I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 13 19:56:43 -12 2022 I: pbuilder-time-stamp: 1642147003 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bioperl-run_1.7.2-4.dsc] I: copying [./bioperl-run_1.7.2.orig.tar.gz] I: copying [./bioperl-run_1.7.2-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Sep 14 06:37:45 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bioperl-run_1.7.2-4.dsc dpkg-source: info: extracting bioperl-run in bioperl-run-1.7.2 dpkg-source: info: unpacking bioperl-run_1.7.2.orig.tar.gz dpkg-source: info: unpacking bioperl-run_1.7.2-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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_bowtie.patch dpkg-source: info: applying skip_tests_for_infernal.patch dpkg-source: info: applying skip_tests_for_muscle.patch dpkg-source: info: applying skip_tests_for_ncbi-blast+.patch dpkg-source: info: applying skip_tests_for_maq.patch dpkg-source: info: applying hyphy.patch dpkg-source: info: applying remove_tests_for_ensembl.patch dpkg-source: info: applying fix_bowtie_call.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/51221/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d74225a04b24472fbf8b2b1aa8fa39a6' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='51221' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.6W0sNkjaTk/pbuilderrc_PH2j --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.6W0sNkjaTk/b1 --logfile b1/build.log bioperl-run_1.7.2-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 5.9.0-0.bpo.2-amd64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 9 02:47 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/51221/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), perl, libmodule-build-perl, bioperl, libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libtest-most-perl, libarray-compare-perl, libtree-dagnode-perl, amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate, hmmer, hyphy-mpi, infernal, kalign, maq, mafft, muscle, ncoils, phylip, phyml, primer3, probcons, raxml, samtools, sim4, t-coffee, tigr-glimmer, wise, libwww-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on libalgorithm-diff-perl; however: Package libalgorithm-diff-perl is not installed. pbuilder-satisfydepends-dummy depends on libipc-run-perl; however: Package libipc-run-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on libxml-twig-perl; however: Package libxml-twig-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-most-perl; however: Package libtest-most-perl is not installed. pbuilder-satisfydepends-dummy depends on libarray-compare-perl; however: Package libarray-compare-perl is not installed. pbuilder-satisfydepends-dummy depends on libtree-dagnode-perl; however: Package libtree-dagnode-perl is not installed. pbuilder-satisfydepends-dummy depends on amap-align; however: Package amap-align is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on blast2; however: Package blast2 is not installed. pbuilder-satisfydepends-dummy depends on bowtie; however: Package bowtie is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on emboss; however: Package emboss is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer is not installed. pbuilder-satisfydepends-dummy depends on hyphy-mpi; however: Package hyphy-mpi is not installed. pbuilder-satisfydepends-dummy depends on infernal; however: Package infernal is not installed. pbuilder-satisfydepends-dummy depends on kalign; however: Package kalign is not installed. pbuilder-satisfydepends-dummy depends on maq; however: Package maq is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on muscle; however: Package muscle is not installed. pbuilder-satisfydepends-dummy depends on ncoils; however: Package ncoils is not installed. pbuilder-satisfydepends-dummy depends on phylip; however: Package phylip is not installed. pbuilder-satisfydepends-dummy depends on phyml; however: Package phyml is not installed. pbuilder-satisfydepends-dummy depends on primer3; however: Package primer3 is not installed. pbuilder-satisfydepends-dummy depends on probcons; however: Package probcons is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on sim4; however: Package sim4 is not installed. pbuilder-satisfydepends-dummy depends on t-coffee; however: Package t-coffee is not installed. pbuilder-satisfydepends-dummy depends on tigr-glimmer; however: Package tigr-glimmer is not installed. pbuilder-satisfydepends-dummy depends on wise; however: Package wise is not installed. pbuilder-satisfydepends-dummy depends on libwww-perl; however: Package libwww-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: amap-align{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} bioperl{a} blast2{a} bowtie{a} bsdmainutils{a} bwa{a} ca-certificates{a} clustalw{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} emboss{a} emboss-data{a} emboss-lib{a} exonerate{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} hyphy-common{a} hyphy-mpi{a} infernal{a} intltool-debian{a} kalign{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libarray-compare-perl{a} libb-hooks-op-check-perl{a} libbio-perl-perl{a} libbsd0{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libclass-method-modifiers-perl{a} libcroco3{a} libcurl3-gnutls{a} libdata-stag-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdevel-globaldestruction-perl{a} libdevel-stacktrace-perl{a} libdivsufsort3{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libencode-locale-perl{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexception-class-perl{a} libexpat1{a} libexporter-tiny-perl{a} libfabric1{a} libfile-listing-perl{a} libfile-slurp-tiny-perl{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgd3{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhpdf-2.3.0{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhts2{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhwloc-plugins{a} libhwloc5{a} libibverbs1{a} libicu63{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libio-string-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblmdb0{a} libltdl7{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmariadb3{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmodule-build-perl{a} libmodule-runtime-perl{a} libmoo-perl{a} libncurses6{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenmpi3{a} libparams-classify-perl{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpng16-16{a} libpq5{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} librdmacm1{a} libreadline7{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libstrictures-perl{a} libsub-exporter-progressive-perl{a} libsub-quote-perl{a} libsub-uplevel-perl{a} libtbb2{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtiff5{a} libtimedate-perl{a} libtool{a} libtree-dagnode-perl{a} libtry-tiny-perl{a} libtype-tiny-perl{a} libuchardet0{a} liburi-perl{a} libwebp6{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml-parser-perl{a} libxml-twig-perl{a} libxml2{a} libxpm4{a} m4{a} mafft{a} man-db{a} maq{a} mariadb-common{a} mime-support{a} muscle{a} mysql-common{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} ncoils{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} perl-openssl-defaults{a} phylip{a} phyml{a} po-debconf{a} primer3{a} probcons{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} raxml{a} readline-common{a} samtools{a} sensible-utils{a} sim4{a} t-coffee{a} tigr-glimmer{a} ucf{a} wise{a} wise-data{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run clustalo curl cwltool dialign dialign-tx fsa ibverbs-providers krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclass-xsaccessor-perl libclone-perl libconvert-binary-c-perl libdata-dump-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-form-perl libhtml-format-perl libhtml-tableextract-perl libhttp-daemon-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libmldbm-perl libmodule-signature-perl libopenmpi-dev libpod-readme-perl libpostscript-perl libref-util-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtext-iconv-perl libtie-ixhash-perl libtype-tiny-xs-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-writer-perl libxml-xpath-perl libxml-xpathengine-perl libyaml-perl lynx mustang perl-doc perl-tk poa prank proda publicsuffix ruby