260617-1 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libdb5.3t64_5.3.28+dfsg2-11+b1 libde265-0_1.0.18-1 libdebconfclient0_0.283 libdebhelper-perl_14.2 libdeflate0_1.25-1 libdevel-callchecker-perl_0.009-3+b1 libdevel-stacktrace-perl_2.0500-1 libdivsufsort3_2.0.1-7+b1 libdpkg-perl_1.23.7 libdrm-amdgpu1_2.4.134-2 libdrm-common_2.4.134-2 libdrm2_2.4.134-2 libdynaloader-functions-perl_0.004-2 libeatmydata1_131-2+b2 libedit2_3.1-20260512-1 libelf1t64_0.195-1 libencode-locale-perl_1.05-3 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libexception-class-perl_1.45-1 libexpat1_2.8.2-1 libexporter-tiny-perl_1.006003-1 libfabric1_2.1.0-1.1+b2 libffi8_3.5.2-4 libfido2-1_1.17.0-1 libfile-listing-perl_6.16-1 libfile-slurp-perl_9999.32-2.1 libfile-slurper-perl_0.014-1 libfile-sort-perl_1.01-4 libfile-stripnondeterminism-perl_1.15.1-1 libfontconfig1_2.17.1-5 libfreetype6_2.14.3+dfsg-1 libfuse3-4_3.18.2-2 libgav1-2_0.20.0-2+b1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgd3_2.3.3-13+b2 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sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tigr-glimmer_3.02b-6+b1 tzdata_2026b-1 ucf_3.0056 util-linux_2.42.2-1 wise_2.4.1-28 wise-data_2.4.1-28 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sat, 27 Jun 2026 22:57:39 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bioperl-run Binary: bioperl-run, libbio-perl-run-perl Architecture: all Version: 1.7.3-14 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://metacpan.org/release/BioPerl-Run Standards-Version: 4.7.3 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 5741908702debfb2b787916a18159a5ceeddec2d 20384 bioperl-run_1.7.3-14.debian.tar.xz Checksums-Sha256: 04f11b3a931f625bf80770c3aec1b57658b41cde54573132b58b6179adda7c65 4872163 bioperl-run_1.7.3.orig.tar.gz 5176f6e8d38e77234ba1dd09ca5979dd76b7c08cef3407f7a4f856217a534c89 20384 bioperl-run_1.7.3-14.debian.tar.xz Files: e582f2dc591b947348670ce1479da109 4872163 bioperl-run_1.7.3.orig.tar.gz fb6ed77cf4d5a9e91e5b82cc8e55793a 20384 bioperl-run_1.7.3-14.debian.tar.xz Dgit: 54fbfe4d4e1298b636cc301ceb4c0594734efbc3 debian archive/debian/1.7.3-14 https://git.dgit.debian.org/bioperl-run -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmmvMvgUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpEFBAAqRySyXcODVpreWpgcm4RTTyEr8pd e97JMkiCAE3qqimCP3+GLjcNRGPWfh6NzYVNJuuSgQNyr1fTWNK2I60I/3VxMKIz iVsJ988NDsfmcpMIndr7c1PeZEXYns1+9ANkFR8N3lPRl7iSxGhxQNVUzzSiT5Hb 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info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting bioperl-run in /build/bioperl-run-sInbxY/bioperl-run-1.7.3 dpkg-source: info: unpacking bioperl-run_1.7.3.orig.tar.gz dpkg-source: info: unpacking bioperl-run_1.7.3-14.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 dpkg-source: info: applying update-kalign-invocation.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sat, 27 Jun 2026 22:57:40 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bioperl-run_1.7.3-14 perl-5.44-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bioperl-run_1.7.3-14 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/bioperl-run-sInbxY/bioperl-run-1.7.3 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-af122c90-5134-4ed7-a0ca-179f79731d16 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bioperl-run using existing ../bioperl-run_1.7.3.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bioperl-run in ../bioperl-run_1.7.3-14.debian.tar.xz dpkg-source: info: building bioperl-run in ../bioperl-run_1.7.3-14.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bioperl-run-sInbxY/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/bioperl-run-sInbxY/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config ld="x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bioperl-run-sInbxY/bioperl-run-1.7.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" --install_scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n ]n Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' make[1]: Leaving directory '/build/bioperl-run-sInbxY/bioperl-run-1.7.3' dh_auto_build /usr/bin/perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/bioperl-run-sInbxY/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/oZH6mVXUJl Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG t/Amap.t ...................... 1..18 ok 1 - use Bio::Tools::Run::Alignment::Amap; ok 2 - use Bio::SeqIO; ok 3 - use File::Spec; ok 4 - Found input file ok 5 - An object of class 'Bio::Tools::Run::Alignment::Amap' isa 'Bio::Tools::Run::Alignment::Amap' ok 6 - program_dir returned correct default ok 7 - error_string returned correct default ok 8 - aformat returned correct default ok 9 - outfile_name returned correct default ok 10 - Correct exe default name ok 11 - Correct minimum program version ok 12 - No error occured ok 13 - outfile_name returned something ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 15 - Correct number of seqs returned ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 17 - Correct number of seqs returned ok 18 - Got the correct ave % identity ok t/BEDTools.t .................. 1..423 ok 1 - make a default factory ok 2 - default to command 'bam_to_bed' ok 3 - make a factory using command 'annotate' ok 4 - factory command for 'annotate' is correct ok 5 - all available options for 'annotate' ok 6 - available parameters for 'annotate' ok 7 - available switches for 'annotate' ok 8 - get version for 'annotate' ok 9 - can run command 'annotate' ok 10 - result files exists for command 'annotate' ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' ok 14 - file format of '/tmp/AaiPk3UCXK/z_aR5jdreQ.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' ok 18 - can get the specific object result for command 'annotate' ok 19 - 'returned object is correct for command 'annotate'' isa 'Bio::SeqFeature::Collection' ok 20 - correct number of features for command 'annotate' # TODO maybe adapt reference results to Debian specific dataset ok 21 - make a factory using command 'fasta_from_bed' ok 22 - factory command for 'fasta_from_bed' is correct ok 23 - all available options for 'fasta_from_bed' ok 24 - available parameters for 'fasta_from_bed' ok 25 - available switches for 'fasta_from_bed' ok 26 - get version for 'fasta_from_bed' ok 27 - can run command 'fasta_from_bed' ok 28 - result files exists for command 'fasta_from_bed' ok 29 - can return output format for command 'fasta_from_bed' ok 30 - result claims to be in correct format for command 'fasta_from_bed' ok 31 - can return output file for command 'fasta_from_bed' ok 32 - file format consistent with claim for 'fasta_from_bed' ok 33 - can set want to IO object for command 'fasta_from_bed' ok 34 - can get the basic object result for command 'fasta_from_bed' ok 35 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::Root::IO' ok 36 - can get the specific object result for command 'fasta_from_bed' ok 37 - 'returned object is correct for command 'fasta_from_bed'' isa 'Bio::SeqIO' ok 38 - correct number of sequences for command 'fasta_from_bed' ok 39 - make a factory using command 'overlap' ok 40 - factory command for 'overlap' is correct ok 41 - all available options for 'overlap' ok 42 - available parameters for 'overlap' ok 43 - available switches for 'overlap' ok 44 - get version for 'overlap' ok 45 - can set parameter -columns => '2,3,5,6' ok 46 - can run command 'overlap' ok 47 - result files exists for command 'overlap' ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' ok 51 - file format of '/tmp/kRmSeg4i4a/92dMyiTWWX.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' ok 55 - can get the specific object result for command 'overlap' ok 56 - 'returned object is correct for command 'overlap'' isa 'Bio::SeqFeature::Collection' ok 57 - correct number of features for command 'overlap' # TODO maybe adapt reference results to Debian specific dataset ok 58 - make a factory using command 'bam_to_bed' ok 59 - factory command for 'bam_to_bed' is correct ok 60 - all available options for 'bam_to_bed' ok 61 - available parameters for 'bam_to_bed' ok 62 - available switches for 'bam_to_bed' ok 63 - get version for 'bam_to_bed' ok 64 - can run command 'bam_to_bed' ok 65 - result files exists for command 'bam_to_bed' ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' ok 69 - file format of '/tmp/OmZo_BcOJl/NRY9X_8sjr.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' ok 73 - can get the specific object result for command 'bam_to_bed' ok 74 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::SeqFeature::Collection' ok 75 - correct number of features for command 'bam_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 76 - make a factory using command 'genome_coverage' ok 77 - factory command for 'genome_coverage' is correct ok 78 - all available options for 'genome_coverage' ok 79 - available parameters for 'genome_coverage' ok 80 - available switches for 'genome_coverage' ok 81 - get version for 'genome_coverage' ok 82 - can run command 'genome_coverage' ok 83 - result files exists for command 'genome_coverage' ok 84 - can return output format for command 'genome_coverage' ok 85 - result claims to be in correct format for command 'genome_coverage' ok 86 - can return output file for command 'genome_coverage' ok 87 - make readable output ok 88 - - number of lines # TODO maybe adapt reference results to Debian specific dataset ok 89 - can set want to IO object for command 'genome_coverage' ok 90 - can get the basic object result for command 'genome_coverage' ok 91 - 'returned object is correct for command 'genome_coverage'' isa 'Bio::Root::IO' ok 92 - make a factory using command 'pair_to_pair' ok 93 - factory command for 'pair_to_pair' is correct ok 94 - all available options for 'pair_to_pair' ok 95 - available parameters for 'pair_to_pair' ok 96 - available switches for 'pair_to_pair' ok 97 - get version for 'pair_to_pair' ok 98 - can set parameter -type => 'neither' ok 99 - can run command 'pair_to_pair' ok 100 - result files exists for command 'pair_to_pair' ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' ok 104 - file format of '/tmp/AlHNnskyUk/EZMF98z7Xc.