I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 6 08:02:57 +14 2021 I: pbuilder-time-stamp: 1628186577 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iva_1.0.9+ds-11.dsc] I: copying [./iva_1.0.9+ds.orig.tar.xz] I: copying [./iva_1.0.9+ds-11.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.hdFinxv0/trustedkeys.kbx': General error gpgv: Signature made Wed Dec 23 00:23:23 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-11.dsc dpkg-source: info: extracting iva in iva-1.0.9+ds dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.9+ds-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20052/tmp/hooks/D01_modify_environment starting debug: Running on codethink12-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/20052/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/20052/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=20052 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.FhRGO1UmID/pbuilderrc_r2Du --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.FhRGO1UmID/b2 --logfile b2/build.log --extrapackages usrmerge iva_1.0.9+ds-11.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 6 08:03 sh -> bash lrwxrwxrwx 1 root root 4 Aug 5 23:24 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/20052/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on fastaq (>= 1.6); however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on kmc (>= 3.1); however: Package kmc is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on smalt; however: Package smalt is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk-headless{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} java-common{a} kmc{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbambamc0{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcups2{a} libcurl3-gnutls{a} libdata-stag-perl{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libelf1{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts3{a} libicu67{a} libio-string-perl{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} mummer{a} openjdk-11-jdk-headless{a} openjdk-11-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-networkx{a} python3-nose{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pyparsing{a} python3-pysam{a} python3-setuptools{a} python3.9{a} python3.9-minimal{a} readline-common{a} samtools{a} sensible-utils{a} smalt{a} ucf{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf bioperl-run curl dbus libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk publicsuffix python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 293 MB of archives. After unpacking 571 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 gawk arm64 1:5.1.0-1 [570 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libdata-stag-perl all 0.14-2 [448 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libtest-deep-perl all 1.130-1 [49.3 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libtest-differences-perl all 0.67-1 [18.7 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libsub-uplevel-perl all 0.2800-1.1 [16.5 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libtest-most-perl all 0.37-1 [24.9 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 bioperl all 1.7.7-2 [246 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 java-common all 0.72 [14.5 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libavahi-common-data arm64 0.8-5 [123 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libavahi-common3 arm64 0.8-5 [57.1 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libdbus-1-3 arm64 1.12.20-2 [208 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libavahi-client3 arm64 0.8-5 [60.6 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libcups2 arm64 2.3.3op2-3+deb11u1 [334 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 libnspr4 arm64 2:4.29-1 [105 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libnss3 arm64 2:3.61-1 [1210 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libasound2 arm64 1.2.4-1.1 [326 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libpcsclite1 arm64 1.9.1-1 [59.5 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 openjdk-11-jre-headless arm64 11.0.12+7-2 [36.4 MB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 default-jre-headless arm64 2:1.11-72 [10.9 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 ca-certificates-java all 20190909 [15.7 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 openjdk-11-jdk-headless arm64 11.0.12+7-2 [206 MB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 default-jdk-headless arm64 2:1.11-72 [1100 B] Get: 92 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 fastaq all 3.17.0-3 [47.8 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 kmc arm64 3.1.1+dfsg-3+b2 [689 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libbambamc0 arm64 0.0.50-4 [33.4 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libssl-dev arm64 1.1.1k-1 [1689 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 mummer arm64 3.23+dfsg-7 [640 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 python3-networkx all 2.5+ds-2 [900 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 python3-nose all 1.3.7-7 [133 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 python3-numpy arm64 1:1.19.5-1 [3196 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 python3-packaging all 20.9-2 [33.5 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 python3-pysam arm64 0.15.4+ds-3+b2 [1386 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 smalt arm64 0.7.6-9 [104 kB] Fetched 293 MB in 20s (14.