I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 17 22:48:08 +14 2021 I: pbuilder-time-stamp: 1639730888 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [unicycler_0.4.7+dfsg-2.dsc] I: copying [./unicycler_0.4.7+dfsg.orig.tar.xz] I: copying [./unicycler_0.4.7+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Oct 29 06:31:47 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./unicycler_0.4.7+dfsg-2.dsc dpkg-source: info: extracting unicycler in unicycler-0.4.7+dfsg dpkg-source: info: unpacking unicycler_0.4.7+dfsg.orig.tar.xz dpkg-source: info: unpacking unicycler_0.4.7+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spades.patch dpkg-source: info: applying install_wo_extra_steps.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2951083/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. 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/2951083/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2951083/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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=be86416a788448c782508db3be059ca8 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=2951083 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.IrjtQtjXdf/pbuilderrc_XtJT --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.IrjtQtjXdf/b2 --logfile b2/build.log unicycler_0.4.7+dfsg-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Dec 17 22:48 sh -> bash lrwxrwxrwx 1 root root 4 Nov 8 11:58 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/2951083/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, python3-all, python3-setuptools, default-jdk, bowtie2, ncbi-blast+, pilon, racon, samtools, spades, libseqan2-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on pilon; however: Package pilon is not installed. pbuilder-satisfydepends-dummy depends on racon; however: Package racon is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on spades; however: Package spades is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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: ant{a} ant-optional{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bamtools{a} bowtie2{a} bsdmainutils{a} bwa{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} java-common{a} java-wrappers{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasound2{a} libasound2-data{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbamtools2.5.1{a} libbsd0{a} libcdi-api-java{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcroco3{a} libcups2{a} libcurl3-gnutls{a} libdbus-1-3{a} libdeflate0{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libedit2{a} libedlib0{a} libelf1{a} libexpat1{a} libfastinfoset-java{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libguava-java{a} libguice-java{a} libharfbuzz0b{a} libhat-trie0{a} libhts2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libicu63{a} libistack-commons-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjpeg62-turbo{a} libjsoncpp1{a} libjsoup-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm7{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libngs-java{a} libngs-sdk-dev{a} libngs-sdk2{a} libnlopt0{a} libnspr4{a} libnss3{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libprocps7{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librelaxng-datatype-java{a} librngom-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqan2-dev{a} libsigsegv2{a} libsisu-guice-java{a} libsisu-inject-java{a} libsisu-ioc-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libspoa1.1.5{a} libssh2-1{a} libssl1.1{a} libssw0{a} libstax-ex-java{a} libstreambuffer-java{a} libtbb2{a} libthread-pool0{a} libtool{a} libtxw2-java{a} libuchardet0{a} libwagon-http-java{a} libwagon-provider-api-java{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-sync1{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libyaml-0-2{a} lsb-base{a} m4{a} man-db{a} mime-support{a} ncbi-blast+{a} ncbi-data{a} openjdk-11-jdk{a} openjdk-11-jdk-headless{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} pilon{a} po-debconf{a} procps{a} python{a} python-joblib{a} python-minimal{a} python-yaml{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.7{a} python3.7-minimal{a} racon{a} readline-common{a} samtools{a} scala-library{a} sensible-utils{a} spades{a} ucf{a} unzip{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl cwltool dbus fonts-dejavu-extra krb5-locales libarchive-cpio-perl libasm-java libatk-wrapper-java-jni libcglib-java libglib2.0-data libgpm2 libjansi-java libltdl-dev libmail-sendmail-perl libsasl2-modules libxt-dev lynx psmisc publicsuffix python-lz4 python-numpy python-psutil python-pytest python-simplejson shared-mime-info wget xdg-user-dirs 0 packages upgraded, 250 newly installed, 0 to remove and 0 not upgraded. Need to get 380 MB of archives. After unpacking 931 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.12+7-2~deb10u1 [37.2 MB] Get: 70 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 ant all 1.10.5-2 [2082 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 ant-optional all 1.10.5-2 [379 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 bamtools amd64 2.5.1+dfsg-3 [171 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 bwa amd64 0.7.17-3 [195 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libglvnd0 amd64 1.1.0-1 [48.6 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libdrm-common all 2.4.97-1 [13.8 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libdrm2 amd64 2.4.97-1 [39.7 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libglapi-mesa amd64 18.3.6-2+deb10u1 [66.3 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1+deb10u2 [191 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libxdamage1 amd64 1:1.1.4-3+b3 [14.9 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 118 http://deb.debian.org/debian buster/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libdrm-amdgpu1 amd64 2.4.97-1 [27.3 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libdrm-intel1 