sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | bio-tradis 1.4.5+dfsg2-2 (amd64) Sat, 14 Sep 2024 22:54:32 +0000 | +==============================================================================+ Package: bio-tradis Version: 1.4.5+dfsg2-2 Source Version: 1.4.5+dfsg2-2 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-a34b4292-9d15-45a5-a781-58cfec130687' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bio-tradis_1.4.5+dfsg2-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bio-tradis_1.4.5+dfsg2-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bio-tradis-IG8inV/resolver-nwo5bP' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://localhost:3142/debian sid InRelease [202 kB] Get:3 http://deb.debian.org/debian unstable InRelease [202 kB] Get:4 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [17.4 kB] Get:6 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [17.4 kB] Fetched 570 kB in 6s (89.9 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bio-tradis_1.4.5+dfsg2-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/bio-tradis-IG8inV/bio-tradis-1.4.5+dfsg2' with '<>' I: NOTICE: Log filtering will replace 'build/bio-tradis-IG8inV' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot, libbio-perl-perl, libenv-path-perl, libexception-class-perl, libmoose-perl, libtest-exception-perl, libtest-files-perl, libtest-most-perl, libtest-simple-perl, libtext-csv-perl, libtry-tiny-perl, perl, samtools, smalt, tabix, bwa Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot, libbio-perl-perl, libenv-path-perl, libexception-class-perl, libmoose-perl, libtest-exception-perl, libtest-files-perl, libtest-most-perl, libtest-simple-perl, libtext-csv-perl, libtry-tiny-perl, perl, samtools, smalt, tabix, bwa dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [868 B] Get:5 copy:/<>/apt_archive ./ Packages [880 B] Fetched 2357 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils bwa debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libalgorithm-c3-perl libalgorithm-diff-perl libarchive-zip-perl libb-hooks-op-check-perl libbambamc0 libbio-perl-perl libbrotli1 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconst-fast-perl libcurl3t64-gnutls libdata-compare-perl libdata-optlist-perl libdata-stag-perl libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdynaloader-functions-perl libelf1t64 libenv-path-perl libeval-closure-perl libexception-class-perl libfakeroot libfile-chdir-perl libfile-find-rule-perl libfile-stripnondeterminism-perl libgssapi-krb5-2 libhts3t64 libhtscodecs2 libicu72 libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1t64 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libpipeline1 libpsl5t64 librtmp1 libssh2-1t64 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-files-perl libtest-most-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libtool libtry-tiny-perl libuchardet0 libxml2 m4 man-db po-debconf samtools sensible-utils smalt tabix Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff bioperl libxml-sax-expatxs-perl libscalar-properties-perl krb5-doc krb5-user libscalar-number-perl libtool-doc gfortran | fortran95-compiler gcj-jdk libsub-name-perl m4-doc apparmor less www-browser libmail-box-perl cwltool Recommended packages: curl | wget | lynx libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl libclass-c3-xs-perl ca-certificates perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libdevel-lexalias-perl libarchive-cpio-perl krb5-locales libdevel-partialdump-perl libgpm2 libunicode-utf8-perl publicsuffix libmodule-pluggable-perl libtext-csv-xs-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils bwa debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libalgorithm-c3-perl libalgorithm-diff-perl libarchive-zip-perl libb-hooks-op-check-perl libbambamc0 libbio-perl-perl libbrotli1 libcapture-tiny-perl libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconst-fast-perl libcurl3t64-gnutls libdata-compare-perl libdata-optlist-perl libdata-stag-perl libdebhelper-perl libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdynaloader-functions-perl libelf1t64 libenv-path-perl libeval-closure-perl libexception-class-perl libfakeroot libfile-chdir-perl libfile-find-rule-perl libfile-stripnondeterminism-perl libgssapi-krb5-2 libhts3t64 libhtscodecs2 libicu72 libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1t64 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnumber-compare-perl libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libpipeline1 libpsl5t64 librtmp1 libssh2-1t64 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-files-perl libtest-most-perl libtest-warn-perl libtest2-suite-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl libtool libtry-tiny-perl libuchardet0 libxml2 m4 man-db po-debconf samtools sbuild-build-depends-main-dummy sensible-utils smalt tabix 0 upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 28.3 MB/29.2 MB of archives. After this operation, 104 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get:2 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [976 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.3 kB] Get:4 file:/srv/reprepro perl-5.40/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.1 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:6 file:/srv/reprepro perl-5.40/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.4 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:8 file:/srv/reprepro perl-5.40/main amd64 libclass-load-xs-perl amd64 0.10-2+b4 [14.1 kB] Get:9 file:/srv/reprepro perl-5.40/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB] Get:10 file:/srv/reprepro perl-5.40/main amd64 libclone-perl amd64 0.47-1+b1 [13.8 kB] Get:11 file:/srv/reprepro perl-5.40/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b4 [20.7 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:17 file:/srv/reprepro perl-5.40/main amd64 libmoose-perl amd64 2.2207-1+b2 [766 kB] Get:18 file:/srv/reprepro perl-5.40/main amd64 libpadwalker-perl amd64 2.5-1+b6 [18.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:34 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:54 http://deb.debian.org/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:65 http://deb.debian.org/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:66 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:69 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.0-2 [359 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:80 http://deb.debian.org/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:81 http://deb.debian.org/debian unstable/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdata-compare-perl all 1.29-1 [19.6 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get:85 http://deb.debian.org/debian unstable/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get:87 http://deb.debian.org/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libenv-path-perl all 0.19-4 [19.1 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libfile-chdir-perl all 0.1008-1.2 [11.9 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get:96 http://deb.debian.org/debian unstable/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libtest2-suite-perl all 0.000163-1 [383 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libtest-files-perl all 0.26-1 [21.6 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libtext-csv-perl all 2.04-1 [112 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 smalt amd64 0.7.6-13 [115 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-1 [483 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.3 MB in 0s (131 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 22986 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../002-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../005-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up bwa (0.7.18-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libpadwalker-perl (2.5-1+b6) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libtest2-suite-perl (0.000163-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libio-string-perl (1.08-4) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b4) ... Setting up autotools-dev (20220109.