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20252 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.1.0-1_arm64.deb ... Unpacking gawk (1:5.1.0-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20736 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21133 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../005-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../008-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package m4. Preparing to unpack .../009-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../010-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../011-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../012-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../013-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../014-libio-string-perl_1.08-3.1_all.deb ... Unpacking libio-string-perl (1.08-3.1) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../015-libdata-stag-perl_0.14-2_all.deb ... Unpacking libdata-stag-perl (0.14-2) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../016-libbio-perl-perl_1.7.7-2_all.deb ... Unpacking libbio-perl-perl (1.7.7-2) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../017-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../018-libdevel-stacktrace-perl_2.0400-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../019-libexception-class-perl_1.44-1_all.deb ... Unpacking libexception-class-perl (1.44-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../020-libtest-deep-perl_1.130-1_all.deb ... Unpacking libtest-deep-perl (1.130-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../021-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../022-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../023-libtext-diff-perl_1.45-1_all.deb ... Unpacking libtext-diff-perl (1.45-1) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../024-libtest-differences-perl_0.67-1_all.deb ... Unpacking libtest-differences-perl (0.67-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../025-libsub-uplevel-perl_0.2800-1.1_all.deb ... Unpacking libsub-uplevel-perl (0.2800-1.1) ... Selecting previously unselected package libtest-exception-perl. 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Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../038-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../039-libpng16-16_1.6.37-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../040-libfreetype6_2.10.4+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../041-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../042-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../043-libfontconfig1_2.13.1-4.2_arm64.deb ... 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Setting up libtest-deep-perl (1.130-1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up gawk (1:5.1.0-1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up m4 (1.4.18-5) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up libasound2-data (1.2.4-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libnspr4:arm64 (2:4.29-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:arm64 (0.8-5) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libdbus-1-3:arm64 (1.12.20-2) ... Setting up libbambamc0 (0.0.50-4) ... Setting up libssl-dev:arm64 (1.1.1k-1) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up autopoint (0.21-4) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libpcsclite1:arm64 (1.9.1-1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libasound2:arm64 (1.2.4-1.1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up mummer (3.23+dfsg-7) ... Setting up libsub-uplevel-perl (0.2800-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libbio-perl-perl (1.7.7-2) ... Setting up openssl (1.1.1k-1) ... Setting up libelf1:arm64 (0.183-1) ... Setting up kmc (3.1.1+dfsg-3+b2) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up smalt (0.7.6-9) ... Setting up liblapack3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libavahi-common3:arm64 (0.8-5) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libnss3:arm64 (2:3.61-1) ... Setting up libexception-class-perl (1.44-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libavahi-client3:arm64 (0.8-5) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libtest-most-perl (0.37-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.9.2-3) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up libcups2:arm64 (2.3.3op2-3+deb11u1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up bioperl (1.7.7-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up fastaq (3.17.0-3) ... Setting up debhelper (13.3.4) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-nose (1.3.7-7) ... Setting up python3-packaging (20.9-2) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:arm64 (11.0.12+7-2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jdk-headless:arm64 (11.0.12+7-2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jdk-headless (2:1.11-72) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Processing