amd64 2.4.97-1 [69.8 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libdrm-nouveau2 amd64 2.4.97-1 [26.3 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libdrm-radeon1 amd64 2.4.97-1 [31.1 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libllvm7 amd64 1:7.0.1-8+deb10u2 [13.1 MB] Get: 126 http://deb.debian.org/debian buster/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-dri amd64 18.3.6-2+deb10u1 [6685 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libglx-mesa0 amd64 18.3.6-2+deb10u1 [180 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libgif7 amd64 5.1.4-3 [43.3 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre amd64 11.0.12+7-2~deb10u1 [174 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 default-jre amd64 2:1.11-71 [1044 B] Get: 139 http://deb.debian.org/debian buster/main amd64 openjdk-11-jdk-headless amd64 11.0.12+7-2~deb10u1 [221 MB] Get: 140 http://deb.debian.org/debian buster/main amd64 default-jdk-headless amd64 2:1.11-71 [1104 B] Get: 141 http://deb.debian.org/debian buster/main amd64 openjdk-11-jdk amd64 11.0.12+7-2~deb10u1 [2693 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 default-jdk amd64 2:1.11-71 [1056 B] Get: 143 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 java-wrappers all 0.3 [10.9 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 libaopalliance-java all 20070526-6 [9048 B] Get: 150 http://deb.debian.org/debian buster/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 151 http://deb.debian.org/debian buster/main amd64 libargs4j-java all 2.33-1 [139 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 153 http://deb.debian.org/debian buster/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 154 http://deb.debian.org/debian buster/main amd64 libcdi-api-java all 1.2-2 [54.5 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 156 http://deb.debian.org/debian buster/main amd64 libdom4j-java all 2.1.1-2 [310 kB] Get: 157 http://deb.debian.org/debian buster/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 158 http://deb.debian.org/debian buster/main amd64 libcommons-io-java all 2.6-2+deb10u1 [213 kB] Get: 159 http://deb.debian.org/debian buster/main amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 160 http://deb.debian.org/debian buster/main amd64 libcommons-cli-java all 1.4-1 [55.2 kB] Get: 161 http://deb.debian.org/debian buster/main amd64 libcommons-lang3-java all 3.8-2 [478 kB] Get: 162 http://deb.debian.org/debian buster/main amd64 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get: 163 http://deb.debian.org/debian buster/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 164 http://deb.debian.org/debian buster/main amd64 libguava-java all 19.0-1 [2028 kB] Get: 165 http://deb.debian.org/debian buster/main amd64 libguice-java all 4.2.1-1 [962 kB] Get: 166 http://deb.debian.org/debian buster/main amd64 libmaven-parent-java all 31-2 [5100 B] Get: 167 http://deb.debian.org/debian buster/main amd64 libplexus-utils2-java all 3.1.1-1 [249 kB] Get: 168 http://deb.debian.org/debian buster/main amd64 libwagon-provider-api-java all 3.3.1-2 [50.1 kB] Get: 169 http://deb.debian.org/debian buster/main amd64 libmaven-resolver-java all 1.3.1-1 [549 kB] Get: 170 http://deb.debian.org/debian buster/main amd64 libplexus-cipher-java all 1.7-3 [15.0 kB] Get: 171 http://deb.debian.org/debian buster/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 172 http://deb.debian.org/debian buster/main amd64 libplexus-component-annotations-java all 1.7.1-7 [7536 B] Get: 173 http://deb.debian.org/debian buster/main amd64 libplexus-interpolation-java all 1.25-1 [76.8 kB] Get: 174 http://deb.debian.org/debian buster/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 175 http://deb.debian.org/debian buster/main amd64 libslf4j-java all 1.7.25-3 [143 kB] Get: 176 http://deb.debian.org/debian buster/main amd64 libsisu-inject-java all 0.3.3-1 [347 kB] Get: 177 http://deb.debian.org/debian buster/main amd64 libsisu-plexus-java all 0.3.3-3 [182 kB] Get: 178 http://deb.debian.org/debian buster/main amd64 libmaven3-core-java all 3.6.0-1 [1465 kB] Get: 179 http://deb.debian.org/debian buster/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 180 http://deb.debian.org/debian buster/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 181 http://deb.debian.org/debian buster/main amd64 libcommons-compress-java all 1.18-2+deb10u1 [531 kB] Get: 182 http://deb.debian.org/debian buster/main amd64 libplexus-io-java all 3.1.1-1 [64.6 kB] Get: 183 http://deb.debian.org/debian buster/main amd64 libsnappy1v5 amd64 1.1.7-1 [17.0 kB] Get: 184 http://deb.debian.org/debian buster/main amd64 libsnappy-jni amd64 1.1.7.2-1 [7148 B] Get: 185 http://deb.debian.org/debian buster/main amd64 libsnappy-java all 1.1.7.2-1 [73.7 kB] Get: 186 http://deb.debian.org/debian buster/main amd64 libxz-java all 1.8-2 [141 kB] Get: 187 http://deb.debian.org/debian buster/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 188 http://deb.debian.org/debian buster/main amd64 libsisu-guice-java all 4.2.0-1 [785 kB] Get: 189 http://deb.debian.org/debian buster/main amd64 libsisu-ioc-java all 2.3.0-11 [492 kB] Get: 190 http://deb.debian.org/debian buster/main amd64 libhttpcore-java all 4.4.11-1 [625 kB] Get: 191 http://deb.debian.org/debian buster/main amd64 libcommons-codec-java all 1.11-1 [271 kB] Get: 192 http://deb.debian.org/debian buster/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 193 http://deb.debian.org/debian buster/main amd64 libhttpclient-java all 4.5.7-1+deb10u1 [721 kB] Get: 194 http://deb.debian.org/debian buster/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get: 195 http://deb.debian.org/debian buster/main amd64 libwagon-http-java all 3.3.1-2 [50.5 kB] Get: 196 http://deb.debian.org/debian buster/main amd64 libistack-commons-java all 3.0.6-3 [144 kB] Get: 197 http://deb.debian.org/debian buster/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-8 [163 kB] Get: 198 http://deb.debian.org/debian