shared-mime-info tm-align wget xauth xdg-user-dirs 0 packages upgraded, 211 newly installed, 0 to remove and 0 not upgraded. Need to get 168 MB of archives. After unpacking 864 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u3 [1538 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u1 [117 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u1 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 openssh-client amd64 1:7.9p1-10+deb10u2 [782 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 amap-align amd64 2.2+git20080214.600fc29+dfsg-1 [131 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 bedtools amd64 2.27.1+dfsg-4 [593 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libbio-perl-perl all 1.7.2-3 [4553 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 48 http://deb.debian.org/debian buster/main amd64 libdevel-stacktrace-perl all 2.0300-1 [28.0 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libtest-deep-perl all 1.128-1 [48.8 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libalgorithm-diff-perl all 1.19.03-2 [47.9 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libtest-differences-perl all 0.65-1 [18.1 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libsub-uplevel-perl all 0.2800-1 [16.3 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 bioperl all 1.7.2-3 [418 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get: 66 http://deb.debian.org/debian buster/main amd64 ncbi-blast+-legacy all 2.8.1-1+deb10u1 [10.6 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 blast2 all 1:2.8.1-1+deb10u1 [10.1 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 bowtie amd64 1.2.2+dfsg-4 [1670 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 bwa amd64 0.7.17-3 [195 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u3 [844 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20190110 [157 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 clustalw amd64 2.1+lgpl-6 [282 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u1 [271 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u1 [757 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libgd3 amd64 2.2.5-5.2 [136 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1 [340 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 mysql-common all 5.8+1.0.5 [7324 B] Get: 108 http://deb.debian.org/debian buster/main amd64 mariadb-common all 1:10.3.27-0+deb10u1 [32.2 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libmariadb3 amd64 1:10.3.27-0+deb10u1 [171 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u4 [89.8 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u4 [224 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libpq5 amd64 11.9-0+deb10u1 [167 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 emboss-lib amd64 6.6.0+dfsg-7+b1 [2786 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 emboss-data all 6.6.0+dfsg-7 [61.1 MB] Get: 117 http://deb.debian.org/debian buster/main amd64 emboss amd64 6.6.0+dfsg-7+b1 [1073 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 exonerate amd64 2.4.0-4 [1544 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libdivsufsort3 amd64 2.0.1-4 [44.5 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 hmmer amd64 3.2.1+dfsg-1 [1169 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 hyphy-common all 2.3.14+dfsg-1 [661 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u1 [330 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libibverbs1 amd64 22.1-1 [51.2 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 libpsm2-2 amd64 11.2.78-1 [177 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 librdmacm1 amd64 22.1-1 [65.3 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 libfabric1 amd64 1.6.2-3 [396 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 libhwloc5 amd64 1.11.12-3 [111 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 libhwloc-plugins amd64 1.11.12-3 [17.4 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 libpmix2 amd64 3.1.2-3 [498 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 libopenmpi3 amd64 3.1.3-11 [2191 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 hyphy-mpi amd64 2.3.14+dfsg-1 [919 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 infernal amd64 1.1.2-2 [22.1 MB] Get: 148 http://deb.debian.org/debian buster/main amd64 kalign amd64 1:2.03+20110620-5 [92.9 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get: 151 http://deb.debian.org/debian buster/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get: 152 http://deb.debian.org/debian buster/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get: 156 http://deb.debian.org/debian buster/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 157 http://deb.debian.org/debian buster/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 158 http://deb.debian.org/debian buster/main amd64 librole-tiny-perl all 2.000006-1 [19.4 kB] Get: 159 http://deb.debian.org/debian buster/main amd64 libstrictures-perl all 2.000005-1 [18.3 kB] Get: 160 http://deb.debian.org/debian buster/main amd64 libsub-quote-perl all 2.005001-1 [17.9 kB] Get: 161 http://deb.debian.org/debian buster/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get: 162 http://deb.debian.org/debian buster/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get: 163 http://deb.debian.org/debian buster/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get: 164 http://deb.debian.org/debian buster/main amd64 libarray-compare-perl all 3.0.2-1 [14.5 kB] Get: 165 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 166 http://deb.debian.org/debian buster/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get: 167 http://deb.debian.org/debian buster/main amd64 libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get: 168 http://deb.debian.org/debian buster/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get: 169 http://deb.debian.org/debian buster/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get: 170 http://deb.debian.org/debian buster/main amd64 libfile-slurp-tiny-perl all 0.004-1 [7288 B] Get: 171 http://deb.debian.org/debian buster/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 172 http://deb.debian.org/debian buster/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get: 173 http://deb.debian.org/debian buster/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get: 174 http://deb.debian.org/debian buster/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 175 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-11 [305 kB] Get: 176 http://deb.debian.org/debian buster/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get: 177 http://deb.debian.org/debian buster/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get: 178 http://deb.debian.org/debian buster/main amd64 libhttp-message-perl all 6.18-1 [77.8 kB] Get: 179 http://deb.debian.org/debian buster/main amd64 libhttp-cookies-perl all 6.04-1 [17.8 kB] Get: 180 http://deb.debian.org/debian buster/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 181 http://deb.debian.org/debian buster/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get: 182 http://deb.debian.org/debian buster/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get: 183 http://deb.debian.org/debian buster/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get: 184 http://deb.debian.org/debian buster/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get: 185 http://deb.debian.org/debian buster/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get: 186 http://deb.debian.org/debian buster/main amd64 libnet-http-perl all 6.18-1 [24.5 kB] Get: 187 http://deb.debian.org/debian buster/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 188 http://deb.debian.org/debian buster/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 189 http://deb.debian.org/debian buster/main amd64 libwww-perl all 6.36-2 [188 kB] Get: 190 http://deb.debian.org/debian buster/main amd64 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get: 191 http://deb.debian.org/debian buster/main amd64 libmodule-build-perl all 0.422400-1 [259 kB] Get: 192 http://deb.debian.org/debian buster/main amd64 libtree-dagnode-perl all 1.31-1 [61.4 kB] Get: 193 http://deb.debian.org/debian buster/main amd64 libxml-parser-perl amd64 2.44-4 [213 kB] Get: 194 