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' ok 108 - can get the specific object result for command 'pair_to_pair' ok 109 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::SeqFeature::Collection' ok 110 - correct number of features for command 'pair_to_pair' # TODO maybe adapt reference results to Debian specific dataset ok 111 - make a factory using command 'bed_to_bam' ok 112 - factory command for 'bed_to_bam' is correct ok 113 - all available options for 'bed_to_bam' ok 114 - available parameters for 'bed_to_bam' ok 115 - available switches for 'bed_to_bam' ok 116 - get version for 'bed_to_bam' ok 117 - can run command 'bed_to_bam' ok 118 - result files exists for command 'bed_to_bam' ok 119 - can return output format for command 'bed_to_bam' ok 120 - result claims to be in correct format for command 'bed_to_bam' ok 121 - can return output file for command 'bed_to_bam' ok 122 - can set want to IO object for command 'bed_to_bam' ok 123 - can get the basic object result for command 'bed_to_bam' ok 124 - 'returned object is correct for command 'bed_to_bam'' isa 'Bio::Root::IO' ok 125 - make a factory using command 'graph_union' ok 126 - factory command for 'graph_union' is correct ok 127 - all available options for 'graph_union' ok 128 - available parameters for 'graph_union' ok 129 - available switches for 'graph_union' ok 130 - get version for 'graph_union' ok 131 - can run command 'graph_union' ok 132 - result files exists for command 'graph_union' ok 133 - can return output format for command 'graph_union' ok 134 - result claims to be in correct format for command 'graph_union' ok 135 - can return output file for command 'graph_union' ok 136 - can set want to IO object for command 'graph_union' ok 137 - can get the basic object result for command 'graph_union' ok 138 - 'returned object is correct for command 'graph_union'' isa 'Bio::Root::IO' ok 139 - make a factory using command 'pair_to_bed' ok 140 - factory command for 'pair_to_bed' is correct ok 141 - all available options for 'pair_to_bed' ok 142 - available parameters for 'pair_to_bed' ok 143 - available switches for 'pair_to_bed' ok 144 - get version for 'pair_to_bed' ok 145 - can run command 'pair_to_bed' ok 146 - result files exists for command 'pair_to_bed' ok 147 - can return output format for command 'pair_to_bed' ok 148 - result claims to be in correct format for command 'pair_to_bed' ok 149 - can return output file for command 'pair_to_bed' ok 150 - can set want to IO object for command 'pair_to_bed' ok 151 - can get the basic object result for command 'pair_to_bed' ok 152 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::Root::IO' ok 153 - can get the specific object result for command 'pair_to_bed' ok 154 - 'returned object is correct for command 'pair_to_bed'' isa 'Bio::SeqFeature::Collection' ok 155 - correct number of features for command 'pair_to_bed' # TODO maybe adapt reference results to Debian specific dataset ok 156 - make a factory using command 'bed_to_IGV' ok 157 - factory command for 'bed_to_IGV' is correct ok 158 - all available options for 'bed_to_IGV' ok 159 - available parameters for 'bed_to_IGV' ok 160 - available switches for 'bed_to_IGV' ok 161 - get version for 'bed_to_IGV' ok 162 - can run command 'bed_to_IGV' ok 163 - result files exists for command 'bed_to_IGV' ok 164 - can return output format for command 'bed_to_IGV' ok 165 - result claims to be in correct format for command 'bed_to_IGV' ok 166 - can return output file for command 'bed_to_IGV' ok 167 - can set want to IO object for command 'bed_to_IGV' ok 168 - can get the basic object result for command 'bed_to_IGV' ok 169 - 'returned object is correct for command 'bed_to_IGV'' isa 'Bio::Root::IO' ok 170 - make a factory using command 'group_by' ok 171 - factory command for 'group_by' is correct ok 172 - all available options for 'group_by' ok 173 - available parameters for 'group_by' ok 174 - available switches for 'group_by' ok 175 - get version for 'group_by' ok 176 - can set parameter -group => 1 ok 177 - can set parameter -columns => '2,2,3,3' ok 178 - can set parameter -operations => 'min,max,min,max' ok 179 - can run command 'group_by' ok 180 - result files exists for command 'group_by' ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' ok 184 - file format of '/tmp/JcQ1rLs1OP/uejeAVMqCI.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' ok 188 - can get the specific object result for command 'group_by' ok 189 - 'returned object is correct for command 'group_by'' isa 'Bio::SeqFeature::Collection' ok 190 - correct number of features for command 'group_by' # TODO maybe adapt reference results to Debian specific dataset ok 191 - make a factory using command 'shuffle' ok 192 - factory command for 'shuffle' is correct ok 193 - all available options for 'shuffle' ok 194 - available parameters for 'shuffle' ok 195 - available switches for 'shuffle' ok 196 - get version for 'shuffle' ok 197 - can run command 'shuffle' ok 198 - result files exists for command 'shuffle' ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' ok 202 - file format of '/tmp/oFum8RkhkW/ECysmi3Iq7.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' ok 206 - can get the specific object result for command 'shuffle' ok 207 - 'returned object is correct for command 'shuffle'' isa 'Bio::SeqFeature::Collection' ok 208 - correct number of features for command 'shuffle' # TODO maybe adapt reference results to Debian specific dataset ok 209 - make a factory using command 'b12_to_b6' ok 210 - factory command for 'b12_to_b6' is correct ok 211 - all available options for 'b12_to_b6' ok 212 - available parameters for 'b12_to_b6' ok 213 - available switches for 'b12_to_b6' ok 214 - get version for 'b12_to_b6' ok 215 - can run command 'b12_to_b6' ok 216 - result files exists for command 'b12_to_b6' ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' ok 220 - file format of '/tmp/vOU6g7VLzH/EPz86QY_0a.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' ok 224 - can get the specific object result for command 'b12_to_b6' ok 225 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::SeqFeature::Collection' ok 226 - correct number of features for command 'b12_to_b6' # TODO maybe adapt reference results to Debian specific dataset ok 227 - make a factory using command 'intersect' ok 228 - factory command for 'intersect' is correct ok 229 - all available options for 'intersect' ok 230 - available parameters for 'intersect' ok 231 - available switches for 'intersect' ok 232 - get version for 'intersect' ok 233 - can run command 'intersect' ok 234 - result files exists for command 'intersect' ok 235 - can return output format for command 'intersect' ok 236 - result claims to be in correct format for command 'intersect' ok 237 - can return output file for command 'intersect' ok 238 - can set want to IO object for command 'intersect' ok 239 - can get the basic object result for command 'intersect' ok 240 - 'returned object is correct for command 'intersect'' isa 'Bio::Root::IO' ok 241 - can get the specific object result for command 'intersect' ok 242 - 'returned object is correct for command 'intersect'' isa 'Bio::SeqFeature::Collection' not ok 243 - correct number of features for command 'intersect' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'intersect'' # at t/BEDTools.t line 364. # got: '1305' # expected: '72534' ok 244 - make a factory using command 'slop' ok 245 - factory command for 'slop' is correct ok 246 - all available options for 'slop' ok 247 - available parameters for 'slop' ok 248 - available switches for 'slop' ok 249 - get version for 'slop' ok 250 - can set parameter -add_bidirectional => 100 ok 251 - can run command 'slop' ok 252 - result files exists for command 'slop' ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' ok 256 - file format of '/tmp/ANRzDEIIyD/hXjEZTTLGH.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' ok 260 - can get the specific object result for command 'slop' ok 261 - 'returned object is correct for command 'slop'' isa 'Bio::SeqFeature::Collection' ok 262 - correct number of features for command 'slop' # TODO maybe adapt reference results to Debian specific dataset ok 263 - make a factory using command 'closest' ok 264 - factory command for 'closest' is correct ok 265 - all available options for 'closest' ok 266 - available parameters for 'closest' ok 267 - available switches for 'closest' ok 268 - get version for 'closest' ok 269 - can run command 'closest' ok 270 - result files exists for command 'closest' ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' ok 274 - file format of '/tmp/uFhlkQm9hO/gmXjhhPcgE.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' ok 278 - can get the specific object result for command 'closest' ok 279 - 'returned object is correct for command 'closest'' isa 'Bio::SeqFeature::Collection' ok 280 - correct number of features for command 'closest' # TODO maybe adapt reference results to Debian specific dataset ok 281 - make a factory using command 'links' ok 282 - factory command for 'links' is correct ok 283 - all available options for 'links' ok 284 - available parameters for 'links' ok 285 - available switches for 'links' ok 286 - get version for 'links' ok 287 - can run command 'links' ok 288 - result files exists for command 'links' ok 289 - can return output format for command 'links' ok 290 - result claims to be in correct format for command 'links' ok 291 - can return output file for command 'links' ok 292 - make readable output ok 293 - - html tag line ok 294 - - number of lines ok 295 - can set want to IO object for command 'links' ok 296 - can get the basic object result for command 'links' ok 297 - 'returned object is correct for command 'links'' isa 'Bio::Root::IO' ok 298 - make a factory using command 'sort' ok 299 - factory command for 'sort' is correct ok 300 - all available options for 'sort' ok 301 - available parameters for 'sort' ok 302 - available switches for 'sort' ok 303 - get version for 'sort' ok 304 - can run command 'sort' ok 305 - result files exists for command 'sort' ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' ok 309 - file format of '/tmp/uyt3t4_OqW/My0mUA2z1o.