buster/main amd64 libcommons-jexl2-java all 2.1.1-4 [257 kB] Get: 199 http://deb.debian.org/debian buster/main amd64 libcommons-lang-java all 2.6-8 [273 kB] Get: 200 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 201 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 202 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 203 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 204 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 205 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 206 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 207 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 208 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 209 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 210 http://deb.debian.org/debian buster/main amd64 libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get: 211 http://deb.debian.org/debian buster/main amd64 libedlib0 amd64 1.2.4-1 [16.1 kB] Get: 212 http://deb.debian.org/debian buster/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 213 http://deb.debian.org/debian buster/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 214 http://deb.debian.org/debian buster/main amd64 libstreambuffer-java all 1.5.4-1 [71.8 kB] Get: 215 http://deb.debian.org/debian buster/main amd64 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get: 216 http://deb.debian.org/debian buster/main amd64 libxsom-java all 2.3.0.1-8 [396 kB] Get: 217 http://deb.debian.org/debian buster/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 218 http://deb.debian.org/debian buster/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get: 219 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 220 http://deb.debian.org/debian buster/main amd64 librngom-java all 2.3.0.1-8 [288 kB] Get: 221 http://deb.debian.org/debian buster/main amd64 libtxw2-java all 2.3.0.1-8 [134 kB] Get: 222 http://deb.debian.org/debian buster/main amd64 libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get: 223 http://deb.debian.org/debian buster/main amd64 libjaxb-java all 2.3.0.1-8 [1966 kB] Get: 224 http://deb.debian.org/debian buster/main amd64 libngs-sdk2 amd64 2.9.3-1 [62.7 kB] Get: 225 http://deb.debian.org/debian buster/main amd64 libngs-sdk-dev amd64 2.9.3-1 [111 kB] Get: 226 http://deb.debian.org/debian buster/main amd64 libngs-java amd64 2.9.3-1 [79.9 kB] Get: 227 http://deb.debian.org/debian buster/main amd64 libhtsjdk-java all 2.18.2+dfsg-2 [1499 kB] Get: 228 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get: 229 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get: 230 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get: 231 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get: 232 http://deb.debian.org/debian buster/main amd64 libnlopt0 amd64 2.4.2+dfsg-8+b1 [165 kB] Get: 233 http://deb.debian.org/debian buster/main amd64 libseqan2-dev all 2.4.0+dfsg-11 [1220 kB] Get: 234 http://deb.debian.org/debian buster/main amd64 libspoa1.1.5 amd64 1.1.5-1 [29.3 kB] Get: 235 http://deb.debian.org/debian buster/main amd64 libssw0 amd64 1.1-2 [16.5 kB] Get: 236 http://deb.debian.org/debian buster/main amd64 libthread-pool0 amd64 1.0.0-2 [8532 B] Get: 237 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get: 238 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 239 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get: 240 http://deb.debian.org/debian buster/main amd64 scala-library all 2.11.12-4 [9589 kB] Get: 241 http://deb.debian.org/debian buster/main amd64 pilon all 1.23+dfsg-1 [421 kB] Get: 242 http://deb.debian.org/debian buster/main amd64 python-joblib all 0.13.0-2 [190 kB] Get: 243 http://deb.debian.org/debian buster/main amd64 python-yaml amd64 3.13-2 [127 kB] Get: 244 http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 [1068 B] Get: 245 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 246 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Get: 247 http://deb.debian.org/debian buster/main amd64 racon amd64 1.3.2-1+b1 [52.9 kB] Get: 248 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get: 249 http://deb.debian.org/debian buster/main amd64 spades amd64 3.13.0+dfsg2-2 [4755 kB] Get: 250 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 380 MB in 14s (27.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../003-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../007-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... 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Selecting previously unselected package ca-certificates-java. Preparing to unpack .../015-ca-certificates-java_20190405_all.deb ... Unpacking ca-certificates-java (20190405) ... Selecting previously unselected package java-common. Preparing to unpack .../016-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../017-libavahi-common-data_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../018-libavahi-common3_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../019-libdbus-1-3_1.12.20-0+deb10u1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Selecting previously unselected package libavahi-client3:amd64. 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Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../026-libcups2_2.2.10-6+deb10u4_amd64.deb ... Unpacking libcups2:amd64 (2.2.10-6+deb10u4) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../027-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../028-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../029-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../030-libfreetype6_2.9.1-3+deb10u2_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u2) ... Selecting previously unselected package fonts-dejavu-core. 