http://deb.debian.org/debian buster/main amd64 libxml-twig-perl all 1:3.50-1.1 [179 kB] Get: 195 http://deb.debian.org/debian buster/main amd64 mafft amd64 7.407-2 [999 kB] Get: 196 http://deb.debian.org/debian buster/main amd64 maq amd64 0.7.1-8 [313 kB] Get: 197 http://deb.debian.org/debian buster/main amd64 muscle amd64 1:3.8.1551-2 [245 kB] Get: 198 http://deb.debian.org/debian buster/main amd64 ncoils amd64 2002-7 [21.9 kB] Get: 199 http://deb.debian.org/debian buster/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get: 200 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 201 http://deb.debian.org/debian buster/main amd64 phylip amd64 1:3.697+dfsg-1 [910 kB] Get: 202 http://deb.debian.org/debian buster/main amd64 phyml amd64 3:3.3.20180621-2 [1653 kB] Get: 203 http://deb.debian.org/debian buster/main amd64 primer3 amd64 2.4.0-2 [180 kB] Get: 204 http://deb.debian.org/debian buster/main amd64 probcons amd64 1.12-12 [116 kB] Get: 205 http://deb.debian.org/debian buster/main amd64 raxml amd64 8.2.12+dfsg-1 [1275 kB] Get: 206 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get: 207 http://deb.debian.org/debian buster/main amd64 sim4 amd64 0.0.20121010-5 [396 kB] Get: 208 http://deb.debian.org/debian buster/main amd64 t-coffee amd64 12.00.7fb08c2-4 [1520 kB] Get: 209 http://deb.debian.org/debian buster/main amd64 tigr-glimmer amd64 3.02b-2 [282 kB] Get: 210 http://deb.debian.org/debian buster/main amd64 wise-data all 2.4.1-21 [109 kB] Get: 211 http://deb.debian.org/debian buster/main amd64 wise amd64 2.4.1-21 [978 kB] Fetched 168 MB in 3s (53.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. 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Setting up liblmdb0:amd64 (0.9.22-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Setting up libpciaccess0:amd64 (0.14-1) ... Setting up mysql-common (5.8+1.0.5) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up probcons (1.12-12) ... Setting up libdynaloader-functions-perl (0.003-1) ... Setting up libtest-deep-perl (1.128-1) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up mafft (7.407-2) ... Setting up libalgorithm-diff-perl (1.19.03-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up bwa (0.7.17-3) ... 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libdivsufsort3:amd64 (2.0.1-4) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up tigr-glimmer (3.02b-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Setting up exonerate (2.4.0-4) ... Setting up bedtools (2.27.1+dfsg-4) ... Setting up liburi-perl (1.76-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up maq (0.7.1-8) ... Setting up raxml (8.2.12+dfsg-1) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libevent-pthreads-2.1-6:amd64 (2.1.8-stable-4) ... Setting up libhttp-date-perl (6.02-1) ... 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Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up hmmer (3.2.1+dfsg-1) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u1) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up libhttp-message-perl (6.18-1) ... 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Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python (2.7.16-1) ... Setting up bioperl (1.7.2-3) ... Setting up librdmacm1:amd64 (22.1-1) ... Setting up libhts2:amd64 (1.9-11) ... Setting up bowtie (1.2.2+dfsg-4) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003004-2) ... Setting up po-debconf (1.0.21) ... Setting up samtools (1.9-4) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up libarray-compare-perl (3.0.2-1) ... Setting up libgd3:amd64 (2.2.5-5.2) ... Setting up emboss-lib (6.6.0+dfsg-7+b1) ... Setting up ncbi-blast+-legacy (2.8.1-1+deb10u1) ... Setting up libfabric1 (1.6.2-3) ... Setting up emboss (6.6.0+dfsg-7+b1) ... Setting up libopenmpi3:amd64 (3.1.3-11) ... Setting up hyphy-mpi (2.3.14+dfsg-1) ... Setting up blast2 (1:2.8.1-1+deb10u1) ... Setting up openmpi-bin (3.1.3-11) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up phyml (3:3.3.20180621-2) ... Setting up dh-autoreconf (19) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up libwww-perl (6.36-2) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libxml-parser-perl (2.44-4) ... Setting up libxml-twig-perl (1:3.50-1.1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/bioperl-run-1.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.2-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bioperl-run-1.7.2' dh_auto_configure -- --install_scripts perl Build.PL --installdirs vendor --config "optimize=-g -O2 -ffile-prefix-map=/build/bioperl-run-1.7.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/bioperl-run-1.7.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts Checking prerequisites... recommends: * Bio::FeatureIO is not installed * Config::Any is not installed * File::Sort is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. 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 '1.007002' make[1]: Leaving directory '/build/bioperl-run-1.7.2' dh_auto_build perl Build Building BioPerl-Run debian/rules override_dh_auto_test make[1]: Entering directory '/build/bioperl-run-1.7.2' mkdir t.skip for t in Blat Eponine Glimmer2 Gumby RepeatMasker Phyml Hyphy BWA 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 \ HOME_4_TCOFFEE=/tmp COILSDIR=/usr/share/ncoils/ \ dh_auto_test --no-parallel perl Build test --verbose 1 AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: t/data/cysprot.fa Computing posterior matrices Building DAG Starting the sequence annealing process Creating candidate edge list Adding edges to the DAG AMAP version AMAP.2.2 - align multiple protein sequences and print to standard output PROBCONS Written by Chuong Do AMAP algorithm implemented by Ariel Schwartz Using parameter set: initDistrib[] = { 0.400000006 0.3000000119 0.3000000119 } gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } Loading sequence file: /tmp/4_YCgTJlHM 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/AnalysisFactory_soap.t ...... skipped: Network tests have not been requested t/Analysis_soap.t ............. skipped: Network tests have not been requested t/BEDTools.t .................. skipped: The optional module Bio::Tools::Run::BEDTools (or dependencies thereof) was not installed t/Bowtie.t .................... 1..61 ok 1 - make a factory using command 'assemble' 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 - set an exclusive group parameter ok 16 - parameter really set ok 17 - set an incompatible parameter ok 18 - parameter really set ok 19 - original exclusive parameter really unset ok 20 - parameters changed ok 21 - all available options ok 22 - available parameters ok 23 - available switches ok 24 - parameters changed ok 25 - all available options ok 26 - available parameters ok 27 - available switches ok 28 - get_parameters correct ok 29 - command attribute set ok 30 - internal command array set ok 31 - internal prefix hash set ok 32 - commands filtered by prefix ok 33 - translate_params: options correct ok 34 - make unpaired reads bowtie factory ok 35 - read raw sequence ok 36 - bowtie success ok 37 - read fasta sequence ok 38 - bowtie success ok 39 - read fastq sequence ok 40 - bowtie success ok 41 - make paired reads bowtie factory ok 42 - read paired fasta sequence ok 43 - bowtie success ok 44 - read paired fastq sequence ok 45 - bowtie success ok 46 - make a single alignment factory ok 47 - command attribute set ok 48 - seed mismatch param set ok 49 - seed length param set ok 50 - quality mismatch param set ok 51 - return type set ok 52 - make file based alignment ok 53 - make readable output ok 54 - number of alignments ok 55 - change mode ok 56 - make a crossbow alignment factory ok 57 - command attribute set ok 58 - make a single alignment factory ok 59 ok 60 - make variable based alignment ok 61 - bowtie success ok # Required executable for Bio::Tools::Run::Cap3 is not present t/Cap3.t ...................... 