Sun Jan 16 19:42:43 UTC 2022 I: starting to build unicycler/bullseye/amd64 on jenkins on '2022-01-16 19:42' Sun Jan 16 19:42:43 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_21/42008/console.log Sun Jan 16 19:42:43 UTC 2022 I: Downloading source for bullseye/unicycler=0.4.8+dfsg-2 --2022-01-16 19:42:44-- http://cdn-fastly.deb.debian.org/debian/pool/main/u/unicycler/unicycler_0.4.8%2bdfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2294 (2.2K) Saving to: ‘unicycler_0.4.8+dfsg-2.dsc’ 0K .. 100% 27.2M=0s 2022-01-16 19:42:44 (27.2 MB/s) - ‘unicycler_0.4.8+dfsg-2.dsc’ saved [2294/2294] Sun Jan 16 19:42:44 UTC 2022 I: unicycler_0.4.8+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: unicycler Binary: unicycler, unicycler-data Architecture: any all Version: 0.4.8+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Liubov Chuprikova Homepage: https://github.com/rrwick/Unicycler Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/unicycler Vcs-Git: https://salsa.debian.org/med-team/unicycler.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), dh-python, python3-all, python3-setuptools, default-jdk, bcftools, bowtie2, miniasm, ncbi-blast+, pilon, racon, samtools, spades (>= 3.13.1), libseqan2-dev, zlib1g-dev Package-List: unicycler deb science optional arch=any unicycler-data deb science optional arch=all Checksums-Sha1: cac78dcddd5a1fc7412979a2845837283d974914 14638264 unicycler_0.4.8+dfsg.orig.tar.xz 987be077833ca6e7a9f3df2a34b8a4021ca237fa 11640 unicycler_0.4.8+dfsg-2.debian.tar.xz Checksums-Sha256: 82f259d95fbff7a6bf610c90abcff82357e139ffa104bae20f40d207d49fb58a 14638264 unicycler_0.4.8+dfsg.orig.tar.xz f19415d06ec5c4396e9367c8a62cad642be0e23ce38f6b7502ee955890803378 11640 unicycler_0.4.8+dfsg-2.debian.tar.xz Files: b3990233cfbb19b66c6caa68c564953b 14638264 unicycler_0.4.8+dfsg.orig.tar.xz 532ab6cb325721783d39159c54777bb9 11640 unicycler_0.4.8+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl3nb9gRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGEjg//Zcst+F/gU7kqWnkpuZK6BJcCchVsA6gg ROTinm6OlxPGHcd7cqEBDqBmNcs/dqwJeCbd7KCB0yf8fZCsiBiEgrZkQ+BbfC1y TS+zSYkbn+EkEzALehoBwOPVcWS5kbqylce/gNAVDQtgD8Xuf7erCKEsEPNSqHVp nDxhOi3HM3S5147QQTvGq4Q68CshNi/aSTrNA1hLgQw0MIYlI/MDTlykS6ItOk1U 0WuNBlcGfuO9a3jG27L9szfMMzv3u8dGBLazak3ASdCiY/pcIjzZEL19w3cfFdk6 pTas41K4cHoaTcgN4jtIyPF+vxnp8J1HMQoDUvZ2ETspOy7o7vHjBiqC1Hre1nX7 LpQ65YI89uy3ndfGFlclEUCS0DfS8d27D9SqoJkX318HWRYujR6kok6DBdfoIDT7 bHX1qzVnSccrUMxKIK5Ifo3yNOrnvCb3xhtgjAdcOgsujYoaJMPUtnOVu/HLB+4Y SQ203IaebLJaghxyvYPmirsNtWjTNufmUIJjYiUpBUsu9KK2ZRawPHLH320nBHSD cWYJvFsX5aeKvm0Enu1kCxssu8UG8xstqtniB80lqwiNhAxiwXwzP0yb1UNT2Vnb rFYCFAz9XXCjTqWKdH7j9Naj58Ok3S/mDCBs2e/MhNpJ/yLR8EQtYJhZlfwEMMxj +W7bYn+1dn8= =9T8W -----END PGP SIGNATURE----- Sun Jan 16 19:42:44 UTC 2022 I: Checking whether the package is not for us Sun Jan 16 19:42:45 UTC 2022 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun Jan 16 19:42:45 UTC 2022 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun Jan 16 19:48:01 UTC 2022 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 16 07:42:46 -12 2022 I: pbuilder-time-stamp: 1642362166 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [unicycler_0.4.8+dfsg-2.dsc] I: copying [./unicycler_0.4.8+dfsg.orig.tar.xz] I: copying [./unicycler_0.4.8+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.4t48fvdy/trustedkeys.kbx': General error gpgv: Signature made Tue Dec 3 20:35:36 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./unicycler_0.4.8+dfsg-2.dsc dpkg-source: info: extracting unicycler in unicycler-0.4.8+dfsg dpkg-source: info: unpacking unicycler_0.4.8+dfsg.orig.tar.xz dpkg-source: info: unpacking unicycler_0.4.8+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 dpkg-source: info: applying append_flags I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/995712/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ae234d2fc2ca4b99a4188c7f4c0add6d' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='995712' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/pbuilderrc_m1Hr --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/b1 --logfile b1/build.log unicycler_0.4.8+dfsg-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/995712/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-compat (= 12), dh-python, python3-all, python3-setuptools, default-jdk, bcftools, bowtie2, miniasm, ncbi-blast+, pilon, racon, samtools, spades (>= 3.13.1), 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 ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on 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 bcftools; however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on miniasm; however: Package miniasm 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 (>= 3.13.1); 