triggers for libc-bin (2.31-13) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (3228 kB/s) Selecting previously unselected package libnumber-compare-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 27490 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/iva-1.0.9+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iva_1.0.9+ds-11_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iva-1.0.9+ds' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /build/iva-1.0.9+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/iva-1.0.9+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/iva-1.0.9+ds' chmod a-x /build/iva-1.0.9+ds/iva/read_trim/adapters.fasta chmod a+x /build/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh chmod a+x /build/iva-1.0.9+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /build/iva-1.0.9+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/GetFastaStats.java]] [parsing completed 119ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/SizeFasta.java]] [parsing completed 8ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 6ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/Utils.java]] [parsing completed 35ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]] [parsing completed 38ms] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.scripting.nashorn.shell/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/jdk.rmic/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.aot/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/jdk.pack/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.scripting.nashorn/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.naming.ldap/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-arm64/lib/modules,.] [loading /modules/java.base/java/io/BufferedReader.class] [loading /modules/java.base/java/io/FileInputStream.class] [loading /modules/java.base/java/io/InputStreamReader.class] [loading /modules/java.base/java/text/DecimalFormat.class] [loading /modules/java.base/java/text/NumberFormat.class] [loading /modules/java.base/java/util/ArrayList.class] [loading /modules/java.base/java/util/Arrays.class] [loading /modules/java.base/java/util/HashMap.class] [loading /modules/java.base/java/lang/Object.class] [loading /modules/java.base/java/lang/String.class] [loading /modules/java.base/java/lang/Integer.class] [loading /modules/java.base/java/lang/Exception.class] [loading /modules/java.base/java/lang/StringBuffer.class] [loading /modules/java.management/java/lang/management/ManagementFactory.class] [loading /modules/java.management/java/lang/management/MemoryMXBean.class] [loading /modules/java.base/java/io/File.class] [loading /modules/java.base/java/io/FileReader.class] [loading /modules/java.base/java/lang/Boolean.class] [loading /modules/java.base/java/lang/Enum.class] [loading /modules/java.base/java/lang/Comparable.class] [loading /modules/java.base/java/io/Serializable.class] [loading /modules/java.base/java/util/Collections.class] [loading /modules/java.base/java/lang/Deprecated.class] [loading /modules/java.base/java/lang/annotation/Retention.class] [loading /modules/java.base/java/lang/annotation/RetentionPolicy.class] [loading /modules/java.base/java/lang/annotation/Target.class] [loading /modules/java.base/java/lang/annotation/ElementType.class] [checking GetFastaStats] [loading /modules/java.base/java/lang/AutoCloseable.class] [loading /modules/java.base/java/util/Map.class] [loading /modules/java.base/java/lang/Throwable.class] [loading /modules/java.base/java/lang/CharSequence.class] [loading /modules/java.base/java/io/Reader.class] [loading /modules/java.base/java/lang/Readable.class] [loading /modules/java.base/java/io/Closeable.class] [loading /modules/java.base/java/lang/Number.class] [loading /modules/java.base/java/lang/Cloneable.class] [loading /modules/java.base/java/util/AbstractMap.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/function/IntFunction.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [loading /modules/java.base/java/util/Iterator.class] [wrote /build/iva-1.0.9+ds/iva/gage/GetFastaStats$ContigAt.class] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /build/iva-1.0.9+ds/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /build/iva-1.0.9+ds/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /build/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils$Pair.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils$Translate.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /build/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/iva-1.0.9+ds/iva/gage/getScaffoldStats.class] [total 2364ms] dh_auto_build -- I: pybuild base:232: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/mapping.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/test_data_runner.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/seed_processor.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/seed.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/read_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/qc_external.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/qc.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/mummer.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/kraken.