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' ok 313 - can get the specific object result for command 'sort' ok 314 - 'returned object is correct for command 'sort'' isa 'Bio::SeqFeature::Collection' ok 315 - correct number of features for command 'sort' # TODO maybe adapt reference results to Debian specific dataset ok 316 - make a factory using command 'complement' ok 317 - factory command for 'complement' is correct ok 318 - all available options for 'complement' ok 319 - available parameters for 'complement' ok 320 - available switches for 'complement' ok 321 - get version for 'complement' ok 322 - can run command 'complement' ok 323 - result files exists for command 'complement' ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' ok 327 - file format of '/tmp/IVGA5RfNhP/1BzzNduteO.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' ok 331 - can get the specific object result for command 'complement' ok 332 - 'returned object is correct for command 'complement'' isa 'Bio::SeqFeature::Collection' ok 333 - correct number of features for command 'complement' # TODO maybe adapt reference results to Debian specific dataset ok 334 - make a factory using command 'mask_fasta_from_bed' ok 335 - factory command for 'mask_fasta_from_bed' is correct ok 336 - all available options for 'mask_fasta_from_bed' ok 337 - available parameters for 'mask_fasta_from_bed' ok 338 - available switches for 'mask_fasta_from_bed' ok 339 - get version for 'mask_fasta_from_bed' ok 340 - can run command 'mask_fasta_from_bed' ok 341 - result files exists for command 'mask_fasta_from_bed' ok 342 - can return output format for command 'mask_fasta_from_bed' ok 343 - result claims to be in correct format for command 'mask_fasta_from_bed' ok 344 - can return output file for command 'mask_fasta_from_bed' ok 345 - file format consistent with claim for 'mask_fasta_from_bed' ok 346 - can set want to IO object for command 'mask_fasta_from_bed' ok 347 - can get the basic object result for command 'mask_fasta_from_bed' ok 348 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::Root::IO' ok 349 - can get the specific object result for command 'mask_fasta_from_bed' ok 350 - 'returned object is correct for command 'mask_fasta_from_bed'' isa 'Bio::SeqIO' ok 351 - correct number of sequences for command 'mask_fasta_from_bed' ok 352 - make a factory using command 'subtract' ok 353 - factory command for 'subtract' is correct ok 354 - all available options for 'subtract' ok 355 - available parameters for 'subtract' ok 356 - available switches for 'subtract' ok 357 - get version for 'subtract' ok 358 - can run command 'subtract' ok 359 - result files exists for command 'subtract' ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' ok 363 - file format of '/tmp/gDggDVH47e/FRkJH_Qfuu.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' ok 367 - can get the specific object result for command 'subtract' ok 368 - 'returned object is correct for command 'subtract'' isa 'Bio::SeqFeature::Collection' not ok 369 - correct number of features for command 'subtract' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'subtract'' # at t/BEDTools.t line 364. # got: '1802' # expected: '57959' ok 370 - make a factory using command 'coverage' ok 371 - factory command for 'coverage' is correct ok 372 - all available options for 'coverage' ok 373 - available parameters for 'coverage' ok 374 - available switches for 'coverage' ok 375 - get version for 'coverage' ok 376 - can run command 'coverage' ok 377 - result files exists for command 'coverage' ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' ok 381 - file format of '/tmp/4jHzkax6Wa/VO0465Xs9A.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' ok 385 - can get the specific object result for command 'coverage' ok 386 - 'returned object is correct for command 'coverage'' isa 'Bio::SeqFeature::Collection' not ok 387 - correct number of features for command 'coverage' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'coverage'' # at t/BEDTools.t line 364. # got: '828' # expected: '57261' ok 388 - make a factory using command 'merge' ok 389 - factory command for 'merge' is correct ok 390 - all available options for 'merge' ok 391 - available parameters for 'merge' ok 392 - available switches for 'merge' ok 393 - get version for 'merge' ok 394 - can run command 'merge' ok 395 - result files exists for command 'merge' ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' ok 399 - file format of '/tmp/gMFRocL7tL/N7M6TcSp0E.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' ok 403 - can get the specific object result for command 'merge' ok 404 - 'returned object is correct for command 'merge'' isa 'Bio::SeqFeature::Collection' ok 405 - correct number of features for command 'merge' # TODO maybe adapt reference results to Debian specific dataset ok 406 - make a factory using command 'window' ok 407 - factory command for 'window' is correct ok 408 - all available options for 'window' ok 409 - available parameters for 'window' ok 410 - available switches for 'window' ok 411 - get version for 'window' ok 412 - can run command 'window' ok 413 - result files exists for command 'window' ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' ok 417 - file format of '/tmp/GgZ5JmJpdT/7OZ1XjZTQr.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' ok 421 - can get the specific object result for command 'window' ok 422 - 'returned object is correct for command 'window'' isa 'Bio::SeqFeature::Collection' not ok 423 - correct number of features for command 'window' # TODO maybe adapt reference results to Debian specific dataset # Failed (TODO) test 'correct number of features for command 'window'' # at t/BEDTools.t line 364. # got: '1331' # expected: '74998' ok # You named your test '71'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '91'. You shouldn't use numbers for your test names. # Very confusing. t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 ok 4 ok 5 - 71 ok 6 - 91 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present ok Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 7%] 4000 Cells done [ 9%] 5000 Cells done [12%] 6000 Cells done [14%] 7000 Cells done [17%] 8000 Cells done [19%] 9000 Cells done [21%] 10000 Cells done [24%] 11000 Cells done [26%] 12000 Cells done [29%] 13000 Cells done [31%] 14000 Cells done [34%] 15000 Cells done [36%] 16000 Cells done [38%] 17000 Cells done [41%] 18000 Cells done [43%] 19000 Cells done [46%] 20000 Cells done [48%] 21000 Cells done [51%] 22000 Cells done [53%] 23000 Cells done [55%] 24000 Cells done [58%] 25000 Cells done [60%] 26000 Cells done [63%] 27000 Cells done [65%] 28000 Cells done [68%] 29000 Cells done [70%] 30000 Cells done [72%] 31000 Cells done [75%] 32000 Cells done [77%] 33000 Cells done [80%] 34000 Cells done [82%] 35000 Cells done [85%] 36000 Cells done [87%] 37000 Cells done [89%] 38000 Cells done [92%] 39000 Cells done [94%] 40000 Cells done [97%] 41000 Cells done [99%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode Find start end points: 1000 Cells done [ 2%] 2000 Cells done [ 4%] 3000 Cells done [ 6%] 4000 Cells done [ 8%] 5000 Cells done [10%] 6000 Cells done [12%] 7000 Cells done [14%] 8000 Cells done [17%] 9000 Cells done [19%] 10000 Cells done [21%] 11000 Cells done [23%] 12000 Cells done [25%] 13000 Cells done [27%] 14000 Cells done [29%] 15000 Cells done [32%] 16000 Cells done [34%] 17000 Cells done [36%] 18000 Cells done [38%] 19000 Cells done [40%] 20000 Cells done [42%] 21000 Cells done [44%] 22000 Cells done [46%] 23000 Cells done [49%] 24000 Cells done [51%] 25000 Cells done [53%] 26000 Cells done [55%] 27000 Cells done [57%] 28000 Cells done [59%] 29000 Cells done [61%] 30000 Cells done [64%] 31000 Cells done [66%] 32000 Cells done [68%] 33000 Cells done [70%] 34000 Cells done [72%] 35000 Cells done [74%] 36000 Cells done [76%] 37000 Cells done [79%] 38000 Cells done [81%] 39000 Cells done [83%] 40000 Cells done [85%] 41000 Cells done [87%] 42000 Cells done [89%] 43000 Cells done [91%] 44000 Cells done [93%] 45000 Cells done [96%] 46000 Cells done [98%][0,0][0,0] Score 0 Recovering alignment: [0,0][0,0] Explicit read offWarning Error Major problem (!) - in DnaMatchBlock read off, position 0,0 state 0 no source found! Warning Error In DnaMatchBlock hidden read off, between 0:0,0:0 - at got bad read off. Problem! Warning Error In full dc, at 0:0,0:0 got a bad hidden explicit read off... Warning Error Major problem (!) - in DnaMatchBlock matrix to special read off, position 0,0 state 0 no source found! Warning Error Problem in reading off special state system, hit a non start state (or an internal error) in a single alignment mode t/DBA.t ....................... 1..5 ok 1 - use Bio::Tools::Run::Alignment::DBA; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::DBA' isa 'Bio::Tools::Run::Alignment::DBA' ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present ok -- namet is "-sequence" associated seqall qualifiers -- namet is "-outfile" associated outfile qualifiers t/EMBOSS.t .................... 1..31 ok 1 - use Bio::Root::IO; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - use Bio::Factory::EMBOSS; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok t/Exonerate.t ................. 1..89 ok 1 - use Bio::Tools::Run::Alignment::Exonerate; ok 2 - An object of class 'Bio::Tools::Run::Alignment::Exonerate' isa 'Bio::Tools::Run::Alignment::Exonerate' ok 3 ok 4 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - An object of class 'Bio::SearchIO::exonerate' isa 'Bio::SearchIO' ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok t/FastTree.t .................. 1..9 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::FastTree; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - Tree is defined ok 6 - Number of nodes is correct ok 7 - Tree is defined ok 8 - Tree is defined ok 9 - Tree is defined ok # Required executable for Bio::Tools::Run::FootPrinter is not present t/FootPrinter.t ............... 