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} bcftools{a} bowtie2{a} bsdextrautils{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} libbrotli1{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} libcups2{a} libcurl3-gnutls{a} libdbus-1-3{a} libdebhelper-perl{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} libguava-java{a} libguice-java{a} libharfbuzz0b{a} libhat-trie0{a} libhts3{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libicu67{a} libistack-commons-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjpeg62-turbo{a} libjsoncpp24{a} libjsoup-java{a} libjsr305-java{a} liblcms2-2{a} libldap-2.4-2{a} libllvm11{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} libmd0{a} libmpdec3{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} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{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-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libspoa7.0.0{a} libssh2-1{a} libssw0{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libtbb2{a} libtool{a} libtxw2-java{a} libuchardet0{a} libvulkan1{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-shm0{a} libxcb-sync1{a} libxcb-xfixes0{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} libz3-4{a} m4{a} man-db{a} media-types{a} miniasm{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} python3{a} python3-all{a} python3-distutils{a} python3-joblib{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3-yaml{a} python3.9{a} python3.9-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: alsa-topology-conf alsa-ucm-conf curl dbus fonts-dejavu-extra libarchive-cpio-perl libatk-wrapper-java-jni libglib2.0-data libgpm2 libjansi-java libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libxt-dev lynx mesa-vulkan-drivers minimap psmisc publicsuffix python3-numpy python3-psutil python3-pytest python3-simplejson rampler shared-mime-info wget xdg-user-dirs 0 packages upgraded, 238 newly installed, 0 to remove and 0 not upgraded. Need to get 397 MB of archives. After unpacking 854 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1k-1+deb11u1 [851 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u1 [1305 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909 [15.7 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5 [124 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5 [58.4 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.20-2 [219 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5 [62.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u1 [350 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.12+7-2 [37.3 MB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 ant all 1.10.9-4 [2118 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 ant-optional all 1.10.9-4 [381 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-9 [158 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 bamtools amd64 2.5.1+dfsg-9 [183 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 bcftools amd64 1.11-1 [617 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 bwa amd64 0.7.17-6+b1 [212 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1 [203 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.12+7-2 [176 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get: 140 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jdk-headless amd64 11.0.12+7-2 [217 MB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 default-jdk-headless amd64 2:1.11-72 [1100 B] Get: 142 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jdk amd64 11.0.12+7-2 [7101 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 default-jdk amd64 2:1.11-72 [1056 B] Get: 144 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26 [171 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 java-wrappers all 0.3 [10.9 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libaopalliance-java all 20070526-6 [9048 B] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 152 http://deb.debian.org/debian bullseye/main amd64 libargs4j-java all 2.33-1.1 [137 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 155 http://deb.debian.org/debian bullseye/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 libdom4j-java all 2.1.3-1 [310 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 libcommons-io-java all 2.8.0-1 [279 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 libcommons-cli-java all 1.4-2 [57.3 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 libcommons-lang3-java all 3.11-1 [550 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libguava-java all 29.0-6 [2419 kB] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libmaven-parent-java all 31-2 [5100 B] Get: 168 http://deb.debian.org/debian bullseye/main amd64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 169 http://deb.debian.org/debian bullseye/main amd64 libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 174 http://deb.debian.org/debian bullseye/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 libslf4j-java all 1.7.30-1 [144 kB] Get: 177 http://deb.debian.org/debian bullseye/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 178 http://deb.debian.org/debian bullseye/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 179 http://deb.debian.org/debian bullseye/main amd64 libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 180 http://deb.debian.org/debian bullseye/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 181 http://deb.debian.org/debian bullseye/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 182 http://deb.debian.org/debian bullseye/main amd64 libcommons-compress-java all 1.20-1 [574 kB] Get: 183 http://deb.debian.org/debian bullseye/main amd64 libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 184 http://deb.debian.org/debian bullseye/main amd64 libsnappy1v5 amd64 1.1.8-1 [17.9 kB] Get: 185 http://deb.debian.org/debian