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Setting up libhttpcore-java (4.4.11-1) ... Setting up libngs-java (2.9.3-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libdrm-common (2.4.97-1) ... Setting up libcdi-api-java (1.2-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libsnappy-jni (1.1.7.2-1) ... Setting up libssw0:amd64 (1.1-2) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libargs4j-java (2.33-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libdom4j-java (2.1.1-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libwagon-provider-api-java (3.3.1-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up java-wrappers (0.3) ... Setting up libtool (2.4.6-9) ... Setting up libmbedx509-0:amd64 (2.16.0-1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:amd64 (1.13.1-2) ... Setting up libmaven-parent-java (31-2) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libmbedtls12:amd64 (2.16.0-1) ... Setting up libavahi-common3:amd64 (0.7-4+deb10u1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up libcommons-lang-java (2.6-8) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libxcb-present0:amd64 (1.13.1-2) ... Setting up libcommons-jexl2-java (2.1.1-4) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up libguava-java (19.0-1) ... Setting up libxcb-sync1:amd64 (1.13.1-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up racon (1.3.2-1+b1) ... Setting up libstreambuffer-java (1.5.4-1) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libcommons-lang3-java (3.8-2) ... Setting up autoconf (2.69-11) ... Setting up libxcb-dri2-0:amd64 (1.13.1-2) ... Setting up librngom-java (2.3.0.1-8) ... Setting up libdrm2:amd64 (2.4.97-1) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up bamtools (2.5.1+dfsg-3) ... Setting up libllvm7:amd64 (1:7.0.1-8+deb10u2) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libsnappy-java (1.1.7.2-1) ... Setting up libxsom-java (2.3.0.1-8) ... Setting up libcommons-codec-java (1.11-1) ... Setting up libavahi-client3:amd64 (0.7-4+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.97-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.13.1-2) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up libdrm-nouveau2:amd64 (2.4.97-1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.18-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcommons-io-java (2.6-2+deb10u1) ... Setting up libdrm-radeon1:amd64 (2.4.97-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libdrm-intel1:amd64 (2.4.97-1) ... Setting up libgl1-mesa-dri:amd64 (18.3.6-2+deb10u1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libsisu-ioc-java (2.3.0-11) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up libguice-java (4.2.1-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libcups2:amd64 (2.2.10-6+deb10u4) ... Setting up libhttpclient-java (4.5.7-1+deb10u1) ... Setting up libwagon-http-java (3.3.1-2) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up libplexus-io-java (3.1.1-1) ... Setting up libxdamage1:amd64 (1:1.1.4-3+b3) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-all (3.7.3-1) ... Setting up libsisu-inject-java (0.3.3-1) ... Setting up samtools (1.9-4) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up libsisu-plexus-java (0.3.3-3) ... Setting up python-joblib (0.13.0-2) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up python-yaml (3.13-2) ... Setting up libglx-mesa0:amd64 (18.3.6-2+deb10u1) ... Setting up libglx0:amd64 (1.1.0-1) ... Setting up libmaven3-core-java (3.6.0-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libgl1:amd64 (1.1.0-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up spades (3.13.0+dfsg2-2) ... Setting up default-jre-headless (2:1.11-71) ... Setting up openjdk-11-jre-headless:amd64 (11.0.12+7-2~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.12+7-2~deb10u1) ... Setting up openjdk-11-jdk-headless:amd64 (11.0.12+7-2~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre (2:1.11-71) ... Setting up dh-autoreconf (19) ... Setting up default-jdk-headless (2:1.11-71) ... Setting up ant (1.10.5-2) ... Setting up openjdk-11-jdk:amd64 (11.0.12+7-2~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem 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:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.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: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:Taiwan_GRCA.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_Root_CA_-_G2.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:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.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_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.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:EE_Certification_Centre_Root_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. Setting up debhelper (12.1.1) ... Setting up default-jdk (2:1.11-71) ... Setting up ant-optional (1.10.5-2) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libistack-commons-java (3.0.6-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Setting up libtxw2-java (2.3.0.1-8) ... Setting up libjaxb-java (2.3.0.1-8) ... Setting up libhtsjdk-java (2.18.2+dfsg-2) ... Setting up pilon (1.23+dfsg-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... 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... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/unicycler-0.4.7+dfsg/ && 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 > ../unicycler_0.4.7+dfsg-2_source.changes dpkg-buildpackage: info: source package unicycler dpkg-buildpackage: info: source version 0.4.7+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Liubov Chuprikova dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/unicycler-0.4.7+dfsg' find . -name __pycache__ -type d | xargs rm -rf make distclean make[2]: Entering directory '/build/unicycler-0.4.7+dfsg' Platform: Linux Compiler: g++ 8.3.0 rm -f unicycler/src/string_functions.o unicycler/src/start_end_align.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align.o unicycler/src/scrub.o unicycler/src/scoredalignment.o unicycler/src/ref_seqs.o unicycler/src/random_alignments.o unicycler/src/path_align.o unicycler/src/overlap_align.o unicycler/src/minimap_align.o unicycler/src/minimap/sketch.o unicycler/src/minimap/sdust.o unicycler/src/minimap/misc.o unicycler/src/minimap/map.