1..24 ok 1 - use Bio::Tools::Run::FootPrinter; ok 2 - use Bio::SeqIO; ok 3 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 4 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 5 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 6 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 7 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 8 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 9 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 10 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 11 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 12 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 13 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 14 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 15 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 16 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 17 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 18 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 19 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 20 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 21 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 22 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 23 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok 24 # skip Required executable for Bio::Tools::Run::FootPrinter is not present ok # Required environment variable $GENEMARK_MODELS is not set t/Genemark.hmm.prokaryotic.t .. 1..99 ok 1 - use Bio::Tools::Run::Genemark; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 # skip Required environment variable $GENEMARK_MODELS is not set ok 5 # skip Required environment variable $GENEMARK_MODELS is not set ok 6 # skip Required environment variable $GENEMARK_MODELS is not set ok 7 # skip Required environment variable $GENEMARK_MODELS is not set ok 8 # skip Required environment variable $GENEMARK_MODELS is not set ok 9 # skip Required environment variable $GENEMARK_MODELS is not set ok 10 # skip Required environment variable $GENEMARK_MODELS is not set ok 11 # skip Required environment variable $GENEMARK_MODELS is not set ok 12 # skip Required environment variable $GENEMARK_MODELS is not set ok 13 # skip Required environment variable $GENEMARK_MODELS is not set ok 14 # skip Required environment variable $GENEMARK_MODELS is not set ok 15 # skip Required environment variable $GENEMARK_MODELS is not set ok 16 # skip Required environment variable $GENEMARK_MODELS is not set ok 17 # skip Required environment variable $GENEMARK_MODELS is not set ok 18 # skip Required environment variable $GENEMARK_MODELS is not set ok 19 # skip Required environment variable $GENEMARK_MODELS is not set ok 20 # skip Required environment variable $GENEMARK_MODELS is not set ok 21 # skip Required environment variable $GENEMARK_MODELS is not set ok 22 # skip Required environment variable $GENEMARK_MODELS is not set ok 23 # skip Required environment variable $GENEMARK_MODELS is not set ok 24 # skip Required environment variable $GENEMARK_MODELS is not set ok 25 # skip Required environment variable $GENEMARK_MODELS is not set ok 26 # skip Required environment variable $GENEMARK_MODELS is not set ok 27 # skip Required environment variable $GENEMARK_MODELS is not set ok 28 # skip Required environment variable $GENEMARK_MODELS is not set ok 29 # skip Required environment variable $GENEMARK_MODELS is not set ok 30 # skip Required environment variable $GENEMARK_MODELS is not set ok 31 # skip Required environment variable $GENEMARK_MODELS is not set ok 32 # skip Required environment variable $GENEMARK_MODELS is not set ok 33 # skip Required environment variable $GENEMARK_MODELS is not set ok 34 # skip Required environment variable $GENEMARK_MODELS is not set ok 35 # skip Required environment variable $GENEMARK_MODELS is not set ok 36 # skip Required environment variable $GENEMARK_MODELS is not set ok 37 # skip Required environment variable $GENEMARK_MODELS is not set ok 38 # skip Required environment variable $GENEMARK_MODELS is not set ok 39 # skip Required environment variable $GENEMARK_MODELS is not set ok 40 # skip Required environment variable $GENEMARK_MODELS is not set ok 41 # skip Required environment variable $GENEMARK_MODELS is not set ok 42 # skip Required environment variable $GENEMARK_MODELS is not set ok 43 # skip Required environment variable $GENEMARK_MODELS is not set ok 44 # skip Required environment variable $GENEMARK_MODELS is not set ok 45 # skip Required environment variable $GENEMARK_MODELS is not set ok 46 # skip Required environment variable $GENEMARK_MODELS is not set ok 47 # skip Required environment variable $GENEMARK_MODELS is not set ok 48 # skip Required environment variable $GENEMARK_MODELS is not set ok 49 # skip Required environment variable $GENEMARK_MODELS is not set ok 50 # skip Required environment variable $GENEMARK_MODELS is not set ok 51 # skip Required environment variable $GENEMARK_MODELS is not set ok 52 # skip Required environment variable $GENEMARK_MODELS is not set ok 53 # skip Required environment variable $GENEMARK_MODELS is not set ok 54 # skip Required environment variable $GENEMARK_MODELS is not set ok 55 # skip Required environment variable $GENEMARK_MODELS is not set ok 56 # skip Required environment variable $GENEMARK_MODELS is not set ok 57 # skip Required environment variable $GENEMARK_MODELS is not set ok 58 # skip Required environment variable $GENEMARK_MODELS is not set ok 59 # skip Required environment variable $GENEMARK_MODELS is not set ok 60 # skip Required environment variable $GENEMARK_MODELS is not set ok 61 # skip Required environment variable $GENEMARK_MODELS is not set ok 62 # skip Required environment variable $GENEMARK_MODELS is not set ok 63 # skip Required environment variable $GENEMARK_MODELS is not set ok 64 # skip Required environment variable $GENEMARK_MODELS is not set ok 65 # skip Required environment variable $GENEMARK_MODELS is not set ok 66 # skip Required environment variable $GENEMARK_MODELS is not set ok 67 # skip Required environment variable $GENEMARK_MODELS is not set ok 68 # skip Required environment variable $GENEMARK_MODELS is not set ok 69 # skip Required environment variable $GENEMARK_MODELS is not set ok 70 # skip Required environment variable $GENEMARK_MODELS is not set ok 71 # skip Required environment variable $GENEMARK_MODELS is not set ok 72 # skip Required environment variable $GENEMARK_MODELS is not set ok 73 # skip Required environment variable $GENEMARK_MODELS is not set ok 74 # skip Required environment variable $GENEMARK_MODELS is not set ok 75 # skip Required environment variable $GENEMARK_MODELS is not set ok 76 # skip Required environment variable $GENEMARK_MODELS is not set ok 77 # skip Required environment variable $GENEMARK_MODELS is not set ok 78 # skip Required environment variable $GENEMARK_MODELS is not set ok 79 # skip Required environment variable $GENEMARK_MODELS is not set ok 80 # skip Required environment variable $GENEMARK_MODELS is not set ok 81 # skip Required environment variable $GENEMARK_MODELS is not set ok 82 # skip Required environment variable $GENEMARK_MODELS is not set ok 83 # skip Required environment variable $GENEMARK_MODELS is not set ok 84 # skip Required environment variable $GENEMARK_MODELS is not set ok 85 # skip Required environment variable $GENEMARK_MODELS is not set ok 86 # skip Required environment variable $GENEMARK_MODELS is not set ok 87 # skip Required environment variable $GENEMARK_MODELS is not set ok 88 # skip Required environment variable $GENEMARK_MODELS is not set ok 89 # skip Required environment variable $GENEMARK_MODELS is not set ok 90 # skip Required environment variable $GENEMARK_MODELS is not set ok 91 # skip Required environment variable $GENEMARK_MODELS is not set ok 92 # skip Required environment variable $GENEMARK_MODELS is not set ok 93 # skip Required environment variable $GENEMARK_MODELS is not set ok 94 # skip Required environment variable $GENEMARK_MODELS is not set ok 95 # skip Required environment variable $GENEMARK_MODELS is not set ok 96 # skip Required environment variable $GENEMARK_MODELS is not set ok 97 # skip Required environment variable $GENEMARK_MODELS is not set ok 98 # skip Required environment variable $GENEMARK_MODELS is not set ok 99 # skip Required environment variable $GENEMARK_MODELS is not set ok These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values t/Genewise.t .................. 1..17 ok 1 - use Bio::Tools::Run::Genewise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Genewise' isa 'Bio::Tools::Run::Genewise' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok # Required environment variable $GENSCANDIR is not set t/Genscan.t ................... 1..6 ok 1 - use Bio::Tools::Run::Genscan; ok 2 - use Bio::Root::IO; ok 3 # skip Required environment variable $GENSCANDIR is not set ok 4 # skip Required environment variable $GENSCANDIR is not set ok 5 # skip Required environment variable $GENSCANDIR is not set ok 6 # skip Required environment variable $GENSCANDIR is not set ok # Required executable for Bio::Tools::Run::Phylo::Gerp is not present t/Gerp.t ...................... 1..33 ok 1 - use Bio::Tools::Run::Phylo::Gerp; ok 2 - use Bio::AlignIO; ok 3 - use Bio::TreeIO; ok 4 - use Bio::Root::Utilities; ok 5 - Found input alignment file ok 6 - Found input tree file ok 7 - An object of class 'Bio::Tools::Run::Phylo::Gerp' isa 'Bio::Tools::Run::Phylo::Gerp' ok 8 - has a created method not in args supplied to new ok 9 - quiet was set ok 10 - program_dir returned correct default ok 11 - Correct exe default name ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 20 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 21 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 22 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 23 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 24 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 25 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 26 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 27 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 28 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 29 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 30 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 31 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 32 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok 33 # skip Required executable for Bio::Tools::Run::Phylo::Gerp is not present ok t/Glimmer3.t .................. 