1..91 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Cap3' isa 'Bio::Tools::Run::Cap3' ok 4 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 ok 48 ok 49 ok 50 ok 51 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 52 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 53 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 54 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 55 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 56 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 57 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 58 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 59 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 60 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 61 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 62 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 63 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 64 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 65 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 66 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 67 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 68 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 69 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 70 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 71 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 72 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 73 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 74 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 75 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 76 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 77 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 78 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 79 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 80 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 81 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 82 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 83 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 84 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 85 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 86 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 87 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 88 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 89 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 90 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok 91 # skip Required executable for Bio::Tools::Run::Cap3 is not present ok # You named your test '71'. You shouldn't use numbers for your test names. # Very confusing. # You named your test '91'. You shouldn't use numbers for your test names. # Very confusing. t/Coil.t ...................... 1..6 ok 1 - use Bio::Tools::Run::Coil; ok 2 - use Bio::SeqIO; ok 3 ok 4 ok 5 - 71 ok 6 - 91 ok t/Consense.t .................. 1..8 ok 1 - use Bio::Tools::Run::Phylo::Phylip::Consense; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::Consense' isa 'Bio::Tools::Run::Phylo::Phylip::Consense' ok 4 - could not set rooted option consense: can't find input tree file "intree" Please enter a new file name>  Consensus tree program, version 3.697 Settings for this run: C Consensus type (MRe, strict, MR, Ml): Majority rule (extended) O Outgroup root: No, use as outgroup species 1 R Trees to be treated as Rooted: No T Terminal type (IBM PC, ANSI, none): ANSI 1 Print out the sets of species: Yes 2 Print indications of progress of run: Yes 3 Print out tree: Yes 4 Write out trees onto tree file: Yes Are these settings correct? (type Y or the letter for one to change)  Consensus tree program, version 3.697 Settings for this run: C Consensus type (MRe, strict, MR, Ml): Majority rule (extended) R Trees to be treated as Rooted: Yes T Terminal type (IBM PC, ANSI, none): ANSI 1 Print out the sets of species: Yes 2 Print indications of progress of run: Yes 3 Print out tree: Yes 4 Write out trees onto tree file: Yes Are these settings correct? (type Y or the letter for one to change) Consensus tree written to file "outtree" Output written to file "outfile" Done. ok 5 ok 6 ok 7 ok 8 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 t/DrawGram.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawGram; ok 2 - use Bio::TreeIO; ok 3 ok 4 ok 5 ok 6 ok t/DrawTree.t .................. 1..6 ok 1 - use Bio::Tools::Run::Phylo::Phylip::DrawTree; ok 2 - use Bio::TreeIO; ok 3 ok 4 ok 5 ok 6 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 # Required executable for Bio::Tools::Run::Phylo::FastTree is not present 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 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::FastTree is not present 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 version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. reading from STDIN: found 0 sequences reading from t/data/cysprot.fa: found 7 sequences Output file: /tmp/o1r4U7rTIk/GEjQwdNLQG, in (null) format. Aligning 7 protein sequences with these parameters: 54.94940948 gap open penalty 8.52492046 gap extension 4.42409992 terminal gap penalty 0.20000000 bonus Alignment will be written to file:'/tmp/o1r4U7rTIk/GEjQwdNLQG'. Distance Calculation: 5 percent done 10 percent done 14 percent done 19 percent done 24 percent done 29 percent done 33 percent done 38 percent done 43 percent done 48 percent done 52 percent done 57 percent done 62 percent done 67 percent done 71 percent done 76 percent done 81 percent done 86 percent done 90 percent done 95 percent done 100 percent done Alignment: 0 percent done 14 percent done 29 percent done 43 percent done 57 percent done 71 percent done 100 percent done Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann Kalign is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. reading from STDIN: found 0 sequences reading from /tmp/Xg4Nr5NDgy: found 7 sequences Output file: /tmp/o1r4U7rTIk/GEjQwdNLQG, in (null) format. Aligning 7 protein sequences with these parameters: 54.94940948 gap open penalty 8.52492046 gap extension 4.42409992 terminal gap penalty 0.20000000 bonus Alignment will be written to file:'/tmp/o1r4U7rTIk/GEjQwdNLQG'. Distance Calculation: 5 percent done 10 percent done 14 percent done 19 percent done 24 percent done 29 percent done 33 percent done 38 percent done 43 percent done 48 percent done 52 percent done 57 percent done 62 percent done 67 percent done 71 percent done 76 percent done 81 percent done 86 percent done 90 percent done 95 percent done 100 percent done Alignment: 0 percent done 14 percent done 29 percent done 43 percent done 57 percent done 71 percent done 100 percent done t/Kalign.t .................... 1..8 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 8 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 Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845, line 1. t/Maq.t ....................... 1..52 ok 1 - make a factory using command 'assemble' 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 - make fasta2bfa conversion factory ok 27 - convert refseq to bfa ok 28 - maq success ok 29 - make fastq2bfq conversion factory ok 30 - convert r1.fq to bfa ok 31 - maq success ok 32 - convert r2.fq to bfa ok 33 - maq success ok 34 - make map factory ok 35 - map single-end reads ok 36 - map paired-end reads ok 37 - make mapmerge factory ok 38 - merge maps ok 39 - make assemble factory ok 40 - assemble consensus ok 41 - make mapview converter ok 42 - convert mmap ok 43 - make consensus->fastq converter ok 44 - convert consensus -> fastq ok 45 - make an assembly factory ok 46 - command attribute set ok 47 - map param set ok 48 - asm param set ok 49 - c2q param set ok 50 - make full assy ok 51 - number of contigs ok 52 - number of singlets ok t/Match.t ..................... skipped: The optional module Config::Any (or dependencies thereof) was not installed # 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::Meme is not present t/Meme.t ...................... 