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/minimap/bseq.o unicycler/src/miniasm_assembly.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asg.o unicycler/src/kmers.o unicycler/src/global_align.o unicycler/src/consensus_align.o rm -f unicycler/cpp_functions.so make[2]: Leaving directory '/build/unicycler-0.4.7+dfsg' make[1]: Leaving directory '/build/unicycler-0.4.7+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --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:217: python3.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/unicycler-0.4.7+dfsg' make make[2]: Entering directory '/build/unicycler-0.4.7+dfsg' Platform: Linux Compiler: g++ 8.3.0 g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/string_functions.o unicycler/src/string_functions.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/start_end_align.o unicycler/src/start_end_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align_exhaustive.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/semi_global_align.o unicycler/src/semi_global_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/scrub.o unicycler/src/scrub.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/ref_seqs.o unicycler/src/ref_seqs.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/random_alignments.o unicycler/src/random_alignments.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/path_align.o unicycler/src/path_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/overlap_align.o unicycler/src/overlap_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap_align.o unicycler/src/minimap_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/sketch.o unicycler/src/minimap/sketch.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/sdust.o unicycler/src/minimap/sdust.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/misc.o unicycler/src/minimap/misc.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/map.o unicycler/src/minimap/map.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/kthread.o unicycler/src/minimap/kthread.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/index.o unicycler/src/minimap/index.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/bseq.o unicycler/src/minimap/bseq.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm_assembly.o unicycler/src/miniasm_assembly.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asm.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/kmers.o unicycler/src/kmers.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/global_align.o unicycler/src/global_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/consensus_align.o unicycler/src/consensus_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/unicycler-0.4.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-soname,unicycler/cpp_functions.so -o unicycler/cpp_functions.so unicycler/src/string_functions.o unicycler/src/start_end_align.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align.o unicycler/src/scrub.o unicycler/src/scoredalignment.o unicycler/src/ref_seqs.o unicycler/src/random_alignments.o unicycler/src/path_align.o unicycler/src/overlap_align.o unicycler/src/minimap_align.o unicycler/src/minimap/sketch.o unicycler/src/minimap/sdust.o unicycler/src/minimap/misc.o unicycler/src/minimap/map.o unicycler/src/minimap/kthread.o unicycler/src/minimap/index.o unicycler/src/minimap/bseq.o unicycler/src/miniasm_assembly.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asg.o unicycler/src/kmers.o unicycler/src/global_align.o unicycler/src/consensus_align.o -shared -lz make[2]: Leaving directory '/build/unicycler-0.4.7+dfsg' dh_auto_build I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/misc.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/version.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/vcf_func.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_scrub.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_polish.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_check.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_align.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/string_graph.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/spades_func.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/settings.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/read_ref.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/pilon_func.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/path_finding.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/minimap_alignment.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/miniasm_assembly.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/log.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/cpp_wrappers.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_spades_contig.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_miniasm.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_loop_unroll.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_long_read_simple.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_long_read.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_common.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/blast_func.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/assembly_graph_segment.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/assembly_graph_copy_depth.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/assembly_graph.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/alignment.