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libtext-diff-perl (1.45-2) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libenv-path-perl (0.19-4) ... Setting up libbambamc0:amd64 (0.0.50-6+b1) ... Setting up autopoint (0.22.5-2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libfile-chdir-perl (0.1008-1.2) ... Setting up sensible-utils (0.0.24) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up tabix (1.20+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libtext-csv-perl (2.04-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up smalt (0.7.6-13) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ... Setting up libdata-compare-perl (1.29-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up libcurl3t64-gnutls:amd64 (8.10.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmodule-runtime-perl (0.016-2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up debhelper (13.20) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libtest-files-perl (0.26-1) ... Setting up libclass-load-perl (0.25-2) ... Setting up samtools (1.20-3) ... Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b4) ... Setting up libmoose-perl:amd64 (2.2207-1+b2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bwa_0.7.18-1 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-4 cpp-14-x86-64-linux-gnu_14.2.0-4 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-4 g++-14-x86-64-linux-gnu_14.2.0-4 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-4 gcc-14-base_14.2.0-4 gcc-14-x86-64-linux-gnu_14.2.0-4 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 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libsub-exporter-progressive-perl_0.001013-3 libsub-install-perl_0.929-1 libsub-uplevel-perl_0.2800-3 libsystemd0_256.6-1 libtasn1-6_4.19.0-3+b2 libtest-deep-perl_1.204-1 libtest-differences-perl_0.71-1 libtest-exception-perl_0.43-3 libtest-files-perl_0.26-1 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtest2-suite-perl_0.000163-1 libtext-csv-perl_2.04-1 libtext-diff-perl_1.45-2 libtext-glob-perl_0.11-3 libtinfo6_6.5-2 libtool_2.4.7-7 libtry-tiny-perl_0.32-1 libtsan2_14.2.0-4 libubsan1_14.2.0-4 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunistring5_1.2-1 libuuid1_2.40.2-8 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 smalt_0.7.6-13 sysvinit-utils_3.10-2 tabix_1.20+ds-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-8 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bio-tradis Binary: bio-tradis Architecture: all Version: 1.4.5+dfsg2-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/sanger-pathogens/Bio-Tradis Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git Build-Depends: debhelper-compat (= 13) Build-Depends-Indep: libbio-perl-perl, libenv-path-perl, libexception-class-perl, libmoose-perl, libtest-exception-perl, libtest-files-perl, libtest-most-perl, libtest-simple-perl, libtext-csv-perl, libtry-tiny-perl, perl, samtools, smalt, tabix, bwa Package-List: bio-tradis deb perl optional arch=all Checksums-Sha1: 8dc680ab6fafa5205030a15c0e8986fb0428f671 7876340 bio-tradis_1.4.5+dfsg2.orig.tar.xz 2a1eadb27d76c6ec3c148df87ddbaa0d885d931a 6096 bio-tradis_1.4.5+dfsg2-2.debian.tar.xz Checksums-Sha256: 2ae1058a077eb8753dea148079c82ac8335c1488886cfbf2a6fe534b7f7c076e 7876340 bio-tradis_1.4.5+dfsg2.orig.tar.xz 32dd5c211c5e7a1180e8050b1da7c0d0b12c5531bd11c61eb2fc837e8f92265c 6096 bio-tradis_1.4.5+dfsg2-2.debian.tar.xz Files: c31ec74b7db82cd7bf39386caf70859f 7876340 bio-tradis_1.4.5+dfsg2.orig.tar.xz b60da3af535d0d1ca443981c7c214475 6096 bio-tradis_1.4.5+dfsg2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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No public key dpkg-source: warning: cannot verify inline signature for ./bio-tradis_1.4.5+dfsg2-2.dsc: no acceptable signature found dpkg-source: info: extracting bio-tradis in /<> dpkg-source: info: unpacking bio-tradis_1.4.5+dfsg2.orig.tar.xz dpkg-source: info: unpacking bio-tradis_1.4.5+dfsg2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying samtools1.10 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bio-tradis_1.4.5+dfsg2-2 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bio-tradis_1.4.5+dfsg2-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-a34b4292-9d15-45a5-a781-58cfec130687 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package bio-tradis dpkg-buildpackage: info: source version 1.4.5+dfsg2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bio-tradis using existing ./bio-tradis_1.4.5+dfsg2.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bio-tradis in bio-tradis_1.4.5+dfsg2-2.debian.tar.xz dpkg-source: info: building bio-tradis in bio-tradis_1.4.5+dfsg2-2.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro" Checking if your kit is complete... Warning: the following files are missing in your kit: BioTraDISTutorial.pdf Please inform the author. Generating a Unix-style Makefile Writing Makefile for Bio::Tradis Writing MYMETA.yml and MYMETA.json dh_auto_build make -j2 make[1]: Entering directory '/<>' cp lib/Bio/Tradis/Exception.pm blib/lib/Bio/Tradis/Exception.pm cp lib/Bio/Tradis.pm blib/lib/Bio/Tradis.pm cp lib/Bio/Tradis/AddTagsToSeq.pm blib/lib/Bio/Tradis/AddTagsToSeq.pm cp lib/Bio/Tradis/TradisPlot.pm blib/lib/Bio/Tradis/TradisPlot.pm cp lib/Bio/Tradis/Analysis/Exceptions.pm blib/lib/Bio/Tradis/Analysis/Exceptions.pm cp lib/Bio/Tradis/CommandLine/AddTags.pm blib/lib/Bio/Tradis/CommandLine/AddTags.pm cp lib/Bio/Tradis/FilterTags.pm blib/lib/Bio/Tradis/FilterTags.pm cp lib/Bio/Tradis/Parser/Bam.pm blib/lib/Bio/Tradis/Parser/Bam.pm cp lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm blib/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm cp lib/Bio/Tradis/CommandLine/FilterFastqTags.pm blib/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm cp lib/Bio/Tradis/Analysis/InsertSite.pm blib/lib/Bio/Tradis/Analysis/InsertSite.pm cp lib/Bio/Tradis/CommandLine/TradisAnalysis.pm blib/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm cp lib/Bio/Tradis/RunTradis.pm blib/lib/Bio/Tradis/RunTradis.pm cp lib/Bio/Tradis/CommandLine/PlotCombine.pm blib/lib/Bio/Tradis/CommandLine/PlotCombine.pm cp lib/Bio/Tradis/Samtools.pm blib/lib/Bio/Tradis/Samtools.pm