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/kmers.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/kcount.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/graph.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/external_progs.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/egg_extract.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/edge.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/contig_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/contig.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/common.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/assembly.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/__init__.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/colsum.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt.config -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.9 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.9 copying and adjusting scripts/iva_qc -> build/scripts-3.9 copying and adjusting scripts/iva -> build/scripts-3.9 changing mode of build/scripts-3.9/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.9/iva_qc from 644 to 755 changing mode of build/scripts-3.9/iva from 644 to 755 make[1]: Leaving directory '/build/iva-1.0.9+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iva-1.0.9+ds' python3 setup.py test Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info creating iva.egg-info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' running build_ext /build/iva-1.0.9+ds/iva/mapping.py:159: DeprecationWarning: invalid escape sequence \^ s = re.sub('\^.', '', s) /build/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \( 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /build/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \( 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /build/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \( 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /build/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \( 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /build/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /build/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \. self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /build/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W return re.sub('\W', '_', s).strip('_') test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly) Test _contig_contained_in_nucmer_hits ... ok test_contig_names_size_order (assembly_test.TestAssembly) Test _contig_names_size_order ... ok test_contig_worth_extending (assembly_test.TestAssembly) Test _contig_worth_extending ... ok test_coords_to_new_contig (assembly_test.TestAssembly) Test _coords_to_new_contig ... ok test_extend_contigs_with_bam (assembly_test.TestAssembly) test _extend_contigs_with_bam ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_get_contig_order_by_orfs (assembly_test.TestAssembly) Test get_contig_order_by_orfs ... ok test_get_ref_length (assembly_test.TestAssembly) Test _get_ref_length ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam' ok test_get_ref_length_sam_pair (assembly_test.TestAssembly) Test _get_ref_length_sam_pair ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam' ok test_get_unmapped_pairs (assembly_test.TestAssembly) Test _get_unmapped_pairs ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.bam' ok test_good_intervals_from_strand_coverage (assembly_test.TestAssembly) Test good_intervals_from_strand_coverage ... ok test_init_and_write (assembly_test.TestAssembly) test assembly initialise and write to file ... ok test_map_reads (assembly_test.TestAssembly) test _map_reads ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.assembly_test.out.bam' ok test_merge_overlapping_contigs (assembly_test.TestAssembly) Test _merge_overlapping_contigs ... ok test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.4.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.5.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.4.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.5.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.4.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/tmp.filter_reads.p1hc7sh9/out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.5.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/tmp.trim_strand_biased_ends.yh7ltkwd/out.unsorted.bam' ok test_remove_contained_contigs (assembly_test.TestAssembly) Test _remove_contained_contigs ... ok test_remove_contig (assembly_test.TestAssembly) Test _remove_contig ... ok test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly) Test _remove_contig_from_nucmer_hits ... ok test_subcontigs_from_strand_bias (assembly_test.TestAssembly) Test _subcontigs_from_strand_bias ... ok test_trim_contig_for_strand_bias (assembly_test.TestAssembly) Test _trim_contig_for_strand_bias ... ok test_trim_contigs (assembly_test.TestAssembly) Test trim_contigs ... ok test_trim_strand_biased_ends (assembly_test.TestAssembly) Test _trim_strand_biased_ends ... ok test_worth_extending (assembly_test.TestAssembly) Test worth_extending ... ok test_add_left_kmer (contig_test.TestContig) Test add_left_kmer ... ok test_add_right_kmer (contig_test.TestContig) Test add_right_kmer ... ok test_extend (contig_test.TestContig) Test extend ... ok