bullseye/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 186 http://deb.debian.org/debian bullseye/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 187 http://deb.debian.org/debian bullseye/main amd64 libxz-java all 1.8-2 [141 kB] Get: 188 http://deb.debian.org/debian bullseye/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 189 http://deb.debian.org/debian bullseye/main amd64 libhttpcore-java all 4.4.14-1 [631 kB] Get: 190 http://deb.debian.org/debian bullseye/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 191 http://deb.debian.org/debian bullseye/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 192 http://deb.debian.org/debian bullseye/main amd64 libhttpclient-java all 4.5.13-2 [1233 kB] Get: 193 http://deb.debian.org/debian bullseye/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get: 194 http://deb.debian.org/debian bullseye/main amd64 libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 195 http://deb.debian.org/debian bullseye/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 196 http://deb.debian.org/debian bullseye/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 197 http://deb.debian.org/debian bullseye/main amd64 libcommons-jexl2-java all 2.1.1-5 [256 kB] Get: 198 http://deb.debian.org/debian bullseye/main amd64 libcommons-lang-java all 2.6-9 [273 kB] Get: 199 http://deb.debian.org/debian bullseye/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 200 http://deb.debian.org/debian bullseye/main amd64 libedlib0 amd64 1.2.6-1 [15.7 kB] Get: 201 http://deb.debian.org/debian bullseye/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 202 http://deb.debian.org/debian bullseye/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 203 http://deb.debian.org/debian bullseye/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 204 http://deb.debian.org/debian bullseye/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 205 http://deb.debian.org/debian bullseye/main amd64 libxsom-java all 2.3.0.1-10 [396 kB] Get: 206 http://deb.debian.org/debian bullseye/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 207 http://deb.debian.org/debian bullseye/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get: 208 http://deb.debian.org/debian bullseye/main amd64 librngom-java all 2.3.0.1-10 [288 kB] Get: 209 http://deb.debian.org/debian bullseye/main amd64 libtxw2-java all 2.3.0.1-10 [134 kB] Get: 210 http://deb.debian.org/debian bullseye/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 211 http://deb.debian.org/debian bullseye/main amd64 libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 212 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk2 amd64 2.10.9-1 [59.2 kB] Get: 213 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk-dev amd64 2.10.9-1 [104 kB] Get: 214 http://deb.debian.org/debian bullseye/main amd64 libngs-java amd64 2.10.9-1 [80.4 kB] Get: 215 http://deb.debian.org/debian bullseye/main amd64 libhtsjdk-java all 2.23.0+dfsg-2 [1607 kB] Get: 216 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get: 217 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get: 218 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get: 219 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get: 220 http://deb.debian.org/debian bullseye/main amd64 libnlopt0 amd64 2.7.0-4+b2 [172 kB] Get: 221 http://deb.debian.org/debian bullseye/main amd64 libseqan2-dev all 2.4.0+dfsg-14 [1220 kB] Get: 222 http://deb.debian.org/debian bullseye/main amd64 libspoa7.0.0 amd64 4.0.7+ds-1+b1 [66.8 kB] Get: 223 http://deb.debian.org/debian bullseye/main amd64 libssw0 amd64 1.1-13 [19.7 kB] Get: 224 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 225 http://deb.debian.org/debian bullseye/main amd64 miniasm amd64 0.3+dfsg-2 [30.3 kB] Get: 226 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 227 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get: 228 http://deb.debian.org/debian bullseye/main amd64 scala-library all 2.11.12-4 [9589 kB] Get: 229 http://deb.debian.org/debian bullseye/main amd64 pilon all 1.23+dfsg-2 [500 kB] Get: 230 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 231 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 232 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4 [213 kB] Get: 233 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 234 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Get: 235 http://deb.debian.org/debian bullseye/main amd64 racon amd64 1.4.20-1 [3272 kB] Get: 236 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get: 237 http://deb.debian.org/debian bullseye/main amd64 spades amd64 3.13.1+dfsg-2+b2 [4777 kB] Get: 238 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Fetched 397 MB in 8s (48.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... 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Selecting previously unselected package python3. (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 ... 20943 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../001-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. 