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/__init__.py -> /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler make[1]: Leaving directory '/build/unicycler-0.4.7+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:272: cp -a unicycler-runner.py /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build; cp -a unicycler/cpp_functions.so /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler; cp -a sample_data /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build I: pybuild base:217: cd /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build; python3.7 -m unittest discover -v test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_filter_by_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_all_gfa_link_lines (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_estimated_sequence_len (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_n_segment_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_load_spades_paths (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_all_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_specific_segments_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_fasta_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_gfa (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_add_link_1 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_add_link_2 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_all_segments_below_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_bad_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_change_if_deleted (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_change_if_path_deleted (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_filter_homopolymer_loops (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_connected_components_and_remove_link (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_connected_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_exclusive_inputs (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_exclusive_outputs (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_mean_path_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_next_available_seg_number (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_path_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_simple_path (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_lead_exclusively_from (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_lead_exclusively_to (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_all_possible (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_1 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_2 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_3 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_remove_small_dead_ends (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_seq_from_signed_seg_num (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_expand_repeats_1 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_2 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_3 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_4 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_5 (test.test_assembly_graph.TestExpandRepeats) ... ok test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_11 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_2 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_4 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_6 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_7 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_8 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_graph (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_1 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_2 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_3 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_4 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_5 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_6 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_merge_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_single_copy_segments_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_random_seq_no_start_gene (test.test_blast_func.TestBlastFunc) ... ok test_random_seq_with_exact_gene_forward_strand (test.test_blast_func.TestBlastFunc) ... ok test_random_seq_with_exact_gene_reverse_strand (test.test_blast_func.TestBlastFunc) ... ok test_1bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_1bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_insertion_and_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_long_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_one_mismatch (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_random_seqs (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_shift_big_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_shift_small_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_consensus_different_qualities (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_all (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_deletions_and_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_subs (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_insertions_and_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_two_way_consensus (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_bad_pilon (test.test_dependencies.TestDependencies) ... ok test_bowtie2_build_not_found (test.test_dependencies.TestDependencies) ... ok test_bowtie2_not_found (test.test_dependencies.TestDependencies) ... ok test_java_not_found (test.test_dependencies.TestDependencies) ... ok test_makeblastdb_not_found (test.test_dependencies.TestDependencies) ... ok test_no_pilon (test.test_dependencies.TestDependencies) ... ok test_no_rotate (test.test_dependencies.TestDependencies) ... ok test_pilon_not_found (test.test_dependencies.TestDependencies) ... ok test_samtools_not_found (test.test_dependencies.TestDependencies) ... ok test_spades_not_found (test.test_dependencies.TestDependencies) ... ok test_tblastn_not_found (test.test_dependencies.TestDependencies) ... ok test_verbosity_1 (test.test_dependencies.TestDependencies) ... ok test_verbosity_2 (test.test_dependencies.TestDependencies) ... ok test_basic_options (test.test_help_text.TestBasicHelpText) ... ok test_extended_options (test.test_help_text.TestBasicHelpText) ... ok test_output (test.test_help_text.TestBasicHelpText) ... ok test_return_code (test.test_help_text.TestBasicHelpText) ... ok test_title (test.test_help_text.TestBasicHelpText) ... ok test_error_message (test.test_help_text.TestEmptyCommand) ... ok test_output (test.test_help_text.TestEmptyCommand) ... ok test_return_code (test.test_help_text.TestEmptyCommand) ... ok test_basic_options (test.test_help_text.TestExtendedHelpText) ... ok test_extended_options (test.test_help_text.TestExtendedHelpText) ... ok test_output (test.test_help_text.TestExtendedHelpText) ... ok test_return_code (test.test_help_text.TestExtendedHelpText) ... ok test_title (test.test_help_text.TestExtendedHelpText) ... ok test_contig_placement_1 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_2 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_3 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_4 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_add_line_breaks_to_sequence (test.test_misc.TestMiscFunctions) ... ok test_colour (test.test_misc.TestMiscFunctions) ... ok test_convert_fastq_to_fasta (test.test_misc.TestMiscFunctions) ... ok test_flip_number_order (test.test_misc.TestMiscFunctions) ... ok test_float_to_str (test.test_misc.TestMiscFunctions) ... ok test_get_all_files_in_current_dir (test.test_misc.TestMiscFunctions) ... ok test_get_compression_type (test.test_misc.TestMiscFunctions) ... ok test_get_nice_header (test.test_misc.TestMiscFunctions) ... ok test_get_num_agreement (test.test_misc.TestMiscFunctions) ... ok test_get_percentile (test.test_misc.TestMiscFunctions) ... ok test_get_random_base (test.test_misc.TestMiscFunctions) ... ok test_get_random_sequence (test.test_misc.TestMiscFunctions) ... ok test_get_sequence_file_type (test.test_misc.TestMiscFunctions) ... ok test_int_to_str (test.test_misc.TestMiscFunctions) ... ok test_is_header_spades_format (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_1 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_2 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_3 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_4 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_5 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_6 (test.test_misc.TestMiscFunctions) ... ok test_len_without_format (test.test_misc.TestMiscFunctions) ... ok test_load_fasta (test.test_misc.TestMiscFunctions) ... ok test_load_fasta_with_full_header (test.test_misc.TestMiscFunctions) ... ok test_remove_formatting (test.test_misc.TestMiscFunctions) ... ok test_reverse_complement (test.test_misc.TestMiscFunctions) ... ok test_round_to_nearest_odd (test.test_misc.TestMiscFunctions) ... ok test_score_function (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_1 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_2 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_3 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_4 (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_capitals (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fa (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fasta (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fastq (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fastq_extra_dots (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fna (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fq (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_other_fasta (test.test_misc.TestMiscFunctions) ... ok test_weighted_average (test.test_misc.TestMiscFunctions) ... ok test_weighted_average_list (test.test_misc.TestMiscFunctions) ... ok test_absolute_paths (test.test_options.TestUnicyclerOptions) ... ok test_defaults (test.test_options.TestUnicyclerOptions) ... ok test_modes (test.test_options.TestUnicyclerOptions) ... ok test_relative_paths (test.test_options.TestUnicyclerOptions) ... ok test_long_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_medium_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_short_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_end_to_end (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_end_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_start_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_tough_alignment_0 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_1 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_10 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_15 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_3 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_4 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_5 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_7 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_8 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_9 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_bad_fastq_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_bad_fastq_2 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_count_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_count_2 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_lengths_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_lengths_2 (test.test_spades_func.TestSPAdesFunc) ... ok ---------------------------------------------------------------------- Ran 223 tests in 70.870s OK I: pybuild pybuild:298: rm /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler-runner.py; rm -r /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/sample_data; rm -r /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/__pycache__ create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/unicycler-0.4.7+dfsg' dh_auto_install --destdir=debian/unicycler I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/unicycler-0.4.7+dfsg/debian/unicycler running install running build running build_py running install_lib creating /build/unicycler-0.4.7+dfsg/debian/unicycler/usr creating /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib creating /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7 creating /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages creating /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/cpp_functions.so -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/__init__.