test_init (contig_test.TestContig) Test init ... ok test_len (contig_test.TestContig) Test len ... ok test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim) Test _coverage_to_trimmed_coords ... ok test_trim_ends (contig_trim_test.TestContigTrim) Test _trim_ends ... ok test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ... ok test_change_hit_coords_with_intersection (edge_test.TestEdge) test test_change_hit_coords_with_intersection ... ok test_make_contig_first (edge_test.TestEdge) test make_contig_first ... ok test_make_contig_forwards (edge_test.TestEdge) test make_contig_forwards ... ok test_merge_into (edge_test.TestEdge) test merge_into ... ok test_open_end (edge_test.TestEdge) test open_end ... ok test_reverse (edge_test.TestEdge) test reverse ... ok test_copy_dir (egg_extract_test.TestEggExtract) test copy_dir ... ok test_copy_dir_unzipped (egg_extract_test.TestEggExtract) test copy_dir_unzipped ... ok test_copy_dir_zipped (egg_extract_test.TestEggExtract) test copy_dir_zipped ... ok test_copy_file (egg_extract_test.TestEggExtract) test copy_file ... ok test_copy_file_unzipped (egg_extract_test.TestEggExtract) test _copy_file_unzipped ... ok test_copy_file_zipped (egg_extract_test.TestEggExtract) test _copy_file_zipped ... ok test_init_and_write (egg_extract_test.TestEggExtract) test __init__ ... ok test_blastn_version (external_progs_test.TestExternalProgs) Test blastn version ... ok test_delta_filter_in_path (external_progs_test.TestExternalProgs) Test delta-filter in path ... ok test_kmc_dump_in_path (external_progs_test.TestExternalProgs) Test kmc_dump in path ... ok test_kmc_dump_version (external_progs_test.TestExternalProgs) Test kmc_dump version ... ok test_kmc_in_path (external_progs_test.TestExternalProgs) Test kmc in path ... ok test_kmc_version (external_progs_test.TestExternalProgs) Test kmc version ... ok test_makeblastdb_version (external_progs_test.TestExternalProgs) Test makeblastdb version ... ok test_nucmer_in_path (external_progs_test.TestExternalProgs) Test nucmer in path ... ok test_nucmer_version (external_progs_test.TestExternalProgs) Test nucmer version ... ok test_r_version (external_progs_test.TestExternalProgs) Test R versions ... ok test_samtools_in_path (external_progs_test.TestExternalProgs) Test samtools in path ... ok test_samtools_original_version (external_progs_test.TestExternalProgs) Test samtools original version ... ok test_samtools_version (external_progs_test.TestExternalProgs) Test samtools version ... ok test_show_coords_in_path (external_progs_test.TestExternalProgs) Test show-coords in path ... ok test_smalt_in_path (external_progs_test.TestExternalProgs) Test smalt in path ... ok test_smalt_version (external_progs_test.TestExternalProgs) Test smalt version ... ok test_add_and_get_edges (graph_test.TestGraph) test adding and getting edges ... ok test_connected_components (graph_test.TestGraph) test connected_components ... ok test_degree (graph_test.TestGraph) test degree ... ok test_edges_are_consistent (graph_test.TestGraph) test edges_are_consistent ... ok test_find_simple_path (graph_test.TestGraph) test find_simple_path ... ok test_get_nodes (graph_test.TestGraph) test get_nodes ... ok test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph) test merged_coords_from_simple_nonredundant_path ... ok test_node_to_coords (graph_test.TestGraph) test _node_to_coords ... ok test_remove_middle_node (graph_test.TestGraph) test remove_middle_node ... ok test_remove_node (graph_test.TestGraph) test remove_node ... ok test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph) test remove_redundant_nodes_from_simple_path ... ok test_simple_path_is_consistent (graph_test.TestGraph) test simple_path_is_consistent ... ok test_counts_file_to_fasta (kcount_test.TestKcount) Test _counts_file_to_fasta ... ok test_head_fastaq_fa (kcount_test.TestKcount) Test head_fastaq with FASTA input ... ok test_head_fastaq_fq (kcount_test.TestKcount) Test head_fastaq with FASTQ input ... ok test_kmc_to_kmer_counts (kcount_test.TestKcount) Test _kmc_to_kmer_counts ... ok test_median (kcount_test.TestKcount) Test _median() ... ok test_append (kmers_test.TestKmers) Test append ... ok test_commonest_kmers (kmers_test.TestKmers) ... ok test_extend (kmers_test.TestKmers) Test extend ... ok test_extension (kmers_test.TestKmers) Test extension ... ok test_init (kmers_test.TestKmers) Test __init__ ... ok test_kmer_dict (kmers_test.TestKmers) Test kmer_dict ... ok test_append_to_file (kraken_test.TestKraken) test _append_to_file ... ok test_count_cds_from_embl (kraken_test.TestKraken) test count_cds_from_embl ... ok test_genbank_to_taxon_and_gi (kraken_test.TestKraken) test _genbank_to_taxon_and_gi ... ok test_get_most_common_species_dir (kraken_test.TestKraken) Test get_most_common_species ... ok test_get_parent_taxons (kraken_test.TestKraken) test _get_parent_taxons ... ok test_load_extra_ref_info (kraken_test.TestKraken) test _load_extra_ref_info ... ok test_replace_fasta_header (kraken_test.TestKraken) test _replace_fasta_header ... ok test_species_to_dir (kraken_test.TestKraken) test species_to_dir ... ok test_bam_file_to_fasta_pair_files (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files with a region ... ok test_bam_file_to_region_fasta (mapping_test.TestMapping) Test bam_file_to_region_fasta ... ok test_bam_to_fasta (mapping_test.TestMapping) Test bam_to_fasta ... ok test_can_extend (mapping_test.TestMapping) Test can_extend ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_consensus_base (mapping_test.TestMapping) Test consensus_base ... ok test_consensus_base_both_strands (mapping_test.TestMapping) Test consensus_base_both_strands ... ok test_find_incorrect_ref_bases (mapping_test.TestMapping) Test find_incorrect_ref_bases ... ok test_get_bam_region_coverage_fwd (mapping_test.TestMapping) Test get_bam_region_coverage forward strand ... ok test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping) Test get_bam_region_coverage both strands ... ok test_get_bam_region_coverage_rev (mapping_test.TestMapping) Test get_bam_region_coverage reverse strand ... ok test_get_pair_type (mapping_test.TestMapping) Test get_pair_type ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_get_ref_name (mapping_test.TestMapping) Test get_ref_name ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_map_reads (mapping_test.TestMapping) Test mapping reads ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam' ok test_map_reads_and_sort (mapping_test.TestMapping) Test mapping reads and sort BAM ... ok test_map_reads_wth_flag (mapping_test.TestMapping) Test map_reads with required flag ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.flag12.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam' ok test_remove_indels (mapping_test.TestMapping) Test _remove_indels ... ok test_sam_to_fasta (mapping_test.TestMapping) Test sam_to_fasta ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_smalt_in_path (mapping_test.TestMapping) Test that samtools is in the user's path ... ok test_soft_clipped (mapping_test.TestMapping) Test soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_strip_mpileup_coverage_string (mapping_test.TestMapping) Test strip_mpileup_coverage_string ... ok test_total_ref_length_from_bam (mapping_test.TestMapping) Test _total_ref_length_from_bam ... [E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/iva/tests/data/mapping_test.total_ref_length_from_bam.bam' ok test_file_read (mummer_test.TestMummer) test file_read ... ok test_is_at_ends (mummer_test.TestMummer) Test is_at_ends ... ok test_is_self_hit (mummer_test.TestMummer) Test is_self_hit ... ok test_on_same_strand (mummer_test.TestMummer) test on_same_strand ... ok test_qry_coords (mummer_test.TestMummer) Test qry_coords ... ok test_ref_coords (mummer_test.TestMummer) Test ref_coords ... ok test_run_nucmer (mummer_test.TestMummer) test run_nucmer ... ok test_sort (mummer_test.TestMummer) test sort ... ok test_swap (mummer_test.TestMummer) test swap ... ok test_to_graph_edge (mummer_test.TestMummer) Test to_graph_edge ... ok test_run_gage (qc_external_test.TestQcExternal) test run_gage ... ok test_run_ratt (qc_external_test.TestQcExternal) test run_ratt ... ok test_calculate_cds_assembly_stats (qc_test.TestQc) test _calculate_cds_assembly_stats ... ok test_calculate_contig_placement (qc_test.TestQc) test calculate_contig_placement ... ok test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc) test _calculate_ref_positions_covered_by_contigs ... ok test_calculate_ref_read_coverage (qc_test.TestQc) test _calculate_ref_read_coverage ... ok test_calculate_ref_read_region_coverage (qc_test.TestQc) test _calculate_ref_read_region_coverage ... ok test_calculate_refseq_assembly_stats (qc_test.TestQc) test _calculate_refseq_assembly_stats ... ok test_calculate_should_have_assembled (qc_test.TestQc) test _calculate_should_have_assembled ... ok test_contig_placement_in_reference (qc_test.TestQc) test _contig_placement_in_reference ... ok test_contigs_and_bases_that_hit_ref (qc_test.TestQc) test _contigs_and_bases_that_hit_ref ... ok test_cov_to_R_string (qc_test.TestQc) test _cov_to_R_string ... ok test_coverage_list_to_low_cov_intervals (qc_test.TestQc) test _coverage_list_to_low_cov_intervals ... ok test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc) test _get_R_plot_contig_order_from_contig_placement ... ok test_get_contig_hits_to_reference (qc_test.TestQc) test _get_contig_hits_to_reference ... ok test_get_overlapping_qry_hits (qc_test.TestQc) test _get_overlapping_qry_hits ... ok test_get_ref_cds_from_gff (qc_test.TestQc) test _get_ref_cds_from_gff ... ok test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc) test _get_unique_and_repetitive_from_contig_hits ... ok test_gff_and_fasta_to_cds (qc_test.TestQc) test _gff_and_fasta_to_cds ... ok test_has_orf (qc_test.TestQc) test _has_orf ... ok test_hash_nucmer_hits_by_ref (qc_test.TestQc) test _hash_nucmer_hits_by_ref ... ok test_ids_in_order_from_fai (qc_test.TestQc) test _ids_in_order_from_fai ... ok test_invert_list (qc_test.TestQc) test _invert_list ... ok test_map_cds_to_assembly (qc_test.TestQc) test _map_cds_to_assembly ... ok test_mummer_coords_file_to_dict (qc_test.TestQc) test _mummer_coords_file_to_dict ... ok test_write_cds_seqs (qc_test.TestQc) test _write_cds_seqs ... ok test_write_fasta_contigs_hit_ref (qc_test.TestQc) test _write_fasta_contigs_hit_ref ... ok test_write_fasta_contigs_not_hit_ref (qc_test.TestQc) test _write_fasta_contigs_not_hit_ref ... ok