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Unpacking default-jre-headless (2:1.11-72) ... Selecting previously unselected package ant. Preparing to unpack .../037-ant_1.10.9-4_all.deb ... Unpacking ant (1.10.9-4) ... Selecting previously unselected package ant-optional. Preparing to unpack .../038-ant-optional_1.10.9-4_all.deb ... Unpacking ant-optional (1.10.9-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../039-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../040-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../041-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../042-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. 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Setting up spades (3.13.1+dfsg-2+b2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:amd64 (11.0.12+7-2) ... 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) ... Setting up openjdk-11-jdk-headless:amd64 (11.0.12+7-2) ... 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 (2:1.11-72) ... Setting up default-jdk-headless (2:1.11-72) ... Setting up ant (1.10.9-4) ... Setting up openjdk-11-jdk:amd64 (11.0.12+7-2) ... 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 (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up default-jdk (2:1.11-72) ... Setting up ant-optional (1.10.9-4) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Setting up libhtsjdk-java (2.23.0+dfsg-2) ... Setting up pilon (1.23+dfsg-2) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/unicycler-0.4.8+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../unicycler_0.4.8+dfsg-2_source.changes dpkg-buildpackage: info: source package unicycler dpkg-buildpackage: info: source version 0.4.8+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/unicycler-0.4.8+dfsg' find . -name __pycache__ -type d | xargs rm -rf make distclean make[2]: Entering directory '/build/unicycler-0.4.8+dfsg' Platform: Linux Compiler: g++ 10.2.1 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-0.4.8+dfsg' make[1]: Leaving directory '/build/unicycler-0.4.8+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:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/unicycler-0.4.8+dfsg' make make[2]: Entering directory '/build/unicycler-0.4.8+dfsg' Platform: Linux Compiler: g++ 10.2.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/string_functions.o unicycler/src/string_functions.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/start_end_align.o unicycler/src/start_end_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+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++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/semi_global_align.o unicycler/src/semi_global_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/scrub.o unicycler/src/scrub.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/ref_seqs.o unicycler/src/ref_seqs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/random_alignments.o unicycler/src/random_alignments.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/path_align.o unicycler/src/path_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/overlap_align.o unicycler/src/overlap_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap_align.o unicycler/src/minimap_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/sketch.o unicycler/src/minimap/sketch.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/sdust.o unicycler/src/minimap/sdust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/misc.o unicycler/src/minimap/misc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/map.o unicycler/src/minimap/map.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/kthread.o unicycler/src/minimap/kthread.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/index.o unicycler/src/minimap/index.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/bseq.o unicycler/src/minimap/bseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm_assembly.o unicycler/src/miniasm_assembly.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/kmers.o unicycler/src/kmers.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/global_align.o unicycler/src/global_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-0.4.8+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 -fdebug-prefix-map=/build/unicycler-0.4.8+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 -Wl,-z,relro -Wl,-z,now -shared -lz make[2]: Leaving directory '/build/unicycler-0.4.8+dfsg' dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/unicycler.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/misc.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/version.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/vcf_func.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/unicycler_scrub.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/unicycler_polish.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/unicycler_check.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/unicycler_align.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/string_graph.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/spades_func.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/settings.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/read_ref.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/pilon_func.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/path_finding.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/minimap_alignment.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/miniasm_assembly.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/log.