cp lib/Bio/Tradis/Map.pm blib/lib/Bio/Tradis/Map.pm cp lib/Bio/Tradis/Parser/Cigar.pm blib/lib/Bio/Tradis/Parser/Cigar.pm cp lib/Bio/Tradis/CommandLine/PlotTradis.pm blib/lib/Bio/Tradis/CommandLine/PlotTradis.pm cp lib/Bio/Tradis/CommandLine/RunMapping.pm blib/lib/Bio/Tradis/CommandLine/RunMapping.pm cp lib/Bio/Tradis/Parser/Fastq.pm blib/lib/Bio/Tradis/Parser/Fastq.pm cp lib/Bio/Tradis/RemoveTags.pm blib/lib/Bio/Tradis/RemoveTags.pm cp lib/Bio/Tradis/CombinePlots.pm blib/lib/Bio/Tradis/CombinePlots.pm cp lib/Bio/Tradis/DetectTags.pm blib/lib/Bio/Tradis/DetectTags.pm cp lib/Bio/Tradis/CommandLine/CheckTags.pm blib/lib/Bio/Tradis/CommandLine/CheckTags.pm cp lib/Bio/Tradis/CommandLine/TradisBam.pm blib/lib/Bio/Tradis/CommandLine/TradisBam.pm cp bin/add_tradis_tags blib/script/add_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/add_tradis_tags cp bin/bacteria_tradis blib/script/bacteria_tradis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bacteria_tradis cp bin/check_tradis_tags blib/script/check_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/check_tradis_tags cp bin/combine_tradis_plots blib/script/combine_tradis_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/combine_tradis_plots cp bin/filter_tradis_tags blib/script/filter_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/filter_tradis_tags cp bin/remove_tradis_tags blib/script/remove_tradis_tags "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/remove_tradis_tags cp bin/tradis_comparison.R blib/script/tradis_comparison.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_comparison.R cp bin/tradis_essentiality.R blib/script/tradis_essentiality.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_essentiality.R cp bin/tradis_gene_insert_sites blib/script/tradis_gene_insert_sites "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_gene_insert_sites cp bin/tradis_merge_plots blib/script/tradis_merge_plots "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_merge_plots cp bin/tradis_plot blib/script/tradis_plot "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/tradis_plot Manifying 9 pod documents Manifying 25 pod documents make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test || true make -j2 test TEST_VERBOSE=1 make[2]: Entering directory '/<>' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/Bio/Tradis/*.t t/Bio/Tradis/Analysis/*.t t/Bio/Tradis/CommandLine/*.t t/Bio/Tradis/Parser/*.t # # Versions for all modules listed in MYMETA.json (including optional ones): # # === Configure Requires === # # Module Want Have # ------------------- ---- ---- # ExtUtils::MakeMaker any 7.70 # # === Build Requires === # # Module Want Have # ------------------- ---- ---- # ExtUtils::MakeMaker any 7.70 # # === Test Requires === # # Module Want Have # ------------------- ---- -------- # Env::Path 0.18 0.19 # ExtUtils::MakeMaker any 7.70 # File::Spec any 3.90 # Test::Exception any 0.43 # Test::Files any 0.26 # Test::More any 1.302199 # Test::Most any 0.38 # # === Test Recommends === # # Module Want Have # ---------- -------- -------- # CPAN::Meta 2.120900 2.150010 # # === Runtime Requires === # # Module Want Have # ---------------- ---- ------ # Bio::Seq any 1.7.8 # Bio::SeqIO any 1.7.8 # Cwd any 3.90 # Data::Dumper any 2.189 # Exception::Class any 1.45 # File::Basename any 2.86 # File::Path any 2.18 # File::Spec any 3.90 # File::Temp any 0.2311 # FindBin any 1.54 # Getopt::Long any 2.57 # Moose any 2.2207 # Text::CSV any 2.04 # Try::Tiny any 0.32 # strict any 1.13 # warnings any 1.70 # t/00-report-prereqs.t ...................... 1..1 ok 1 ok # Failed test 'checking file contents' # at /usr/share/perl5/Test/Files.pm line 376. # --- t/data/output.sam # +++ t/data/AddTags/expected_tradis.sam # @@ -15,9 +15,7 @@ # @PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' # @PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false # @PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 # -@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -H t/data/AddTags/sample_sm_tr.bam # -@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -h -S -b -o t/data/output.bam tmp.20240914225451.sam # -@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h -o t/data/output.sam t/data/output.bam # +@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.bam # MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 60M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCCTGACTCTTA HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABAFFFFFBBCCC X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG # MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3FFFFFCCCCB X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG # MS5_9521:1:2101:3627:15042#14 16 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA HHHGHHHGHHGGHHHHHHHHHHHHHHGGGGGGGGGGGGFFCFFFFBBBAAFFFFFCBAAA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:AAA>AAAA XT:A:U tq:Z:AAABCFFFFF tr:Z:TAAGAGTCAG # Failed test 'checking file contents' # at /usr/share/perl5/Test/Files.pm line 376. # --- t/data/AddTags/sample_sm_no_tr.sam # +++ t/data/output.sam # @@ -15,7 +15,9 @@ # @PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' # @PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false # @PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 # -@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -h -o t/data/AddTags/sample_sm_no_tr.sam t/data/AddTags/sample_sm_no_tr.bam # +@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -H t/data/AddTags/sample_sm_tr.bam # +@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -h -S -b -o t/data/output.bam tmp.20240914225451.sam # +@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h -o t/data/output.sam t/data/output.bam # MS5_9521:1:1101:10072:14269#14 16 ENA|AE004091|AE004091.2 5 37 60M * 0 0 AAGAGACCGGCGATTCTAGTGAAATCGAACGGGCAGGTCAATTTCCAACCCTGACTCTTA HHHGGGGGGGHHHHHHHHHHHGHHHGHHGGGGGGGGGGFFFBFFCBAABAFFFFFBBCCC X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:BBCDECBC XT:A:U tq:Z:CCCBBFFFFF tr:Z:TAAGAGTCAG # MS5_9521:1:1103:26809:18585#14 1040 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA 5FGGHHGEGHFEHHHHHGFHHGHGGHGFGGFCGEGBBAFC?DFFFBBBB3FFFFFCCCCB X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:CCCCCCCC XT:A:U tq:Z:BCCCCFFFFF tr:Z:TAAGAGTCAG # MS5_9521:1:2101:3627:15042#14 16 ENA|AE004091|AE004091.2 23 37 60M * 0 0 GTGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATCTGACTCTTA HHHGHHHGHHGGHHHHHHHHHHHHHHGGGGGGGGGGGGFFCFFFFBBBAAFFFFFCBAAA X0:i:1 X1:i:0 BC:Z:TCTCGGTT MD:Z:50 RG:Z:1#14 XG:i:0 NM:i:0 XM:i:0 XO:i:0 QT:Z:AAA>AAAA XT:A:U tq:Z:AAABCFFFFF tr:Z:TAAGAGTCAG [E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?)) [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Input/output error [E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta : No such file or directory [E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta' [W::cram_get_ref] Failed to populate reference for id 0 [E::cram_decode_slice] Unable to fetch reference #0:5-193 [E::cram_next_slice] Failure to decode slice samtools view: error reading file "t/data/AddTags/sample_sm_tr.cram": No such file or directory [E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?)) [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Input/output