1..25 ok 1 - use Bio::Tools::Run::Meme; ok 2 - An object of class 'Bio::Tools::Run::Meme' isa 'Bio::Tools::Run::Meme' ok 3 - has a created method not in args ok 4 - mod param was set ok 5 - dna 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::Meme is not present ok 9 # skip Required executable for Bio::Tools::Run::Meme is not present ok 10 # skip Required executable for Bio::Tools::Run::Meme is not present ok 11 # skip Required executable for Bio::Tools::Run::Meme is not present ok 12 # skip Required executable for Bio::Tools::Run::Meme is not present ok 13 # skip Required executable for Bio::Tools::Run::Meme is not present ok 14 # skip Required executable for Bio::Tools::Run::Meme is not present ok 15 # skip Required executable for Bio::Tools::Run::Meme is not present ok 16 # skip Required executable for Bio::Tools::Run::Meme is not present ok 17 # skip Required executable for Bio::Tools::Run::Meme is not present ok 18 # skip Required executable for Bio::Tools::Run::Meme is not present ok 19 # skip Required executable for Bio::Tools::Run::Meme is not present ok 20 # skip Required executable for Bio::Tools::Run::Meme is not present ok 21 # skip Required executable for Bio::Tools::Run::Meme is not present ok 22 # skip Required executable for Bio::Tools::Run::Meme is not present ok 23 # skip Required executable for Bio::Tools::Run::Meme is not present ok 24 # skip Required executable for Bio::Tools::Run::Meme is not present ok 25 # skip Required executable for Bio::Tools::Run::Meme is not present ok # Required executable for Bio::Tools::Run::Minimo is not present t/Minimo.t .................... 1..72 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Minimo' isa 'Bio::Tools::Run::Minimo' ok 4 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 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 26 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 27 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 28 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 29 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 30 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 31 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 32 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 33 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 34 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 35 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 36 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 37 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 38 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 39 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 40 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 41 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 42 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 43 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 44 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 45 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 46 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 47 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 48 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 49 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 50 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 51 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 52 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 53 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 54 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 55 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 56 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 57 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 58 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 59 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 60 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 61 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 62 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 63 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 64 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 65 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 66 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 67 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 68 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 69 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 70 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 71 # skip Required executable for Bio::Tools::Run::Minimo is not present ok 72 # skip Required executable for Bio::Tools::Run::Minimo is not present ok # Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present t/Molphy.t .................... 1..10 ok 1 - use Bio::Tools::Phylo::Molphy; ok 2 - use Bio::Tools::Run::Phylo::Molphy::ProtML; ok 3 - use Bio::AlignIO; ok 4 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 5 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 6 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present ok t/Muscle.t .................... 1..8 ok 1 - use Bio::Tools::Run::Alignment::Muscle; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Bio::Root::IO; ok 5 - use POSIX; ok 6 ok 7 - Code tested only on muscle versions > 3.6 ok 8 - log file ok 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 - An object of class 'Bio::Tools::Run::Phylo::Phylip::Neighbor' isa 'Bio::Tools::Run::Phylo::Phylip::Neighbor' ok 4 - couldn't set factory parameter ok 5 - couldn't set factory parameter ok 6 - couldn't set factory parameter ok 7 - couldn't set factory parameter ok 8 - couldn't set factory parameter ok 9 - couldn't set factory parameter ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - failed creating tree by neighbor protdist: can't find input file "infile" Please enter a new file name>  Protein distance algorithm, version 3.697 Settings for this run: P Use JTT, PMB, PAM, Kimura, categories model? Jones-Taylor-Thornton matrix G Gamma distribution of rates among positions? No C One category of substitution rates? Yes W Use weights for positions? No M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI)? ANSI 1 Print out the data at start of run No 2 Print indications of progress of run Yes Are these settings correct? (type Y or the letter for one to change) Computing distances: S01 S02 . S03 .. S04 ... S05 .... S06 ..... S07 ...... S08 ....... S09 ........ S10 ......... S11 .......... S12 ........... S13 ............ S14 ............. Output written to file "outfile" Done. ok 18 - failed to assign serial names ok 19 - failed to restore original names ok # Required executable for Bio::Tools::Run::Newbler is not present t/Newbler.t ................... 1..98 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Newbler' isa 'Bio::Tools::Run::Newbler' ok 4 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 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 54 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 55 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 56 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 57 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 58 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 59 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 60 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 61 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 62 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 63 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 64 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 65 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 66 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 67 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 68 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 69 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 70 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 71 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 72 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 73 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 74 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 75 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 76 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 77 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 78 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 79 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 80 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 81 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 82 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 83 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 84 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 85 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 86 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 87 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 88 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 89 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 90 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 91 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 92 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 93 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 94 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 95 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 96 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 97 # skip Required executable for Bio::Tools::Run::Newbler is not present ok 98 # skip Required executable for Bio::Tools::Run::Newbler 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 # Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present 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 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present ok t/PhastCons.t ................. skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Phrap is not present t/Phrap.t ..................... 