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/cpp_wrappers.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/bridge_spades_contig.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/bridge_miniasm.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/bridge_loop_unroll.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/bridge_long_read_simple.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/bridge_long_read.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/bridge_common.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/blast_func.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/assembly_graph_segment.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/assembly_graph_copy_depth.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/assembly_graph.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/alignment.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler copying unicycler/__init__.py -> /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler make[1]: Leaving directory '/build/unicycler-0.4.8+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:284: cp -a unicycler-runner.py /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build; cp -a unicycler/cpp_functions.so /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler; cp -a sample_data /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build I: pybuild base:232: cd /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build; python3.9 -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) Tests that each segment's forward links match up with its reverse complement's reverse ... 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) This test saves the graph to GFA, loads the GFA graph and then compares the two graphs to ... 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) Tests that each segment's forward links match up with its reverse complement's reverse ... 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) Tests that the common sequence in segments 3 and 4 (just a C) is moved onto segment 2. ... ok test_expand_repeats_2 (test.test_assembly_graph.TestExpandRepeats) Tests that the common sequence in segments 7 and 8 (GATTAGCG) is moved onto segment 6. ... ok test_expand_repeats_3 (test.test_assembly_graph.TestExpandRepeats) Tests that the common sequence on both strands of segment 1 is moved onto segment 2. ... ok test_expand_repeats_4 (test.test_assembly_graph.TestExpandRepeats) Tests that segment 5 isn't changed, because moving its common sequence (from each strand) ... ok test_expand_repeats_5 (test.test_assembly_graph.TestExpandRepeats) Tests that paths through the graph are unchanged by the repeat expansion. ... ok test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 9638 has been removed. ... ok test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segments 9125 and 9126 have been removed (results in a 3-way split). ... ok test_remove_zero_length_segs_11 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segments 8854 and 8855 have been removed (in a simple path). ... ok test_remove_zero_length_segs_2 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 5849 has been removed. ... ok test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 6513 has not been removed (it's a junction point). ... ok test_remove_zero_length_segs_4 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that both segments 8851 and 8852 have been removed. ... ok test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 4907 has not been removed (it's a junction point and a dead end). ... ok test_remove_zero_length_segs_6 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 10029 has been removed (it's a dead end but not a junction). ... ok test_remove_zero_length_segs_7 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 9822 has been removed (it's on a simple path). ... ok test_remove_zero_length_segs_8 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 1 has been removed (it's isolated and unconnected). ... ok test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments) Tests that segment 8232 has been removed. ... 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) Tests a particular part of the graph with merging and splitting. ... ok test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) Tests a particular part of the graph with merging and splitting. ... ok test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) Tests a particular part of the graph with merging and splitting. ... ok test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) Tests large contigs from the largest replicon, all of which should have a copy depth of 1. ... ok test_single_copy_segments_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) Tests single copy contigs from a smaller, higher depth replicon. They should have a copy ... 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) This test aligns two random sequences of different length, making sure that the scores are ... ok test_shift_big_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) This test has a 20 bp insertion near the start and a 20 bp deletion near the end, shifting ... ok test_shift_small_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) This test uses the same sequences as the previous test, but uses a smaller bandwidth than ... 