1..111 ok 1 - use Bio::Tools::Run::Glimmer; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Glimmer' isa 'Bio::Tools::Run::Glimmer' ok 5 - An object of class 'Bio::Tools::Glimmer' isa 'Bio::Tools::Glimmer' ok 6 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 7 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 8 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 9 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 10 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 11 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 12 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 13 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 14 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 15 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 16 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 17 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 18 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 19 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 20 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 21 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 22 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 23 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 24 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 25 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 26 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 27 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 28 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 29 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 30 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 31 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 32 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 33 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 34 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 35 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 36 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 37 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 38 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 39 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 40 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 41 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 42 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 43 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 44 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 45 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 46 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 47 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 48 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 49 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 50 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 51 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 52 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 53 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 54 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 55 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 56 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 57 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 58 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 59 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 60 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 61 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 62 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 63 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 64 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 65 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 66 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 67 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 68 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 69 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 72 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 73 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 74 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 75 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 76 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 77 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 78 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 79 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 80 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 81 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 82 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 83 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 84 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 85 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 86 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 87 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 88 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 89 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 90 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 91 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 92 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 93 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 94 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 95 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 96 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 97 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 98 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 99 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 100 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 101 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 102 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 103 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 104 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 105 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic' ok # Required executable for Bio::Tools::Run::Hmmer is not present t/Hmmer.t ..................... 1..27 ok 1 - use Bio::Tools::Run::Hmmer; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer' ok 5 ok 6 ok 7 ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present ok t/Infernal.t .................. 1..3 ok 1 - use Bio::Tools::Run::Infernal; ok 2 - use Bio::SeqIO; ok 3 - use Bio::AlignIO; ok Kalign (3.5.1) Copyright (C) 2006-2026 Timo Lassmann Licensed under the Apache License, Version 2.0. See the COPYING file or http://www.apache.org/licenses/LICENSE-2.0 Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 [2026-06-27 23:01:19] : LOG : Detected protein sequences. [2026-06-27 23:01:19] : LOG : Read 7 sequences from standard input. [2026-06-27 23:01:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2026-06-27 23:01:19] : LOG : Calculating pairwise distances [2026-06-27 23:01:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2026-06-27 23:01:19] : LOG : Building guide tree. [2026-06-27 23:01:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2026-06-27 23:01:19] : LOG : Anchor consistency: K=5, weight=2.0 [2026-06-27 23:01:19] : LOG : Aligning [2026-06-27 23:01:19] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 Kalign (3.5.1) Copyright (C) 2006-2026 Timo Lassmann Licensed under the Apache License, Version 2.0. See the COPYING file or http://www.apache.org/licenses/LICENSE-2.0 Please cite: Lassmann, Timo. "Kalign 3: multiple sequence alignment of large data sets." Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 [2026-06-27 23:01:19] : LOG : Detected protein sequences. [2026-06-27 23:01:19] : LOG : Read 7 sequences from standard input. [2026-06-27 23:01:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2026-06-27 23:01:19] : LOG : Calculating pairwise distances [2026-06-27 23:01:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2026-06-27 23:01:19] : LOG : Building guide tree. [2026-06-27 23:01:19] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 [2026-06-27 23:01:19] : LOG : Anchor consistency: K=5, weight=2.0 [2026-06-27 23:01:19] : LOG : Aligning [2026-06-27 23:01:19] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 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 ok 5 ok 6 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/CtLPdlvk6H 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/WJsgodkrg8 Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (6) CATL_RAT -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (4) CATH_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (6) CATL_RAT -- done. Computing posterior matrix: (2) ALEU_HORVU vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (4) CATH_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (3) CATH_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (4) CATH_RAT vs. (5) CATL_HUMAN -- done. Computing posterior matrix: (4) CATH_RAT vs. (6) CATL_RAT -- done. Computing posterior matrix: (4) CATH_RAT vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (6) CATL_RAT -- done. Computing posterior matrix: (5) CATL_HUMAN vs. (7) PAPA_CARPA -- done. Computing posterior matrix: (6) CATL_RAT vs. (7) PAPA_CARPA -- done. Trained parameter set: initDistrib[] = { 0.8318762183 5.24617426e-05 5.24617426e-05 0.08400939405 0.08400939405 } gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.8318762183 5.246169894e-05 5.246169894e-05 0.08400939405 0.08400939405 } gapOpen[] = { 0.01386300847 0.01386300847 0.006556313485 0.006556313485 } gapExtend[] = { 0.360332042 0.360332042 0.7831901312 0.7831901312 } Loading sequence file: /tmp/RSi1UYchOe Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # You named your test '15'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '340'. You shouldn't use numbers for your test names. # Very confusing. t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 - An object of class 'Bio::SeqFeature::FeaturePair' isa 'Bio::SeqFeatureI' ok 6 - 15 ok 7 - 340 ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present t/ProtPars.t .................. 1..11 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars' ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present ok # Required executable for Bio::Tools::Run::Pseudowise is not present t/Pseudowise.t ................ 