error [E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta : No such file or directory [E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta' [W::cram_get_ref] Failed to populate reference for id 0 [E::cram_decode_slice] Unable to fetch reference #0:5-193 [E::cram_next_slice] Failure to decode slice samtools view: error reading file "t/data/AddTags/sample_sm_tr.cram": No such file or directory [E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?)) [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Input/output error [E::fai_build3_core] Failed to open the file /nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta : No such file or directory [E::refs_load_fai] Failed to open reference file '/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta' [W::cram_get_ref] Failed to populate reference for id 0 [E::cram_decode_slice] Unable to fetch reference #0:5-203 [E::cram_next_slice] Failure to decode slice samtools view: error reading file "t/data/AddTags/expected_tradis.cram": No such file or directory # Failed test 'checking file contents' # at /usr/share/perl5/Test/Files.pm line 376. # --- t/data/output.sam # +++ t/data/AddTags/expected_tradis.sam # @@ -1,4 +1,6 @@ # @HD VN:1.4 SO:coordinate # +@RG ID:1#14 PL:ILLUMINA PU:130320_MS5_9521_A_MS0205701-050V2_1#14 LB:6982965 DS:ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2013-03-20T00:00:00+0000 SM:ERS222909 CN:SC # +@SQ SN:ENA|AE004091|AE004091.2 LN:6264404 UR:file:/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta AS:PAO1 M5:7f8b730b8a08ebf1eeb7f0de561f0a91 SP:Pseudomonas aeruginosa # @PG ID:SCS PN:MiSeq Control Software DS:Controlling software on instrument VN:2.2.0 # @PG ID:basecalling PN:RTA PP:SCS DS:Basecalling Package VN:1.17.28.0 # @PG ID:Illumina2bam PN:Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:V1.10 CL:uk.ac.sanger.npg.illumina.Illumina2bam INTENSITY_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities BASECALLS_DIR=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BaseCalls LANE=1 OUTPUT=/dev/stdout SAMPLE_ALIAS=ERS222824,ERS222825,ERS222825,ERS222824,ERS222909,ERS222910 LIBRARY_NAME=6983166 STUDY_NAME=ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ BARCODE_SEQUENCE_TAG_NAME=tr BARCODE_QUALITY_TAG_NAME=tq SECOND_BARCODE_SEQUENCE_TAG_NAME=BC SECOND_BARCODE_QUALITY_TAG_NAME=QT COMPRESSION_LEVEL=0 CREATE_MD5_FILE=true GENERATE_SECONDARY_BASE_CALLS=false PF_FILTER=true READ_GROUP_ID=1 SEQUENCING_CENTER=SC PLATFORM=ILLUMINA VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false # @@ -13,8 +15,4 @@ # @PG ID:picard_markduplicates PN:Picard PP:samtools_sort VN:1.72(1230) CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR' # @PG ID:ChangeBamHeader PN:ChangeBamHeader PP:picard_markduplicates DS:Add extra PGs into bam header, or change SM, LB or DS tag in RG line in header and this only works with one read group in the input bam. VN:V1.10 CL:uk.ac.sanger.npg.picard.ChangeBamHeader INPUT=/dev/stdin OUTPUT=/dev/stdout PG=[ID:samtools_sort;PN:samtools;VN:0.1.18 (r982:295);CL:/software/solexa/bin/aligners/samtools/samtools-0.1.18/samtools sort /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14.bam /nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted, ID:picard_markduplicates;PN:Picard;VN:1.72(1230);CL:/software/java/bin/java -Xmx6000m -jar /software/solexa/bin/aligners/picard/picard-tools-1.72/MarkDuplicates.jar INPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb/sorted.bam OUTPUT=/dev/stdout METRICS_FILE=/tmp/kShEyfoGW1 ASSUME_SORTED='true' COMPRESSION_LEVEL='0' MAX_FILE_HANDLES_FOR_READ_ENDS_MAP='900' READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' REMOVE_DUPLICATES='false' VALIDATION_STRINGENCY='SILENT' VERBOSITY='ERROR'] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 QUIET=false MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false # @PG ID:BamTagStripper PN:BamTagStripper PP:ChangeBamHeader DS:Strip a list of tags in bam/sam record. By default, any tags containing lowercase letters will be stripped and other tags will be kept. A list of tags can be given to keep or strip VN:V1.10 CL:uk.ac.sanger.npg.picard.BamTagStripper INPUT=/dev/stdin OUTPUT=/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/9521_1#14_mk.bam TAG_TO_KEEP=[a3, ah, br, qr, tq, tr] TAG_TO_STRIP=[OQ] TMP_DIR=[/nfs/sf49/ILorHSorMS_sf49/analysis/130320_MS5_9521_A_MS0205701-050V2/Data/Intensities/BAM_basecalls_20130321-070041/no_cal/archive/lane1/E2jaMSXizb] VERBOSITY=INFO VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true CREATE_MD5_FILE=true QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 # -@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -H t/data/AddTags/sample_sm_tr.cram # +@PG ID:samtools PN:samtools PP:BamTagStripper VN:1.20 CL:samtools view -h -o t/data/AddTags/expected_tradis.sam t/data/AddTags/expected_tradis.cram # -@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -h -S -C -o t/data/output.cram tmp.20240914225451.sam # -@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools view -h -o t/data/output.sam t/data/output.cram # -@SQ SN:ENA|AE004091|AE004091.2 LN:6264404 UR:file:/nfs/srpipe_references/references/Pseudomonas_aeruginosa/PAO1/all/fasta/AE004091.fasta AS:PAO1 M5:7f8b730b8a08ebf1eeb7f0de561f0a91 SP:Pseudomonas aeruginosa # -@RG ID:1#14 PL:ILLUMINA PU:130320_MS5_9521_A_MS0205701-050V2_1#14 LB:6982965 DS:ERP002335: http://www.sanger.ac.uk/resources/downloads/bacteria/citrobacter-rodentium.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ DT:2013-03-20T00:00:00+0000 SM:ERS222909 CN:SC # Looks like you failed 3 tests of 15. t/Bio/Tradis/AddTagsToSeq.t ................ ok 1 - use Bio::Tradis::AddTagsToSeq; ok 2 - creating object ok 3 - correctly select the bam output switch ok 4 - testing output ok 5 - checking file existence not ok 6 - checking file contents ok 7 - creating object ok 8 - checking file existence not ok 9 - checking file contents ok 10 - number of reads as expected ok 11 - creating object with cram file ok 12 - correctly select the cram output switch ok 13 - testing output ok 14 - checking file existence not ok 15 - checking file contents 1..15 Dubious, test returned 3 (wstat 768, 0x300) Failed 3/15 subtests t/Bio/Tradis/Analysis/InsertSite.t ......... ok 1 - use Bio::Tradis::Analysis::InsertSite; ok 2 ok 3 ok 4 - check main sequence insert_site values first value ok 5 - check main sequence insert_site value before site ok 6 - check main sequence insert_site values for reverse reads only ok 7 - various values ok 8 - various values ok 9 - various values ok 10 - various values ok 11 - various values ok 12 - check empty plasmid insert_site values first value ok 13 - check empty plasmid insert_site values last value ok 14 - check plasmid with 1 read insert_site values first value ok 15 - check plasmid with 1 read insert_site values first base of read ok 16 - check plasmid with 1 read insert_site values after last base of read ok 17 - check plasmid with 1 read insert_site values last value ok 18 - check another empty plasmid insert_site values first value ok 19 - check another empty plasmid insert_site values last value ok 20 ok 21 ok 22 - check forward read ok 23 - check reverse read 1..23 ok [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? [tabix] the index file exists. Please use '-f' to overwrite. t/Bio/Tradis/CombinePlots.t ................ ok 1 - use Bio::Tradis::CombinePlots; ok 2 - creating object ok 3 - combining plots ok 4 - checking first combined plot file exists ok 5 - checking second combined plot file exists ok 6 - checking stats file exists ok 7 - checking first file contents ok 8 - checking second file contents ok 9 - checking stats file contents ok 10 - creating object ok 11 - combining plots ok 12 - checking first combined plot file exists ok 13 - checking tabix sorted combined plot file exists ok 14 - checking tabix index file exists ok 15 - checking zipped file contents ok 16 - checking stats file contents ok 17 - creating object ok 18 - combining plots ok 19 - checking directory exists ok 20 - checking first combined plot file exists ok 21 - checking second combined plot file exists 1..21 ok Attribute (_stats_handle) does not pass the type constraint because: Validation failed for 'FileHandle' with value GLOB(0x55d70d944a68) at reader Bio::Tradis::CommandLine::TradisAnalysis::_stats_handle (defined at lib/Bio/Tradis/CommandLine/TradisAnalysis.pm line 43) line 15 Bio::Tradis::CommandLine::TradisAnalysis::_stats_handle('Bio::Tradis::CommandLine::TradisAnalysis=HASH(0x55d70bd90078)') called at lib/Bio/Tradis/CommandLine/TradisAnalysis.pm line 146 Bio::Tradis::CommandLine::TradisAnalysis::run('Bio::Tradis::CommandLine::TradisAnalysis=HASH(0x55d70bd90078)') called at t/Bio/Tradis/CommandLine/TradisAnalysis.t line 33 # Tests were run but no plan was declared and done_testing() was not seen. # Looks like your test exited with 255 just after 2. t/Bio/Tradis/CommandLine/TradisAnalysis.t .. ok 1 - use Bio::Tradis::CommandLine::TradisAnalysis; ok 2 - creating object Dubious, test returned 255 (wstat 65280, 0xff00) All 2 subtests passed Attempt to call undefined import method with arguments ("") via package "Bio::Tradis::Parser::Bam" (Perhaps you forgot to load the package?) at lib/Bio/Tradis/DetectTags.pm line 9. [E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?)) [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/7f8b730b8a08ebf1eeb7f0de561f0a91": Input/output error t/Bio/Tradis/DetectTags.t .................. ok 1 - use Bio::Tradis::DetectTags; ok 2 - testing tag checker - tradis ok 3 - testing output ok 4 - testing tag checker for cram- tradis ok 5 - testing output cram ok 6 - testing tag checker - no tradis ok 7 - testing output 1..7 ok t/Bio/Tradis/FilterTags.t .................. ok 1 - use Bio::Tradis::FilterTags; ok 2 - creating object ok 3 - testing output ok 4 - checking file existence ok 5 - checking file contents ok 6 - creating object ok 7 - testing output ok 8 - checking file existence ok 9 - checking file contents ok 10 - creating object ok 11 - testing output ok 12 - checking file existence ok 13 - checking file contents ok 14 - creating object ok 15 - testing output ok 16 - checking file existence ok 17 - checking file contents 1..17 ok t/Bio/Tradis/Map.t ......................... ok 1 - use Bio::Tradis::Map; ok 2 - creating object ok 3 - testing reference indexing ok 4 - checking index file existence ok 5 - checking index file existence ok 6 - testing smalt mapping ok 7 - checking index file existence ok 8 - checking file contents ok 9 - creating object ok 10 - testing reference indexing ok 11 - checking index file existence ok 12 - checking index file existence ok 13 - checking index file existence ok 14 - checking index file existence ok 15 - checking index file existence ok 16 - testing bwa mapping ok 17 - checking index file existence ok 18 - checking file contents ok 19 - creating object ok 20 - indexing args correct ok 21 - mapping args correct 1..21 ok t/Bio/Tradis/Parser/Bam.t .................. ok 1 - use Bio::Tradis::Parser::Bam; ok 2 - creating object ok 3 - An object of class 'Bio::Tradis::Parser::Bam' isa 'Bio::Tradis::Parser::Bam' ok 4 - seq_info returns a hash ok 5 - first result detected ok 6 - read_info contains correct info for first line ok 7 - testing flag parsing - mapped ok 8 - testing flag parsing - reverse complement ok 9 - last result detected ok 10 - read_info contains correct info for last line ok 11 - EOF detected 1..11 ok t/Bio/Tradis/Parser/Cigar.t ................ ok 1 - use Bio::Tradis::Parser::Cigar; ok 2 - initialise obj -all matching ok 3 - read start -all matching ok 4 - read end -all matching ok 5 - initialise obj -nothing matching ok 6 - read start -nothing matching ok 7 - read end -nothing matching ok 8 - initialise obj -soft clipping at start ok 9 - read start -soft clipping at start ok 10 - read end -soft clipping at start ok 11 - initialise obj -soft clipping at end ok 12 - read start -soft clipping at end ok 13 - read end -soft clipping at end ok 14 - initialise obj -soft clipping at both ends ok 15 - read start -soft clipping at both ends ok 16 - read end -soft clipping at both ends ok 17 - initialise obj -deletion in middle ok 18 - read start -deletion in middle ok 19 - read end -deletion in middle ok 20 - initialise obj -insertions and deletions ok 21 - read start -insertions and deletions ok 22 - read end -insertions and deletions ok 23 - initialise obj -insertions in the middle ok 24 - read start -insertions in the middle ok 25 - read end -insertions in the middle 1..25 ok t/Bio/Tradis/Parser/Fastq.t ................ ok 1 - use Bio::Tradis::Parser::Fastq; ok 2 - creating object ok 3 - An object of class 'Bio::Tradis::Parser::Fastq' isa 'Bio::Tradis::Parser::Fastq' ok 4 - first result detected ok 5 - read_info contains correct info for first line ok 6 - last result detected ok 7 - read_info contains correct info for last line ok 8 - EOF detected 1..8 ok t/Bio/Tradis/RemoveTags.t .................. ok 1 - use Bio::Tradis::RemoveTags; ok 2 - creating object ok 3 - testing output ok 4 - checking file existence ok 5 - checking file contents ok 6 - creating object ok 7 - testing output ok 8 - checking file existence ok 9 - checking file contents ok 10 - creating object ok 11 - testing output ok 12 - checking file existence ok 13 - checking file contents 1..13 ok # Failed test 'checking mapped file contents' # at /usr/share/perl5/Test/Files.pm line 376. # --- /<>/tmp_run_tradis_tests_pH9fy/tmp1.sam # +++ /<>/tmp_run_tradis_tests_pH9fy/tmp2.sam # @@ -1,5 +1,4 @@ # @SQ SN:AE004091 LN:9840 # -@HD VN:1.5 SO:unsorted GO:query # HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 # HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 # HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 # Looks like you failed 1 test of 45. t/Bio/Tradis/RunTradisBWA.t ................ ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing filtering step ok 4 - checking filtered file existence - Normal files, no mismatch ok 5 - checking filtered file contents - Normal files, no mismatch ok 6 - testing check filtering step ok 7 - complain if no filtered reads ok 8 - complain if filtered reads are empty ok 9 - complain if filtered reads has less than 4 lines ok 10 - complain if filtered reads do not look like a fastq ok 11 - complain if filtered reads are too short ok 12 - check very basic filtered reads validation ok 13 - testing tag removal ok 14 - checking de-tagged file existence - Normal files, no mismatch ok 15 - checking de-tagged file contents - Normal files, no mismatch ok 16 - testing mapping ok 17 - checking SAM existence not ok 18 - checking mapped file contents ok 19 - testing SAM/BAM conversion ok 20 - checking BAM existence ok 21 - testing BAM sorting ok 22 - checking sorted BAM existence - Normal files, no mismatch ok 23 - checking indexed BAM existence - Normal files, no mismatch ok 24 - testing bamcheck ok 25 - checking bamcheck file existence - Normal files, no mismatch ok 26 - testing plotting ok 27 - checking plot file existence - Normal files, no mismatch ok 28 - checking plot file contents - Normal files, no mismatch ok 29 - testing complete analysis - Normal files, no mismatch ok 30 - checking plot file existence - Normal files, no mismatch ok 31 - checking completed pipeline file contents - Normal files, no mismatch ok 32 - creating object - Normal files one mismatch ok 33 - testing complete analysis with mismatch ok 34 - checking plot file existence - Normal files one mismatch ok 35 - checking completed pipeline with mismatch file contents - Normal files one mismatch ok 36 - creating object with gzipped data - Normal files one mismatch ok 37 - testing complete analysis with gzipped data ok 38 - checking plot file existence (gzipped data) - Normal files one mismatch ok 39 - checking mapped bam existence - Normal files one mismatch ok 40 - checking indexed bam file - Normal files one mismatch ok 41 - checking completed pipeline with gzipped data file contents - Normal files one mismatch ok 42 - creating object with custom smalt parameters ok 43 - mapping with custom parameters fine ok 44 - creating object ok 45 - correct error thrown 1..45 Dubious, test returned 1 (wstat 256, 0x100) Failed 1/45 subtests t/Bio/Tradis/RunTradisSmalt.t .............. ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing filtering step ok 4 - checking filtered file existence - Normal files, no mismatch ok 5 - checking filtered file contents - Normal files, no mismatch ok 6 - testing check filtering step ok 7 - complain if no filtered reads ok 8 - complain if filtered reads are empty ok 9 - complain if filtered reads has less than 4 lines ok 10 - complain if filtered reads do not look like a fastq ok 11 - complain if filtered reads are too short ok 12 - check very basic filtered reads validation ok 13 - testing tag removal ok 14 - checking de-tagged file existence - Normal files, no mismatch ok 15 - checking de-tagged file contents - Normal files, no mismatch ok 16 - testing mapping ok 17 - checking SAM existence ok 18 - checking mapped file contents ok 19 - testing SAM/BAM conversion ok 20 - checking BAM existence ok 21 - testing BAM sorting ok 22 - checking sorted BAM existence - Normal files, no mismatch ok 23 - checking indexed BAM existence - Normal files, no mismatch ok 24 - testing bamcheck ok 25 - checking bamcheck file existence - Normal files, no mismatch ok 26 - testing plotting ok 27 - checking plot file existence - Normal files, no mismatch ok 28 - checking plot file contents - Normal files, no mismatch ok 29 - testing complete analysis - Normal files, no mismatch ok 30 - checking plot file existence - Normal files, no mismatch ok 31 - checking completed pipeline file contents - Normal files, no mismatch ok 32 - creating object - Normal files one mismatch ok 33 - testing complete analysis with mismatch ok 34 - checking plot file existence - Normal files one mismatch ok 35 - checking completed pipeline with mismatch file contents - Normal files one mismatch ok 36 - creating object with gzipped data - Normal files one mismatch ok 37 - testing complete analysis with gzipped data ok 38 - checking plot file existence (gzipped data) - Normal files one mismatch ok 39 - checking mapped bam existence - Normal files one mismatch ok 40 - checking indexed bam file - Normal files one mismatch ok 41 - checking completed pipeline with gzipped data file contents - Normal files one mismatch ok 42 - creating object with custom smalt parameters ok 43 - mapping with custom parameters fine ok 44 - creating object with custom smalt parameters ok 45 - correct error thrown 1..45 ok # Failed test 'checking mapped file contents' # at /usr/share/perl5/Test/Files.pm line 376. # --- /<>/tmp_run_tradis_tagless_tests_AWr9c/tmp1.sam # +++ /<>/tmp_run_tradis_tagless_tests_AWr9c/tmp2.sam # @@ -1,5 +1,4 @@ # @SQ SN:AE004091 LN:9840 # -@HD VN:1.5 SO:unsorted GO:query # HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 # HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 # HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 # Looks like you failed 1 test of 22. t/Bio/Tradis/RunTradisTaglessBwa.t ......... ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing mapping ok 4 - checking SAM existence not ok 5 - checking mapped file contents ok 6 - testing SAM/BAM conversion ok 7 - checking BAM existence ok 8 - testing BAM sorting ok 9 - checking sorted BAM existence - Normal files, no mismatch ok 10 - checking indexed BAM existence - Normal files, no mismatch ok 11 - testing bamcheck ok 12 - checking bamcheck file existence - Normal files, no mismatch ok 13 - testing plotting ok 14 - checking plot file existence - Normal files, no mismatch ok 15 - checking plot file contents - Normal files, no mismatch ok 16 - testing complete analysis - Normal files, no mismatch ok 17 - checking plot file existence - Normal files, no mismatch ok 18 - checking completed pipeline file contents - Normal files, no mismatch ok 19 - creating object with custom smalt parameters ok 20 - mapping with custom parameters fine ok 21 - creating object ok 22 - correct error thrown 1..22 Dubious, test returned 1 (wstat 256, 0x100) Failed 1/22 subtests t/Bio/Tradis/RunTradisTaglessSmalt.t ....... ok 1 - use Bio::Tradis::RunTradis; ok 2 - creating object - Normal files, no mismatch ok 3 - testing mapping ok 4 - checking SAM existence ok 5 - checking mapped file contents ok 6 - testing SAM/BAM conversion ok 7 - checking BAM existence ok 8 - testing BAM sorting ok 9 - checking sorted BAM existence - Normal files, no mismatch ok 10 - checking indexed BAM existence - Normal files, no mismatch ok 11 - testing bamcheck ok 12 - checking bamcheck file existence - Normal files, no mismatch ok 13 - testing plotting ok 14 - checking plot file existence - Normal files, no mismatch ok 15 - checking plot file contents - Normal files, no mismatch ok 16 - testing complete analysis - Normal files, no mismatch ok 17 - checking plot file existence - Normal files, no mismatch ok 18 - checking completed pipeline file contents - Normal files, no mismatch ok 19 - creating object with custom smalt parameters ok 20 - mapping with custom parameters fine ok 21 - creating object with custom smalt parameters ok 22 - correct error thrown 1..22 ok t/Bio/Tradis/TradisPlot.t .................. ok 1 - use Bio::Tradis::TradisPlot; ok 2 - creating object ok 3 - testing plotting ok 4 - checking plot file existence ok 5 - checking file contents 1..5 ok t/requires_external.t ...................... 