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) This covers the case where the contig sequences are in the middle of the unitig sequences. ... ok test_contig_placement_2 (test.test_miniasm_assembly.TestContigPlacement) This covers the case where a contig sequence spans the circular junction of the unitig ... ok test_contig_placement_3 (test.test_miniasm_assembly.TestContigPlacement) This covers the case where the a contig sequence starts right at the beginning of the ... ok test_contig_placement_4 (test.test_miniasm_assembly.TestContigPlacement) This covers the case where the a contig sequence ends right at the end of the unitig ... 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) The beginning of the reference in this case is repetitive, which was able to throw off ... ok test_tough_alignment_1 (test.test_semi_global_alignment.TestToughAlignments) This read goes through a repetitive area, which means that the densest area of common ... ok test_tough_alignment_10 (test.test_semi_global_alignment.TestToughAlignments) This is a very low quality read. ... ok test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments) Repeats at one end of the read. ... ok test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments) Repeats at one end of the read. ... ok test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments) This read caused a crash before I added the getMaxSeedChainGapArea function in ... ok test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments) This read caused a crash before I added made a few fixes to the line tracing code. It won't ... ok test_tough_alignment_15 (test.test_semi_global_alignment.TestToughAlignments) This read should hit the same reference twice, even at low sensitivities. ... ok test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments) This read goes through a repetitive area, which means that the densest area of common ... ok test_tough_alignment_3 (test.test_semi_global_alignment.TestToughAlignments) The first line tracing of this alignment is bad but uses all the points. This previously ... ok test_tough_alignment_4 (test.test_semi_global_alignment.TestToughAlignments) Like so many of these tough ones, this case has a read which enters a repetitive region ... ok test_tough_alignment_5 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments) This one misses the right alignment on lower sensitivities because the line tracing never ... ok test_tough_alignment_7 (test.test_semi_global_alignment.TestToughAlignments) This one misses the right alignment on lower sensitivities because the line tracing never ... ok test_tough_alignment_8 (test.test_semi_global_alignment.TestToughAlignments) This has a weird change in slope - the read has a good part and a bad part. Ideally the ... ok test_tough_alignment_9 (test.test_semi_global_alignment.TestToughAlignments) This is a very low quality read. ... 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 52.878s OK I: pybuild pybuild:310: rm /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler-runner.py; rm -r /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/sample_data; rm -r /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_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-0.4.8+dfsg' dh_auto_install --destdir=debian/unicycler I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/unicycler-0.4.8+dfsg/debian/unicycler running install running build running build_py running install_lib creating /build/unicycler-0.4.8+dfsg/debian/unicycler/usr creating /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib creating /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9 creating /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages creating /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/cpp_functions.so -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/__init__.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/alignment.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/assembly_graph.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/assembly_graph_segment.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/blast_func.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/bridge_common.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/bridge_long_read.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/bridge_miniasm.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/bridge_spades_contig.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/cpp_wrappers.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/log.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/miniasm_assembly.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/minimap_alignment.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/path_finding.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/pilon_func.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/read_ref.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/settings.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/spades_func.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/string_graph.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/unicycler_align.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/unicycler_check.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/unicycler_polish.