test_write_ref_coverage_to_files_for_R (qc_test.TestQc) test _write_ref_coverage_to_files_for_R ... ok test_run_trimmomatic (read_trim_test.TestReadTrim) Test run_trimmomatic ... ok test_extend (seed_test.TestSeed) Test extend ... ok test_extend_with_reads_as_single_end (seed_test.TestSeed) Test _extend_with_reads_as_single_end ... ok test_extension_from_read (seed_test.TestSeed) Test _test_extension_from_read ... ok test_extensions_from_reads_file (seed_test.TestSeed) Test _extensions_from_reads_file ... ok test_init (seed_test.TestSeed) test init ... ok test_kmc_in_path (seed_test.TestSeed) Test that kmc is in the user's path ... ok test_len (seed_test.TestSeed) Test len ... ok test_write_fasta (seed_test.TestSeed) Test write_fasta ... ok ---------------------------------------------------------------------- Ran 160 tests in 9.365s OK make[1]: Leaving directory '/build/iva-1.0.9+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/iva-1.0.9+ds/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install running build running build_py running build_scripts running install_lib creating /build/iva-1.0.9+ds/debian/iva/usr creating /build/iva-1.0.9+ds/debian/iva/usr/lib creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9 creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reference.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/main.ratt.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/start.ratt.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/genbank2embl.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/colsum.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/__init__.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/assembly.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/common.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/edge.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/egg_extract.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/external_progs.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/graph.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kcount.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kmers.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kraken.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mummer.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc_external.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed_processor.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_data_runner.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mapping.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/__init__.py to __init__.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/assembly.py to assembly.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/common.py to common.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig.py to contig.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig_trim.py to contig_trim.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/edge.py to edge.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/egg_extract.py to egg_extract.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/external_progs.py to external_progs.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/graph.py to graph.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kcount.py to kcount.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kmers.py to kmers.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kraken.py to kraken.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mummer.py to mummer.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc.py to qc.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc_external.py to qc_external.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim.py to read_trim.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed.py to seed.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed_processor.py to seed_processor.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mapping.py to mapping.cpython-39.pyc running install_egg_info running egg_info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva -> /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva_qc -> /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva_qc_make_db -> /build/iva-1.0.9+ds/debian/iva/usr/bin changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva to 755 changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 755 changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/iva-1.0.9+ds' mkdir -p /build/iva-1.0.9+ds/debian/man PYTHONPATH=. help2man -N -o /build/iva-1.0.9+ds/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /build/iva-1.0.9+ds/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /build/iva-1.0.9+ds/debian/man/iva_qc_make_db.1 \ -n 'make a database as input for iva_qc' \ --no-discard-stderr ./scripts/iva_qc_make_db dh_installman -- make[1]: Leaving directory '/build/iva-1.0.9+ds' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'iva' in '../iva_1.0.9+ds-11_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../iva_1.0.9+ds-11_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/20052/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/20052/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/20052 and its subdirectories I: Current time: Fri Aug 6 08:05:03 +14 2021 I: pbuilder-time-stamp: 1628186703