1..6 ok 1 - awk in PATH ok 2 - samtools in PATH ok 3 - gunzip in PATH ok 4 - gzip in PATH ok 5 - smalt in PATH ok 6 - tabix in PATH ok Test Summary Report ------------------- t/Bio/Tradis/AddTagsToSeq.t (Wstat: 768 (exited 3) Tests: 15 Failed: 3) Failed tests: 6, 9, 15 Non-zero exit status: 3 t/Bio/Tradis/CommandLine/TradisAnalysis.t (Wstat: 65280 (exited 255) Tests: 2 Failed: 0) Non-zero exit status: 255 Parse errors: No plan found in TAP output t/Bio/Tradis/RunTradisBWA.t (Wstat: 256 (exited 1) Tests: 45 Failed: 1) Failed test: 18 Non-zero exit status: 1 t/Bio/Tradis/RunTradisTaglessBwa.t (Wstat: 256 (exited 1) Tests: 22 Failed: 1) Failed test: 5 Non-zero exit status: 1 Files=18, Tests=309, 6 wallclock secs ( 0.08 usr 0.00 sys + 4.72 cusr 1.24 csys = 6.04 CPU) Result: FAIL Failed 4/18 test programs. 5/309 subtests failed. make[2]: *** [Makefile:1077: test_dynamic] Error 255 make[2]: Leaving directory '/<>' dh_auto_test: error: make -j2 test TEST_VERBOSE=1 returned exit code 2 make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bio-tradis/ make -j2 install DESTDIR=/<>/bio-tradis-1.4.5\+dfsg2/debian/bio-tradis AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/<>' Manifying 9 pod documents Manifying 25 pod documents Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Exception.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Samtools.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/FilterTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CombinePlots.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/RemoveTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/AddTagsToSeq.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/TradisPlot.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/RunTradis.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Map.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/DetectTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Cigar.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Bam.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Parser/Fastq.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/InsertSite.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/Analysis/Exceptions.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RunMapping.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotCombine.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/AddTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/PlotTradis.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/CheckTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisAnalysis.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/FilterFastqTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/RemoveFastqTags.pm Installing /<>/debian/bio-tradis/usr/share/perl5/Bio/Tradis/CommandLine/TradisBam.pm Installing /<>/debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/bacteria_tradis.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/tradis_plot.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/tradis_gene_insert_sites.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/add_tradis_tags.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/combine_tradis_plots.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/filter_tradis_tags.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/check_tradis_tags.1p Installing /<>/debian/bio-tradis/usr/share/man/man1/remove_tradis_tags.1p Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::DetectTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Cigar.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CombinePlots.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::FilterFastqTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::AddTagsToSeq.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Samtools.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::FilterTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotCombine.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::InsertSite.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RunMapping.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::AddTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::TradisPlot.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisBam.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Fastq.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RunTradis.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::TradisAnalysis.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::RemoveTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::CheckTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Map.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::PlotTradis.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Exception.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::CommandLine::RemoveFastqTags.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Analysis::Exceptions.3pm Installing /<>/debian/bio-tradis/usr/share/man/man3/Bio::Tradis::Parser::Bam.3pm Installing /<>/debian/bio-tradis/usr/bin/tradis_comparison.R Installing /<>/debian/bio-tradis/usr/bin/combine_tradis_plots Installing /<>/debian/bio-tradis/usr/bin/add_tradis_tags Installing /<>/debian/bio-tradis/usr/bin/filter_tradis_tags Installing /<>/debian/bio-tradis/usr/bin/tradis_plot Installing /<>/debian/bio-tradis/usr/bin/tradis_merge_plots Installing /<>/debian/bio-tradis/usr/bin/bacteria_tradis Installing /<>/debian/bio-tradis/usr/bin/remove_tradis_tags Installing /<>/debian/bio-tradis/usr/bin/check_tradis_tags Installing /<>/debian/bio-tradis/usr/bin/tradis_gene_insert_sites Installing /<>/debian/bio-tradis/usr/bin/tradis_essentiality.R make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done mv debian/bio-tradis/usr/bin/tradis_comparison.R debian/bio-tradis/usr/bin/tradis_comparison mv debian/bio-tradis/usr/bin/tradis_essentiality.R debian/bio-tradis/usr/bin/tradis_essentiality make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman rm debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p* make[1]: Leaving directory '/<>' 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 'bio-tradis' in '../bio-tradis_1.4.5+dfsg2-2_all.deb'. dpkg-genbuildinfo -O../bio-tradis_1.4.5+dfsg2-2_amd64.buildinfo dpkg-genchanges -O../bio-tradis_1.4.5+dfsg2-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-09-14T22:54:59Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bio-tradis_1.4.5+dfsg2-2_amd64.changes: --------------------------------------- Format: 1.8 Date: Thu, 25 Jan 2024 15:34:52 +0100 Source: bio-tradis Binary: bio-tradis Architecture: source all Version: 1.4.5+dfsg2-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bio-tradis - analyse the output from TraDIS analyses of genomic sequences Closes: 1043774 Changes: bio-tradis (1.4.5+dfsg2-2) unstable; urgency=medium . * Fix watch file * Fix clean target Closes: #1043774 * Standards-Version: 4.6.2 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * dh_install now works even without debian/install * r-bioc-edger is back in Debian thus move it to Recommends and drop the outdated debian/NEWS * artemis is available now thus move it to Recommends Checksums-Sha1: dbc9f9a23d3f70275eb4e53875c66df2047b33eb 1355 bio-tradis_1.4.5+dfsg2-2.dsc 