1..127 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::Phrap' isa 'Bio::Tools::Run::Phrap' ok 4 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 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 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 90 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 91 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 92 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 93 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 94 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 95 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 96 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 97 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 98 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 99 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 100 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 101 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 102 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 103 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 104 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 105 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 106 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 107 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 108 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 109 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 110 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 111 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 112 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 113 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 114 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 115 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 116 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 117 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 118 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 119 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 120 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 121 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 122 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 123 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 124 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 125 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 126 # skip Required executable for Bio::Tools::Run::Phrap is not present ok 127 # skip Required executable for Bio::Tools::Run::Phrap 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 ................... skipped: The optional module Clone (or dependencies thereof) was not installed # Required executable for Bio::Tools::Run::Prints is not present t/Prints.t .................... 1..7 ok 1 - use Bio::Tools::Run::Prints; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Prints' isa 'Bio::Tools::Run::Prints' ok 5 # skip Required executable for Bio::Tools::Run::Prints is not present ok 6 # skip Required executable for Bio::Tools::Run::Prints is not present ok 7 # skip Required executable for Bio::Tools::Run::Prints is not present ok # Required executable for Bio::Tools::Run::Alignment::Probalign is not present t/Probalign.t ................. 1..13 ok 1 - use Bio::Tools::Run::Alignment::Probalign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - use Cwd; ok 5 - use POSIX; ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 9 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 10 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 11 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 12 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok 13 # skip Required executable for Bio::Tools::Run::Alignment::Probalign is not present ok PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: t/data/cysprot.fa Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) PROBCONS version 1.12 - align multiple protein sequences and print to standard output Written by Chuong Do Using parameter set: initDistrib[] = { 0.6814756989 8.615339902e-05 8.615339902e-05 0.1591759622 0.1591759622 } gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } Loading sequence file: /tmp/C9vxkdPN53 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/QPb0DkaFWy 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/rKfnM84MAf Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) t/Probcons.t .................. 1..11 ok 1 - use Bio::Tools::Run::Alignment::Probcons; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - Code tested only on probcons versions > 1.09 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok # Required executable for Bio::Tools::Run::Profile is not present t/Profile.t ................... 1..7 ok 1 - use Bio::Tools::Run::Profile; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::Profile' isa 'Bio::Tools::Run::Profile' ok 5 # skip Required executable for Bio::Tools::Run::Profile is not present ok 6 # skip Required executable for Bio::Tools::Run::Profile is not present ok 7 # skip Required executable for Bio::Tools::Run::Profile is not present ok t/Promoterwise.t .............. 1..9 ok 1 - use Bio::Tools::Run::Promoterwise; ok 2 - use Bio::Seq; ok 3 - An object of class 'Bio::Tools::Run::Promoterwise' isa 'Bio::Tools::Run::Promoterwise' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok t/ProtDist.t .................. 1..14 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtDist; ok 2 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 12 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 13 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 14 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok t/ProtPars.t .................. 1..11 ok 1 - use Bio::Tools::Run::Phylo::Phylip::ProtPars; ok 2 - An object of class 'Bio::Tools::Run::Phylo::Phylip::ProtPars' isa 'Bio::Tools::Run::Phylo::Phylip::ProtPars' ok 3 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 4 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 5 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 6 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 7 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 8 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 9 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 10 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok 11 # skip The optional module Bio::Tools::Run::Alignment::Clustalw (or dependencies thereof) was not installed ok # Required executable for Bio::Tools::Run::Pseudowise is not present t/Pseudowise.t ................ 1..18 ok 1 - use Bio::Tools::Run::Pseudowise; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 ok 5 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 6 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 7 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 8 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 9 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 10 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 11 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 12 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 13 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 14 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 15 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 16 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 17 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok 18 # skip Required executable for Bio::Tools::Run::Pseudowise is not present ok # Required executable for Bio::Tools::Run::Phylo::QuickTree is not present t/QuickTree.t ................. 