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/alignment.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/assembly_graph.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/assembly_graph_segment.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/blast_func.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_common.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_long_read.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_miniasm.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_spades_contig.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/cpp_wrappers.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/log.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/miniasm_assembly.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/minimap_alignment.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/path_finding.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/pilon_func.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/read_ref.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/settings.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/spades_func.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/string_graph.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_align.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_check.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_polish.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_scrub.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/vcf_func.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/version.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/misc.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-0.4.7+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler.py -> /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/__init__.py to __init__.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/alignment.py to alignment.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/blast_func.py to blast_func.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/log.py to log.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/path_finding.py to path_finding.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/pilon_func.py to pilon_func.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/read_ref.py to read_ref.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/settings.py to settings.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/spades_func.py to spades_func.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/string_graph.py to string_graph.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_check.py to unicycler_check.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_polish.py to unicycler_polish.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_scrub.py to unicycler_scrub.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/vcf_func.py to vcf_func.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/version.py to version.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/misc.py to misc.cpython-37.pyc byte-compiling /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler.py to unicycler.cpython-37.pyc running install_egg_info running egg_info creating unicycler.egg-info writing unicycler.egg-info/PKG-INFO writing dependency_links to unicycler.egg-info/dependency_links.txt writing entry points to unicycler.egg-info/entry_points.txt writing top-level names to unicycler.egg-info/top_level.txt writing manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'unicycler.egg-info/SOURCES.txt' Copying unicycler.egg-info to /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler-0.4.7.egg-info Skipping SOURCES.txt running install_scripts Installing unicycler script to /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/bin Installing unicycler_align script to /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/bin Installing unicycler_check script to /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/bin Installing unicycler_polish script to /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/bin Installing unicycler_scrub script to /build/unicycler-0.4.7+dfsg/debian/unicycler/usr/bin  __  \ \___  \ ___\  //  ____// _ _ _ _  //_ //\\ | | | | |_| | | // \// \\ | | | | _ __ _ ___ _ _ ___ | | ___ _ __ || (O) || | | | || '_ \ | | / __|| | | | / __|| | / _ \| '__| \\ \_ // | |__| || | | || || (__ | |_| || (__ | || __/| |  \\_____// \____/ |_| |_||_| \___| \__, | \___||_| \___||_|  __/ |  |___/ Unicycler is installed! Example commands: unicycler --help unicycler --help_all unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o path/to/output_dir unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o path/to/output_dir All tools required by Unicycler were found. make[1]: Leaving directory '/build/unicycler-0.4.7+dfsg' dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/unicycler-0.4.7+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/unicycler-0.4.7+dfsg' dh_installinit -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_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/unicycler/usr/lib/python3/dist-packages/unicycler/cpp_functions.so was not linked against librt.so.1 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package unicycler: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package unicycler: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'unicycler' in '../unicycler_0.4.7+dfsg-2_amd64.deb'. dpkg-deb: building package 'unicycler-dbgsym' in '../unicycler-dbgsym_0.4.7+dfsg-2_amd64.deb'. dpkg-deb: building package 'unicycler-data' in '../unicycler-data_0.4.7+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../unicycler_0.4.7+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2951083/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2951083/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/2951083 and its subdirectories I: Current time: Fri Dec 17 22:59:11 +14 2021 I: pbuilder-time-stamp: 1639731551