2a1eadb27d76c6ec3c148df87ddbaa0d885d931a 6096 bio-tradis_1.4.5+dfsg2-2.debian.tar.xz 860f6b38a5e8b37008c47f5b8d44517b6053e3dc 80060 bio-tradis_1.4.5+dfsg2-2_all.deb 050b83a44086d441ed90546efeeadb3df1d994f2 7990 bio-tradis_1.4.5+dfsg2-2_amd64.buildinfo Checksums-Sha256: 785672e52f7de35eca6b82e7e69ee05de89b760f0775c1c82ed05f612ab23042 1355 bio-tradis_1.4.5+dfsg2-2.dsc 32dd5c211c5e7a1180e8050b1da7c0d0b12c5531bd11c61eb2fc837e8f92265c 6096 bio-tradis_1.4.5+dfsg2-2.debian.tar.xz 9b9d3087be8d4d8137fb3b1db0d1fad49d7a8be9da10d7cd74e1d15046344334 80060 bio-tradis_1.4.5+dfsg2-2_all.deb 318bef434dded81d9b9c2a10d9676f9573a43bb73a54fe8ac82d8b012398b222 7990 bio-tradis_1.4.5+dfsg2-2_amd64.buildinfo Files: 91aa1ef09c7199a95de913fa60ea63f1 1355 perl optional bio-tradis_1.4.5+dfsg2-2.dsc b60da3af535d0d1ca443981c7c214475 6096 perl optional bio-tradis_1.4.5+dfsg2-2.debian.tar.xz cf7462e2f84f8868a4d88bcadc64f80a 80060 perl optional bio-tradis_1.4.5+dfsg2-2_all.deb 7e1bd065b09b9f2803eaed0b5abd0ba7 7990 perl optional bio-tradis_1.4.5+dfsg2-2_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bio-tradis Binary: bio-tradis Architecture: all source Version: 1.4.5+dfsg2-2 Checksums-Md5: 91aa1ef09c7199a95de913fa60ea63f1 1355 bio-tradis_1.4.5+dfsg2-2.dsc cf7462e2f84f8868a4d88bcadc64f80a 80060 bio-tradis_1.4.5+dfsg2-2_all.deb Checksums-Sha1: dbc9f9a23d3f70275eb4e53875c66df2047b33eb 1355 bio-tradis_1.4.5+dfsg2-2.dsc 860f6b38a5e8b37008c47f5b8d44517b6053e3dc 80060 bio-tradis_1.4.5+dfsg2-2_all.deb Checksums-Sha256: 785672e52f7de35eca6b82e7e69ee05de89b760f0775c1c82ed05f612ab23042 1355 bio-tradis_1.4.5+dfsg2-2.dsc 9b9d3087be8d4d8137fb3b1db0d1fad49d7a8be9da10d7cd74e1d15046344334 80060 bio-tradis_1.4.5+dfsg2-2_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 14 Sep 2024 22:54:58 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bwa (= 0.7.18-1), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-4), cpp-14-x86-64-linux-gnu (= 14.2.0-4), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-4), g++-14-x86-64-linux-gnu (= 14.2.0-4), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-4), gcc-14-base (= 14.2.0-4), gcc-14-x86-64-linux-gnu (= 14.2.0-4), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libalgorithm-c3-perl (= 0.11-2), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-4), libatomic1 (= 14.2.0-4), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libb-hooks-op-check-perl (= 0.22-3+b2), libbambamc0 (= 0.0.50-6+b1), libbinutils (= 2.43.1-4), libbio-perl-perl (= 1.7.8-1), libblkid1 (= 2.40.2-8), libbrotli1 (= 1.1.0-2+b4), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcapture-tiny-perl (= 0.48-2), libcc1-0 (= 14.2.0-4), libclass-c3-perl (= 0.35-2), libclass-data-inheritable-perl (= 0.08-3), libclass-load-perl (= 0.25-2), libclass-load-xs-perl (= 0.10-2+b4), libclass-xsaccessor-perl (= 1.19-4+b4), libclone-perl (= 0.47-1+b1), libcom-err2 (= 1.47.1-1), libconst-fast-perl (= 0.014-2), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libcurl3t64-gnutls (= 8.10.0-2), libdata-compare-perl (= 1.29-1), libdata-optlist-perl (= 0.114-1), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdeflate0 (= 1.21-1), libdevel-callchecker-perl (= 0.009-1+b1), libdevel-globaldestruction-perl (= 0.14-4), libdevel-overloadinfo-perl (= 0.007-1), libdevel-stacktrace-perl (= 2.0500-1), libdist-checkconflicts-perl (= 0.11-2), libdpkg-perl (= 1.22.11), libdynaloader-functions-perl (= 0.004-1), libelf1t64 (= 0.191-2), libenv-path-perl (= 0.19-4), libeval-closure-perl (= 0.14-3), libexception-class-perl (= 1.45-1), libffi8 (= 3.4.6-1), libfile-chdir-perl (= 0.1008-1.2), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-4), libgcc-s1 (= 14.2.0-4), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-4), libgprofng0 (= 2.43.1-4), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-4), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libio-string-perl (= 1.08-4), libisl23 (= 0.27-1), libitm1 (= 14.2.0-4), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-3+b1), liblsan0 (= 14.2.0-4), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmodule-implementation-perl (= 0.09-2), libmodule-runtime-conflicts-perl (= 0.003-2), libmodule-runtime-perl (= 0.016-2), libmoose-perl (= 2.2207-1+b2), libmount1 (= 2.40.2-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libmro-compat-perl (= 0.15-2), libncurses6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.63.0-1), libnghttp3-9 (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libnumber-compare-perl (= 0.03-3), libp11-kit0 (= 0.25.5-2), libpackage-deprecationmanager-perl (= 0.18-1), libpackage-stash-perl (= 0.40-1), libpackage-stash-xs-perl (= 0.30-1+b4), libpadwalker-perl (= 2.5-1+b6), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libparams-classify-perl (= 0.015-2+b4), libparams-util-perl (= 1.102-3+b1), libpath-tiny-perl (= 0.146-1), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.2.0-4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsmartcols1 (= 2.40.2-8), libssh2-1t64 (= 1.11.0-7), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsub-exporter-perl (= 0.990-1), libsub-exporter-progressive-perl (= 0.001013-3), libsub-install-perl (= 0.929-1), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 256.6-1), libtasn1-6 (= 4.19.0-3+b2), libtest-deep-perl (= 1.204-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-files-perl (= 0.26-1), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtest2-suite-perl (= 0.000163-1), libtext-csv-perl (= 2.04-1), libtext-diff-perl (= 1.45-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtry-tiny-perl (= 0.32-1), libtsan2 (= 14.2.0-4), libubsan1 (= 14.2.0-4), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-8), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), smalt (= 0.7.6-13), sysvinit-utils (= 3.10-2), tabix (= 1.20+ds-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-8), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1706193292" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bio-tradis_1.4.5+dfsg2-2_all.deb -------------------------------- new Debian package, version 2.0. size 80060 bytes: control archive=2844 bytes. 978 bytes, 21 lines control 6111 bytes, 77 lines md5sums Package: bio-tradis Version: 1.4.5+dfsg2-2 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 244 Depends: perl:any, libbio-perl-perl, libexception-class-perl, libmoose-perl, libtext-csv-perl, libtry-tiny-perl, smalt, samtools, tabix, r-base-core, r-cran-getopt, r-cran-mass Recommends: artemis, r-bioc-edger Section: perl Priority: optional Homepage: https://github.com/sanger-pathogens/Bio-Tradis Description: analyse the output from TraDIS analyses of genomic sequences Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. . The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. . 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/srv/debomatic/incoming/bio-tradis_1.4.5+dfsg2-2.dsc Machine Architecture: amd64 Package: bio-tradis Package-Time: 27 Source-Version: 1.4.5+dfsg2-2 Space: 15004 Status: successful Version: 1.4.5+dfsg2-2 -------------------------------------------------------------------------------- Finished at 2024-09-14T22:54:59Z Build needed 00:00:27, 15004k disk space