1..13 ok 1 - use Bio::Tools::Run::Phylo::QuickTree; ok 2 - use Bio::AlignIO; ok 3 - Found input file ok 4 - An object of class 'Bio::Tools::Run::Phylo::QuickTree' isa 'Bio::Tools::Run::Phylo::QuickTree' ok 5 - program_dir returned correct default ok 6 - Correct exe default name ok 7 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 8 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 9 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 10 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 11 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 12 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok 13 # skip Required executable for Bio::Tools::Run::Phylo::QuickTree is not present ok t/Raxml.t ..................... 1..12 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::Raxml; ok 3 - use Bio::AlignIO; ok 4 - Make the object ok 5 - An object of class 'Bio::Tools::Run::Phylo::Raxml' isa 'Bio::Tools::Run::Phylo::Raxml' ok 6 - Tree is defined ok 7 - Tree is defined ok 8 - File containing best tree exists in tempdir ok 9 - Tree is defined ok 10 - Tree is defined ok 11 - Number of nodes is correct ok 12 - Tree is defined ok # DB and mask make tests # run BLAST methods t/SABlastPlus.t ............... 1..71 ok 1 - use Bio::Tools::Run::StandAloneBlastPlus; ok 2 - use Bio::Tools::Run::WrapperBase; ok 3 - use Bio::Tools::Run::WrapperBase::CommandExts; ok 4 - BlastPlus factory ok 5 - make factory ok 6 - test db made with fasta ok 7 - temp db ok 8 - right type ok 9 ok 10 - named db made ok 11 - check_db ok 12 - correct name ok 13 - dbinfo hash returned ok 14 - correct type ok 15 - windowmasker mask made ok 16 - dustmasker mask made ok 17 - check_db with arg ok 18 - db_info with arg ok 19 - protein db made ok 20 - correct type ok 21 - segmasker mask made ok 22 - segmasker mask made; blastdb as data ok 23 ok 24 - protein db made with pre-built mask ok 25 - db_info records mask info ok 26 ok 27 - mask built and db made on construction (windowmasker) ok 28 ok 29 - mask built and db made on construction (segmasker) ok 30 ok 31 - mask built and db made on construction (dustmasker) ok 32 ok 33 ok 34 ok 35 - make db from Bio::SeqIO ok 36 ok 37 - make db from Bio::AlignIO ok 38 ok 39 - make db from \@seqs ok 40 - dbdir : ./a/b; dbname : test; create ok 41 - make db ok 42 ok 43 ok 44 ok 45 ok 46 - run blastn ok 47 - default hit limit ok 48 - return more alignments (arg spec) ok 49 - got more hits ok 50 - run blastn with Bio::Seq query ok 51 - run tblastn ok 52 - tblastn hits ok 53 - run tblastx ok 54 - tblastx hits ok 55 ok 56 - run blastp ok 57 - blastp hits ok 58 - bl2seq (blastn) ok 59 - got hit ok 60 - bl2seq (tblastx) ok 61 - got hit ok 62 - bl2seq (blastx) ok 63 - got hit ok 64 - bl2seq (blastp) ok 65 - no hit ok 66 - bl2seq (blastp) ok 67 - got hit ok 68 - bl2seq (tblastx) - multiple outfmt options ok 69 - bl2seq (tblastx) - multiple outfmt options (use method arg) ok 70 - bl2seq (tblastx) - multiple outfmt options (no explict quotes should also work) ok 71 - bl2seq (tblastx) - multiple outfmt options (a single format number in quotes ok # Required executable for Bio::Tools::Run::Phylo::SLR is not present t/SLR.t ....................... 1..7 ok 1 - use Bio::Root::IO; ok 2 - use Bio::Tools::Run::Phylo::SLR; ok 3 - use Bio::AlignIO; ok 4 - use Bio::TreeIO; ok 5 ok 6 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok 7 # skip Required executable for Bio::Tools::Run::Phylo::SLR is not present ok 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 t/SeqBoot.t ................... 1..9 ok 1 - use Bio::Tools::Run::Phylo::Phylip::SeqBoot; ok 2 - use Bio::AlignIO; ok 3 - An object of class 'Bio::Tools::Run::Phylo::Phylip::SeqBoot' isa 'Bio::Tools::Run::Phylo::Phylip::SeqBoot' ok 4 - couldn't set datatype parameter ok 5 - coludn't set number of replicates ok 6 ok 7 ok 8 - ailed to assign serial names ok 9 - fail to restore original names 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::TigrAssembler is not present # Required executable for Bio::Tools::Run::TigrAssembler is not present t/TigrAssembler.t ............. 1..88 ok 1 - use Bio::SeqIO; ok 2 ok 3 - An object of class 'Bio::Tools::Run::TigrAssembler' isa 'Bio::Tools::Run::TigrAssembler' ok 4 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 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 38 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 39 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 40 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 41 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 42 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 43 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 44 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 45 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 46 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 47 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 48 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 49 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 50 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 51 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 52 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 53 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 54 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 55 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 56 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 57 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 58 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 59 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 60 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 61 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 62 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 63 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 64 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 65 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 66 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 67 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 68 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 69 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 70 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 71 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 72 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 73 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 74 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 75 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 76 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 77 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 78 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 79 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 80 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 81 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 82 ok 83 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 84 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 85 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 86 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 87 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok 88 # skip Required executable for Bio::Tools::Run::TigrAssembler is not present ok # Required executable for Bio::Tools::Run::Tmhmm is not present t/Tmhmm.t ..................... 1..9 ok 1 - use Bio::Tools::Run::Tmhmm; ok 2 - use Bio::SeqIO; ok 3 - An object of class 'Bio::Tools::Run::Tmhmm' isa 'Bio::Tools::Run::Tmhmm' ok 4 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 5 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 6 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 7 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 8 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok 9 # skip Required executable for Bio::Tools::Run::Tmhmm is not present ok t/TribeMCL.t .................. 