1..18 ok 1 - use Bio::Tools::Run::Pseudowise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 ok 5 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 6 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 7 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 8 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 9 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 10 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 11 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 12 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 13 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 14 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 15 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 16 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 17 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 18 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok # Required executable for Bio::Tools::Run::Phylo::QuickTree is not present t/QuickTree.t ................. 1..13 ok 1 - use Bio::Tools::Run::Phylo::QuickTree; ok 2 - use Bio::AlignIO; ok 3 - Found input file ok 4 - An object of class 'Bio::Tools::Run::Phylo::QuickTree' isa 'Bio::Tools::Run::Phylo::QuickTree' ok 5 - program_dir returned correct default ok 6 - Correct exe default name ok 7 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok t/Raxml.t ..................... 1..12 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Raxml; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - An object of class 'Bio::Tools::Run::Phylo::Raxml' isa 'Bio::Tools::Run::Phylo::Raxml' ok 6 - Tree is defined ok 7 - Tree is defined ok 8 - File containing best tree exists in tempdir ok 9 - Tree is defined ok 10 - Tree is defined ok 11 - Number of nodes is correct ok 12 - Tree is defined ok # DB and mask make tests # run BLAST methods t/SABlastPlus.t ............... 1..71 ok 1 - use Bio::Tools::Run::StandAloneBlastPlus; ok 2 - use Bio::Tools::Run::WrapperBase; ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts; ok 4 - BlastPlus factory ok 5 - make factory ok 6 - test db made with fasta ok 7 - temp db ok 8 - right type ok 9 ok 10 - named db made ok 11 - check_db ok 12 - correct name ok 13 - dbinfo hash returned ok 14 - correct type ok 15 - windowmasker mask made ok 16 - dustmasker mask made ok 17 - check_db with arg ok 18 - db_info with arg ok 19 - protein db made ok 20 - correct type ok 21 - segmasker mask made ok 22 - segmasker mask made; blastdb as data ok 23 ok 24 - protein db made with pre-built mask ok 25 - db_info records mask info ok 26 ok 27 - mask built and db made on construction (windowmasker) ok 28 ok 29 - mask built and db made on construction (segmasker) ok 30 ok 31 - mask built and db made on construction (dustmasker) ok 32 ok 33 ok 34 ok 35 - make db from Bio::SeqIO ok 36 ok 37 - make db from Bio::AlignIO ok 38 ok 39 - make db from \@seqs ok 40 - dbdir : ./a/b; dbname : test; create ok 41 - make db ok 42 ok 43 ok 44 ok 45 ok 46 - run blastn ok 47 - default hit limit ok 48 - return more alignments (arg spec) ok 49 - got more hits ok 50 - run blastn with Bio::Seq query ok 51 - run tblastn ok 52 - tblastn hits ok 53 - run tblastx ok 54 - tblastx hits ok 55 ok 56 - run blastp ok 57 - blastp hits ok 58 - bl2seq (blastn) ok 59 - got hit ok 60 - bl2seq (tblastx) ok 61 - got hit ok 62 - bl2seq (blastx) ok 63 - got hit ok 64 - bl2seq (blastp) ok 65 - no hit ok 66 - bl2seq (blastp) ok 67 - got hit ok 68 - bl2seq (tblastx) - multiple outfmt options ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg) ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should also work) ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in quotes ok # Required executable for Bio::Tools::Run::Phylo::SLR is not present t/SLR.t ....................... 1..7 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::SLR; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok t/Samtools.t .................. 1..41 ok 1 - make a factory using command 'pileup' ok 2 - parameters changed on construction ok 3 - access parameter ok 4 - parameters_changed cleared on read ok 5 - set a param not set in constructor ok 6 - parameters_changed set ok 7 - parameter really set ok 8 - original parameter unchanged ok 9 - parameters_changed cleared on read ok 10 - change an original parameter ok 11 - parameter really changed ok 12 - reset parameters with arg ok 13 - original parameters undefined ok 14 - parameter really reset via arg ok 15 - parameters changed ok 16 - all available options ok 17 - available parameters ok 18 - available switches ok 19 - get_parameters correct ok 20 - command attribute set ok 21 - internal command array set ok 22 - internal prefix hash set ok 23 - commands filtered by prefix ok 24 - translate_params: command correct ok 25 - translate_params: options correct ok 26 - merge bam factory instantiated ok 27 - merged bam file created ok 28 - fasta index factory ok 29 - make fasta index ok 30 - fai file present ok 31 - bam -> sam cvt factory ok 32 - convert bam -> sam ok 33 - sam file present and text ok 34 - sam -> bam cvt factory ok 35 - convert sam -> bam ok 36 - bam file present and binary ok 37 - bam sort factory ok 38 - sort bam file ok 39 - bam index factory ok 40 - make bam index ok 41 - bai file present and binary ok # Required executable for Bio::Tools::Run::Seg is not present t/Seg.t ....................... 1..8 ok 1 - use Bio::Tools::Run::Seg; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Seg' isa 'Bio::Tools::Run::Seg' ok 5 # skip Required executable for Bio::Tools::Run::Seg is not present ok 6 # skip Required executable for Bio::Tools::Run::Seg is not present ok 7 # skip Required executable for Bio::Tools::Run::Seg is not present ok 8 # skip Required executable for Bio::Tools::Run::Seg is not present ok # Required executable for Bio::Tools::Run::Phylo::Semphy is not present t/Semphy.t .................... 1..19 ok 1 - use Bio::Tools::Run::Phylo::Semphy; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Semphy' isa 'Bio::Tools::Run::Phylo::Semphy' ok 3 - has a created method not in args ok 4 - ratio param was set via -z ok 5 - jtt switch was set ok 6 - program_dir returned correct default ok 7 - Correct exe default name ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 14 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 15 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 16 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 17 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 18 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok 19 # skip Required executable for Bio::Tools::Run::Phylo::Semphy is not present ok # Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present t/SeqBoot.t ................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot; ok 2 - use Bio::AlignIO; ok 3 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present ok # Required executable for Bio::Tools::Run::Signalp is not present t/Signalp.t ................... 1..7 ok 1 - use Bio::Tools::Run::Signalp; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Signalp' isa 'Bio::Tools::Run::Signalp' ok 5 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 6 # skip Required executable for Bio::Tools::Run::Signalp is not present ok 7 # skip Required executable for Bio::Tools::Run::Signalp is not present ok t/Sim4.t ...................... 1..23 ok 1 - use Bio::Tools::Run::Alignment::Sim4; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::AlignIO; ok 4 - use Bio::SeqIO; ok 5 - An object of class 'Bio::Tools::Run::Alignment::Sim4' isa 'Bio::Tools::Run::Alignment::Sim4' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok # Required executable for Bio::Tools::Run::Simprot is not present t/Simprot.t ................... 1..6 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Simprot; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Simprot is not present ok t/SoapEU-function.t ........... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present t/StandAloneFasta.t ........... 1..15 ok 1 - use Bio::Tools::Run::Alignment::StandAloneFasta; ok 2 - use Bio::SeqIO; ok 3 ok 4 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 14 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok 15 # skip Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present ok # Required executable for Bio::Tools::Run::Tmhmm is not present t/Tmhmm.t ..................... 1..9 ok 1 - use Bio::Tools::Run::Tmhmm; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm' ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok t/TribeMCL.t .................. 1..24 ok 1 - use Bio::Tools::Run::TribeMCL; ok 2 - use Bio::SearchIO; ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa 'Bio::Tools::Run::TribeMCL' ok 4 # skip Tribe Matrix program not found. Skipping tests... ok 5 # skip Tribe Matrix program not found. Skipping tests... ok 6 # skip Tribe Matrix program not found. Skipping tests... ok 7 # skip Tribe Matrix program not found. Skipping tests... ok 8 # skip Tribe Matrix program not found. Skipping tests... ok 9 # skip Tribe Matrix program not found. Skipping tests... ok 10 # skip Tribe Matrix program not found. Skipping tests... ok 11 # skip Tribe Matrix program not found. Skipping tests... ok 12 # skip Tribe Matrix program not found. Skipping tests... ok 13 # skip Tribe Matrix program not found. Skipping tests... ok 14 # skip Tribe Matrix program not found. Skipping tests... ok 15 # skip Tribe Matrix program not found. Skipping tests... ok 16 # skip Tribe Matrix program not found. Skipping tests... ok 17 # skip Tribe Matrix program not found. Skipping tests... ok 18 # skip Tribe Matrix program not found. Skipping tests... ok 19 # skip Tribe Matrix program not found. Skipping tests... ok 20 # skip Tribe Matrix program not found. Skipping tests... ok 21 # skip Tribe Matrix program not found. Skipping tests... ok 22 # skip Tribe Matrix program not found. Skipping tests... ok 23 # skip Tribe Matrix program not found. Skipping tests... ok 24 # skip Tribe Matrix program not found. Skipping tests... ok t/Vista.