1..24 ok 1 - use Bio::Tools::Run::TribeMCL; ok 2 - use Bio::SearchIO; ok 3 - An object of class 'Bio::Tools::Run::TribeMCL' isa 'Bio::Tools::Run::TribeMCL' ok 4 # skip Tribe Matrix program not found. Skipping tests... ok 5 # skip Tribe Matrix program not found. Skipping tests... ok 6 # skip Tribe Matrix program not found. Skipping tests... ok 7 # skip Tribe Matrix program not found. Skipping tests... ok 8 # skip Tribe Matrix program not found. Skipping tests... ok 9 # skip Tribe Matrix program not found. Skipping tests... ok 10 # skip Tribe Matrix program not found. Skipping tests... ok 11 # skip Tribe Matrix program not found. Skipping tests... ok 12 # skip Tribe Matrix program not found. Skipping tests... ok 13 # skip Tribe Matrix program not found. Skipping tests... ok 14 # skip Tribe Matrix program not found. Skipping tests... ok 15 # skip Tribe Matrix program not found. Skipping tests... ok 16 # skip Tribe Matrix program not found. Skipping tests... ok 17 # skip Tribe Matrix program not found. Skipping tests... ok 18 # skip Tribe Matrix program not found. Skipping tests... ok 19 # skip Tribe Matrix program not found. Skipping tests... ok 20 # skip Tribe Matrix program not found. Skipping tests... ok 21 # skip Tribe Matrix program not found. Skipping tests... ok 22 # skip Tribe Matrix program not found. Skipping tests... ok 23 # skip Tribe Matrix program not found. Skipping tests... ok 24 # skip Tribe Matrix program not found. Skipping tests... ok t/Vista.t ..................... 1..7 ok 1 - use Bio::Tools::Run::Vista; ok 2 - use Bio::AlignIO; ok 3 # skip Skipping due to old java version ok 4 # skip Skipping due to old java version ok 5 # skip Skipping due to old java version ok 6 # skip Skipping due to old java version ok 7 # skip Skipping due to old java version ok # Required executable for Bio::Tools::Run::Alignment::Gmap is not present t/gmap-run.t .................. 1..8 ok 1 - use Bio::Tools::Run::Alignment::Gmap; ok 2 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 3 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 4 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 5 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 6 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 7 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok 8 # skip Required executable for Bio::Tools::Run::Alignment::Gmap is not present ok # Required executable for Bio::Tools::Run::tRNAscanSE is not present t/tRNAscanSE.t ................ 1..12 ok 1 - use Bio::Tools::Run::tRNAscanSE; ok 2 - use Bio::Root::IO; ok 3 - use Bio::Seq; ok 4 - An object of class 'Bio::Tools::Run::tRNAscanSE' isa 'Bio::Tools::Run::tRNAscanSE' ok 5 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 6 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 7 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 8 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok All tests successful. Files=70, Tests=1639, 77 wallclock secs ( 0.49 usr 0.14 sys + 69.59 cusr 7.99 csys = 78.21 CPU) Result: PASS mv t.skip/* t rm -rf t.skip make[1]: Leaving directory '/build/bioperl-run-1.7.2' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install perl Build install --destdir /build/bioperl-run-1.7.2/debian/tmp --create_packlist 0 Building BioPerl-Run Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man1/bp_run_protdist.pl.1p Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man1/bp_run_neighbor.pl.1p Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man1/bp_papplmaker.pl.1p Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man1/bp_panalysis.pl.1p Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man1/bp_multi_hmmsearch.pl.1p Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man1/bp_bioperl_application_installer.pl.1p Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/tRNAscanSE.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Vista.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/TribeMCL.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Tmhmm.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/TigrAssembler.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneWUBlast.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlast.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Simprot.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Signalp.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Seg.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/RepeatMasker.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/RNAMotif.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Pseudowise.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Promoterwise.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Profile.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Prints.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primer3.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Primate.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phrap.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Newbler.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Minimo.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Meme.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Mdust.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Match.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Maq.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/MCS.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Infernal.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Hmmer.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Glimmer.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genscan.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genewise.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Genemark.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Eponine.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Ensembl.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/ERPIN.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSacd.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/EMBOSSApplication.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Coil.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Cap3.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Bowtie.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/BWA.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/AssemblerBase.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Samtools/Config.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Semphy.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/SLR.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Raxml.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/QuickTree.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phyml.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/PhyloBase.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/LVB.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gumby.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Gerp.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/FastTree.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Maq/Config.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Bowtie/Config.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/BlastPlus/Config.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/BWA/Config.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/BEDTools/Config.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Analysis/soap.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Sim4.pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/perl5/Bio/Tools/Run/Alignment/Proda.pm Installing 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/build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm Installing /build/bioperl-run-1.7.2/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/bioperl-run-1.7.2/debian/tmp/usr/bin/bp_multi_hmmsearch.pl Installing /build/bioperl-run-1.7.2/debian/tmp/usr/bin/bp_bioperl_application_installer.pl Installing /build/bioperl-run-1.7.2/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/bioperl-run-1.7.2/debian/tmp/usr/bin/bp_run_protdist.pl Installing /build/bioperl-run-1.7.2/debian/tmp/usr/bin/bp_papplmaker.pl dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.2-4_all.deb'. dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.2-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bioperl-run_1.7.2-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/51221 and its subdirectories I: Current time: Thu Jan 13 19:59:16 -12 2022 I: pbuilder-time-stamp: 1642147156