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Vista; ok 2 - use Bio::AlignIO; ok 3 # skip Skipping due to old java version ok 4 # skip Skipping due to old java version ok 5 # skip Skipping due to old java version ok 6 # skip Skipping due to old java version ok 7 # skip Skipping due to old java version ok # Required executable for Bio::Tools::Run::Alignment::Gmap is not present t/gmap-run.t .................. 1..8 ok 1 - use Bio::Tools::Run::Alignment::Gmap; ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok # Required executable for Bio::Tools::Run::tRNAscanSE is not present t/tRNAscanSE.t ................ 1..12 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa 'Bio::Tools::Run::tRNAscanSE' ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok All tests successful. Test Summary Report ------------------- t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 88, 110, 155, 190, 208, 226 262, 280, 315, 333, 405 Files=60, Tests=1652, 258 wallclock secs ( 0.20 usr 0.11 sys + 158.08 cusr 11.63 csys = 170.02 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/bioperl-run-sInbxY/bioperl-run-1.7.3' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install /usr/bin/perl Build install --destdir /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/ESoap/WSDL.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/Result.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Factory/EMBOSS.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Lagan.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probalign.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Blat.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Kalign.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Probcons.pm Installing 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/build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Genewise.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Prints.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Infernal.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Phyml.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::LVB.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::BEDTools.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Lagan.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::FootPrinter.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Amap.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::tRNAscanSE.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneWUBlast.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Seg.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::EMBOSSacd.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Alignment::Blat.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Signalp.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::Tools::Run::Analysis::soap.3pm Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/bioperl-run-sInbxY/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-14_all.deb'. dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-14_all.deb'. dpkg-genbuildinfo -O../bioperl-run_1.7.3-14_amd64.buildinfo dpkg-genchanges -O../bioperl-run_1.7.3-14_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-06-27T23:02:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 27 Jun 2026 23:02:09 +0000 | +------------------------------------------------------------------------------+ bioperl-run_1.7.3-14_amd64.changes: ----------------------------------- Format: 1.8 Date: Mon, 09 Mar 2026 20:43:42 +0100 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: source all Version: 1.7.3-14 Distribution: perl-5.44-throwaway 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: 1129866 Changes: bioperl-run (1.7.3-14) unstable; urgency=medium . * update-kalign-invocation.patch: new. This change adjusts arguments passed to kalign to use stdin as input and stdout as output, per the new command version's usage instructions. (Closes: #1129866) * d/control: drop redundant Priority: optional. * d/control: drop redundant Rules-Requires-Root: no. * d/control: declare compliance to standards version 4.7.3. * d/watch: rework to port to Github uscan template. 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science optional bioperl-run_1.7.3-14.dsc 20a9eaea9bab6c79e6d237799f7ef993 20384 science optional bioperl-run_1.7.3-14.debian.tar.xz 976a3da1f76c3a7c0a9ca8411ff60d30 35108 science optional bioperl-run_1.7.3-14_all.deb 2c15ddfb7857e6eb1d5a5a776dd34348 13559 science optional bioperl-run_1.7.3-14_amd64.buildinfo 4d2e4f7e62ecb4acb41f923ddc363c5f 529152 perl optional libbio-perl-run-perl_1.7.3-14_all.deb +------------------------------------------------------------------------------+ | Buildinfo Sat, 27 Jun 2026 23:02:10 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: bioperl-run Binary: bioperl-run libbio-perl-run-perl Architecture: all source Version: 1.7.3-14 Checksums-Md5: 5e6137b178d57ea91befbdaa9ac8f92e 2187 bioperl-run_1.7.3-14.dsc 976a3da1f76c3a7c0a9ca8411ff60d30 35108 bioperl-run_1.7.3-14_all.deb 4d2e4f7e62ecb4acb41f923ddc363c5f 529152 libbio-perl-run-perl_1.7.3-14_all.deb Checksums-Sha1: 7d6533de78fc04c9c0828500e8101f2b8173e854 2187 bioperl-run_1.7.3-14.dsc 83425c1121890a2ee9599787fc732ca847d66886 35108 bioperl-run_1.7.3-14_all.deb ab7a03fd22ab1a88c3358181bee739029381a9a2 529152 libbio-perl-run-perl_1.7.3-14_all.deb Checksums-Sha256: bf65fe080603490dad4f012040f09d5ac24c716ab29a860d8f82fc426cc554e5 2187 bioperl-run_1.7.3-14.dsc ab4b70839bc8b02fe7df3b45f9a51dc439f8586594939e5f07ecc16d768eeded 35108 bioperl-run_1.7.3-14_all.deb 1a90278899e6ad6f12ce24809b28429255fd64e1fb854a4319b0782c0ac2c1fc 529152 libbio-perl-run-perl_1.7.3-14_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 27 Jun 2026 23:02:09 +0000 Build-Path: /build/bioperl-run-sInbxY/bioperl-run-1.7.3 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: amap-align (= 2.2+git20080214.600fc29+dfsg-2), autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-1), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), bedtools (= 2.31.1+dfsg-3), bedtools-test (= 2.31.1+dfsg-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bioperl (= 1.7.8-4), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), ca-certificates (= 20260601), clustalw (= 2.1+lgpl-7), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.2), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), emboss (= 6.6.0+dfsg-18), emboss-data (= 6.6.0+dfsg-18), emboss-lib (= 6.6.0+dfsg-18), exonerate (= 2.4.0-5+b1), fasttree (= 2.1.11-2), file (= 1:5.47-4), findutils (= 4.10.0-4), fontconfig-config (= 2.17.1-5), fonts-dejavu-core (= 2.37-9), fonts-dejavu-mono (= 2.37-9), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-1), gettext-base (= 1.0-1), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hmmer (= 3.4+dfsg-3), hostname (= 3.25), hyphy-common (= 2.5.69+dfsg-2), hyphy-pt (= 2.5.69+dfsg-2), ibverbs-providers (= 63.0-1.1), infernal (= 1.1.5-3), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), isa-support (= 27+b1), kalign (= 1:3.5.1-1+b1), lagan (= 2.0-10), libabsl20260107 (= 20260107.0-5), libacl1 (= 2.3.2-3), libalgorithm-diff-perl (= 1.201-1), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libaom3 (= 3.13.1-2+b1), libarchive-zip-perl (= 1.68-1), libarray-compare-perl (= 3.0.8-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libavif16 (= 1.4.1-1+b1), libb-hooks-op-check-perl (= 0.22-3+b5), libbinutils (= 2.46.50.20260617-1), libbio-asn1-entrezgene-perl (= 1.730-3), libbio-cluster-perl (= 1.7.3-6), libbio-eutilities-perl (= 1.77-3), libbio-featureio-perl (= 1.6.905-2), libbio-perl-perl (= 1.7.8-4), libbio-perl-run-perl (= 1.7.3-14), libbio-tools-run-alignment-clustalw-perl (= 1.7.4-4), libbio-tools-run-remoteblast-perl (= 1.7.3-3), libbio-variation-perl (= 1.7.5-3), libblas3 (= 3.12.1-7+b2), libblkid1 (= 2.42.2-1), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-3), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1), libcapture-tiny-perl (= 0.50-1), libcbor0.10 (= 0.10.2-2.1+b1), libcc1-0 (= 16.1.0-2), libclang-common-21-dev (= 1:21.1.8-7+b3), libclass-data-inheritable-perl (= 0.10-1), libclass-method-modifiers-perl (= 2.15-1), libclass-xsaccessor-perl (= 1.19-4+b6), libclone-perl (= 0.50-1+b1), libcom-err2 (= 1.47.4-1), libconfig-any-perl (= 0.33-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl3t64-gnutls (= 8.21.0-1), libcurl4-gnutls (= 8.21.0-1), libdata-stag-perl (= 0.14-4), libdav1d7 (= 1.5.3-1+b2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libde265-0 (= 1.0.18-1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.2), libdeflate0 (= 1.25-1), libdevel-callchecker-perl (= 0.009-3+b1), libdevel-stacktrace-perl (= 2.0500-1), libdivsufsort3 (= 2.0.1-7+b1), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.134-2), libdrm-common (= 2.4.134-2), libdrm2 (= 2.4.134-2), libdynaloader-functions-perl (= 0.004-2), libedit2 (= 3.1-20260512-1), libelf1t64 (= 0.195-1), libencode-locale-perl (= 1.05-3), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b2), libexception-class-perl (= 1.45-1), libexpat1 (= 2.8.2-1), libexporter-tiny-perl (= 1.006003-1), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.5.2-4), libfido2-1 (= 1.17.0-1), libfile-listing-perl (= 6.16-1), libfile-slurp-perl (= 9999.32-2.1), libfile-slurper-perl (= 0.014-1), libfile-sort-perl (= 1.01-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libfontconfig1 (= 2.17.1-5), libfreetype6 (= 2.14.3+dfsg-1), libfuse3-4 (= 3.18.2-2), libgav1-2 (= 0.20.0-2+b1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgd3 (= 2.3.3-13+b2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran5 (= 16.1.0-2), libglib2.0-0t64 (= 2.88.2-1), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libheif-plugin-dav1d (= 1.21.2-4), libheif-plugin-libde265 (= 1.21.2-4), libheif1 (= 1.21.2-4), libhogweed6t64 (= 3.10.2-1+b1), libhpdf-2.3.0 (= 2.3.0+dfsg-1.1+b1), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhtml-parser-perl (= 3.83-2+b1), libhtml-tagset-perl (= 3.24-1), libhtml-tree-perl (= 5.07-3), libhts3t64 (= 1.22.1+ds2-1+b2), libhtscodecs2 (= 1.6.6-1), libhttp-cookies-perl (= 6.11-1), libhttp-date-perl (= 6.07-1), libhttp-message-perl (= 7.02-1), libhttp-negotiate-perl (= 6.01-2), libhwasan0 (= 16.1.0-2), libhwloc-plugins (= 2.14.0-2), libhwloc15 (= 2.14.0-2), libibmad5 (= 63.0-1.1), libibumad3 (= 63.0-1.1), libibverbs1 (= 63.0-1.1), libidn2-0 (= 2.3.8-5), libimagequant0 (= 4.4.1-1+b2), libimport-into-perl (= 1.002005-2), libio-html-perl (= 1.004-3), libio-pty-perl (= 1:1.31-1+b1), libio-socket-ssl-perl (= 2.098-1), libio-string-perl (= 1.08-4), libipc-run-perl (= 20260402.0-1), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.0-1), libjbig0 (= 2.1-6.1+b3), libjpeg62-turbo (= 1:3.1.3-4), libk5crypto3 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), liblapack3 (= 3.12.1-7+b2), libldap2 (= 2.6.13+dfsg-1+b1), liblerc4 (= 4.1.0+ds-1), libllvm21 (= 1:21.1.8-7+b3), liblmdb0 (= 0.9.31-1+b3), liblsan0 (= 16.1.0-2), liblwp-mediatypes-perl (= 6.04-2), liblwp-protocol-https-perl (= 6.15-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmariadb3 (= 1:11.8.8-1), libmbedcrypto16 (= 3.6.6-0.1), libmbedtls21 (= 3.6.6-0.1), libmbedx509-7 (= 3.6.6-0.1), libmd0 (= 1.2.0-2), libmodule-build-perl (= 0.423400-3), libmodule-pluggable-perl (= 6.3-1), libmodule-runtime-perl (= 0.018-1), libmoo-perl (= 2.005005-1), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncbi-vdb3 (= 3.2.1+dfsg-2+b1), libncurses6 (= 6.6+20251231-1+b1), libncursesw6 (= 6.6+20251231-1+b1), libnet-http-perl (= 6.24-1), libnet-ssleay-perl (= 1.96-1+b1), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libnl-3-200 (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnuma1 (= 2.0.19-1+b2), libopenmpi40 (= 5.0.10-1), libp11-kit0 (= 0.26.2-3), libpam-modules (= 1.7.0-6), libpam-modules-bin (= 1.7.0-6), libpam-runtime (= 1.7.0-6), libpam0g (= 1.7.0-6), libparams-classify-perl (= 0.015-2+b6), libpciaccess0 (= 0.17-3+b4), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc1-1), libpipeline1 (= 1.5.8-3), libpmix2t64 (= 6.0.0+really5.0.9-3+b1), libpng16-16t64 (= 1.6.58-1), libpq5 (= 18.4-1+b1), libproc2-0 (= 2:4.0.4-9+b2), libprrte-bin (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.22.0-1), libpsm2-2 (= 11.2.185-2.1), libpython3-stdlib (= 3.14.6-1), libpython3.14-minimal (= 3.14.6-1), libpython3.14-stdlib (= 3.14.6-1), libquadmath0 (= 16.1.0-2), librav1e0.8 (= 0.8.1-10), librdmacm1t64 (= 63.0-1.1), libreadline8t64 (= 8.3-4), librole-tiny-perl (= 2.002005-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsharpyuv0 (= 1.5.0-0.1+b2), libsmartcols1 (= 2.42.2-1), libsqlite3-0 (= 3.53.3-1), libssh2-1t64 (= 1.11.1-4), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsub-quote-perl (= 2.006009-1), libsub-uplevel-perl (= 0.2800-3), libsvtav1enc4 (= 4.1.0+dfsg-1), libsystemd-shared (= 261.1-1), libsystemd0 (= 261.1-1), libtasn1-6 (= 4.21.0-2+b1), libtest-deep-perl (= 1.205-1), libtest-differences-perl (= 0.72-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.42-1), libtest-warn-perl (= 0.37-2), libtext-charwidth-perl (= 0.04-12+b1), libtext-csv-perl (= 2.06-1), libtext-diff-perl (= 1.45-2), libtext-wrapi18n-perl (= 0.06-11), libtiff6 (= 4.7.1-3), libtimedate-perl (= 2.3500-1), libtinfo6 (= 6.6+20251231-1+b1), libtool (= 2.5.4-11), libtree-dagnode-perl (= 1.35-1), libtry-tiny-perl (= 0.32-1), libtsan2 (= 16.1.0-2), libtype-tiny-perl (= 2.010001-1), libubsan1 (= 16.1.0-2), libucc1 (= 1.8.0-2), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.21.0-1), libudev1 (= 261.1-1), libunistring5 (= 1.4.2-1), liburi-perl (= 5.35-1), libuuid1 (= 2.42.2-1), libuv1t64 (= 1.52.1-4), libwebp7 (= 1.5.0-0.1+b2), libwww-perl (= 6.83-1), libwww-robotrules-perl (= 6.03-1), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml-dom-perl (= 1.46-2), libxml-dom-xpath-perl (= 0.14-4), libxml-libxml-perl (= 2.0207+dfsg+really+2.0134-8+b1), libxml-namespacesupport-perl (= 1.12-2), libxml-parser-perl (= 2.47-2+b1), libxml-perl (= 0.08-4), libxml-regexp-perl (= 0.04-2), libxml-sax-base-perl (= 1.09-3), libxml-sax-perl (= 1.02+dfsg-5), libxml-simple-perl (= 2.25-2), libxml-twig-perl (= 1:3.54-1), libxml-writer-perl (= 0.900-2), libxml-xpathengine-perl (= 0.14-2), libxml2-16 (= 2.15.3+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libxpm4 (= 1:3.5.19-1), libyuv0 (= 0.0.1922.20260106-1+b1), libz3-4 (= 4.13.3-1.1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.0.13-1), m4 (= 1.4.21-1), mafft (= 7.525-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mariadb-common (= 1:11.8.8-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), mount (= 2.42.2-1), mpi-default-bin (= 1.20), muscle (= 1:5.1.0-1), mysql-common (= 5.8+1.1.1), ncbi-blast+ (= 2.17.0+ds-7), ncbi-blast+-legacy (= 2.17.0+ds-7), ncbi-data (= 6.1.20170106+dfsg2-7), ncbi-vdb-data (= 3.2.1+dfsg-2), ncoils (= 2002-10), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1+b1), netbase (= 6.5), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.3p1-5), openssl (= 3.6.3-1), openssl-provider-legacy (= 3.6.3-1), pal2nal (= 14.1-3), patch (= 2.8-2), perl (= 5.44.0~rc1-1), perl-base (= 5.44.0~rc1-1), perl-modules-5.44 (= 5.44.0~rc1-1), perl-openssl-defaults (= 7+b2), pftools (= 3.2.12-3), phyml (= 3:3.3.20250515-2), po-debconf (= 1.0.22), primer3 (= 2.6.1-6), probcons (= 1.12-15), procps (= 2:4.0.4-9+b2), python3 (= 3.14.6-1), python3-minimal (= 3.14.6-1), python3-numpy (= 1:2.4.6+ds-1), python3-numpy-dev (= 1:2.4.6+ds-1), python3-pybedtools (= 0.10.0-6), python3-pysam (= 0.23.3+ds-2+b1), python3.14 (= 3.14.6-1), python3.14-minimal (= 3.14.6-1), raxml (= 8.2.13+dfsg-3+b1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.4-1), samtools (= 1.22.1-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sim4 (= 0.0.20121010-9), sse4.2-support (= 27+b1), systemd (= 261.1-1), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tigr-glimmer (= 3.02b-6+b1), tzdata (= 2026b-1), ucf (= 3.0056), util-linux (= 2.42.2-1), wise (= 2.4.1-28), wise-data (= 2.4.1-28), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1773085422" +------------------------------------------------------------------------------+ | Package contents Sat, 27 Jun 2026 23:02:10 +0000 | +------------------------------------------------------------------------------+ bioperl-run_1.7.3-14_all.deb ---------------------------- new Debian package, version 2.0. size 35108 bytes: control archive=1348 bytes. 1094 bytes, 15 lines control 1062 bytes, 15 lines md5sums Package: bioperl-run Version: 1.7.3-14 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 88 Depends: perl:any, bioperl (>= 1.7.4), libbio-perl-run-perl (= 1.7.3-14), libbio-featureio-perl, libbio-cluster-perl, libtest-requiresinternet-perl, libbio-eutilities-perl, libbio-tools-run-remoteblast-perl, libsoap-lite-perl, default-jdk-headless Recommends: amap-align, ncbi-blast+-legacy, bwa, exonerate, kalign, maq, mafft, muscle, ncoils, phylip, primer3, probalign, probcons, raxml, sim4, t-coffee, wise, lagan, pal2nal Suggests: gmap, fasta3, trnascan-se, bedtools, bowtie, clustalw, emboss, hmmer, hyphy-pt | hyphy-mpi, infernal, libbio-tools-run-alignment-clustalw-perl, pftools, phyml, samtools, tigr-glimmer Section: science Priority: optional Homepage: https://metacpan.org/release/BioPerl-Run Description: BioPerl wrappers: scripts Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package. drwxr-xr-x root/root 0 2026-03-09 19:43 ./ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/bin/ -rwxr-xr-x root/root 3552 2026-03-09 19:43 ./usr/bin/bp_multi_hmmsearch.pl -rwxr-xr-x root/root 23728 2026-03-09 19:43 ./usr/bin/bp_panalysis.pl -rwxr-xr-x root/root 15037 2026-03-09 19:43 ./usr/bin/bp_papplmaker.pl -rwxr-xr-x root/root 1324 2026-03-09 19:43 ./usr/bin/bp_run_neighbor.pl -rwxr-xr-x root/root 2111 2026-03-09 19:43 ./usr/bin/bp_run_protdist.pl drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/doc/bioperl-run/ -rw-r--r-- root/root 1418 2026-03-09 19:43 ./usr/share/doc/bioperl-run/README.Debian -rw-r--r-- root/root 1279 2026-03-09 19:43 ./usr/share/doc/bioperl-run/changelog.Debian.gz -rw-r--r-- root/root 3103 2019-02-08 17:56 ./usr/share/doc/bioperl-run/changelog.gz -rw-r--r-- root/root 3304 2026-03-09 19:43 ./usr/share/doc/bioperl-run/copyright drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 427 2026-03-09 19:43 ./usr/share/lintian/overrides/bioperl-run drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/man/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/man/man1/ -rw-r--r-- root/root 1592 2026-03-09 19:43 ./usr/share/man/man1/bp_multi_hmmsearch.pl.1p.gz -rw-r--r-- root/root 5943 2026-03-09 19:43 ./usr/share/man/man1/bp_panalysis.pl.1p.gz -rw-r--r-- root/root 3163 2026-03-09 19:43 ./usr/share/man/man1/bp_papplmaker.pl.1p.gz -rw-r--r-- root/root 1173 2026-03-09 19:43 ./usr/share/man/man1/bp_run_neighbor.pl.1p.gz -rw-r--r-- root/root 1399 2026-03-09 19:43 ./usr/share/man/man1/bp_run_protdist.pl.1p.gz libbio-perl-run-perl_1.7.3-14_all.deb ------------------------------------- new Debian package, version 2.0. size 529152 bytes: control archive=5624 bytes. 614 bytes, 14 lines control 17160 bytes, 198 lines md5sums Package: libbio-perl-run-perl Source: bioperl-run Version: 1.7.3-14 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 1723 Depends: perl:any, libbio-perl-perl, libipc-run-perl, libfile-sort-perl Recommends: libalgorithm-diff-perl, libio-string-perl, libxml-twig-perl, libwww-perl Section: perl Priority: optional Homepage: https://metacpan.org/release/BioPerl-Run Description: BioPerl wrappers: modules Contains modules that provide a Perl interface to various bioinformatics applications to allow them to be used with common BioPerl objects. drwxr-xr-x root/root 0 2026-03-09 19:43 ./ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-03-09 19:43 ./usr/share/doc/libbio-perl-run-perl/ -rw-r--r-- root/root 1285 2026-03-09 19:43 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in use +------------------------------------------------------------------------------+ | Summary Sat, 27 Jun 2026 23:02:12 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 19712 Build-Time: 269 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 62 Job: /srv/debomatic/incoming/bioperl-run_1.7.3-14.dsc Machine Architecture: amd64 Package: bioperl-run Package-Time: 345 Source-Version: 1.7.3-14 Space: 19712 Status: successful Version: 1.7.3-14 -------------------------------------------------------------------------------- Finished at 2026-06-27T23:02:09Z Build needed 00:05:45, 19712k disk space