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/unicycler_scrub.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/vcf_func.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/version.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/misc.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler copying /build/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.9_unicycler/build/unicycler/unicycler.py -> /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/__init__.py to __init__.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/alignment.py to alignment.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/blast_func.py to blast_func.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/log.py to log.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/path_finding.py to path_finding.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/pilon_func.py to pilon_func.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/read_ref.py to read_ref.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/settings.py to settings.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/spades_func.py to spades_func.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/string_graph.py to string_graph.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/unicycler_check.py to unicycler_check.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/unicycler_polish.py to unicycler_polish.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/unicycler_scrub.py to unicycler_scrub.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/vcf_func.py to vcf_func.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/version.py to version.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/misc.py to misc.cpython-39.pyc byte-compiling /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler/unicycler.py to unicycler.cpython-39.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-0.4.8+dfsg/debian/unicycler/usr/lib/python3.9/dist-packages/unicycler-0.4.8.egg-info Skipping SOURCES.txt running install_scripts Installing unicycler script to /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_align script to /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_check script to /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_polish script to /build/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_scrub script to /build/unicycler-0.4.8+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-0.4.8+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-0.4.8+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/unicycler-0.4.8+dfsg' dh_installinit -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: debian/unicycler/usr/lib/python3/dist-packages/unicycler/cpp_functions.so contains an unresolvable reference to symbol pthread_create: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) 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-dbgsym' in '../unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb'. dpkg-deb: building package 'unicycler-data' in '../unicycler-data_0.4.8+dfsg-2_all.deb'. dpkg-deb: building package 'unicycler' in '../unicycler_0.4.8+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../unicycler_0.4.8+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: 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/995712 and its subdirectories I: Current time: Sun Jan 16 07:48:01 -12 2022 I: pbuilder-time-stamp: 1642362481 Sun Jan 16 19:48:02 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sun Jan 16 19:48:02 UTC 2022 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sun Jan 16 19:53:20 UTC 2022 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sun Jan 16 19:53:20 UTC 2022 I: unicycler_0.4.8+dfsg-2_amd64.changes: Format: 1.8 Date: Wed, 04 Dec 2019 09:22:18 +0100 Source: unicycler Binary: unicycler unicycler-data unicycler-dbgsym Architecture: all amd64 Version: 0.4.8+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: unicycler - hybrid assembly pipeline for bacterial genomes unicycler-data - hybrid assembly pipeline for bacterial genomes (data package) Closes: 945372 Changes: unicycler (0.4.8+dfsg-2) unstable; urgency=medium . * Autopkgtest: Restrictions: skip-not-installable Closes: #945372 * Remove patches bowtie.patch that are missing from debian/patches/series. * Set upstream metadata fields: Repository-Browse. Checksums-Sha1: 921399e345f015ea513854962fedf431ea79fd28 12042664 unicycler-data_0.4.8+dfsg-2_all.deb f6590f14eaf7531ac242ec46e7350e1a2bcfe099 6888380 unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb 2c70bfd2349c760058a789a6d3640a3e46697f24 11930 unicycler_0.4.8+dfsg-2_amd64.buildinfo 25c834946259cc71548bcc2d182ed52a3bd08a21 885140 unicycler_0.4.8+dfsg-2_amd64.deb Checksums-Sha256: 440f095aa554cae3e1214ad595fcf38490c5f64804a2f8a96de5355663a613fc 12042664 unicycler-data_0.4.8+dfsg-2_all.deb 12c0a77f7dd0f7b2c906428ece7585c16f3a6b9bb4f7d43d6dfc1b7b51478fe4 6888380 unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb adef90a37886effd6f926f27feee2fb67dc5dbe11c8d287860c1a6c3ebb3eab0 11930 unicycler_0.4.8+dfsg-2_amd64.buildinfo da87a66ef23c6ff35d414938852aa9517833dbea23b85d7365f3ec11b4a7faa0 885140 unicycler_0.4.8+dfsg-2_amd64.deb Files: bb4c488079004b384abf56fba65c129a 12042664 science optional unicycler-data_0.4.8+dfsg-2_all.deb 005b4c371b9946de734d2b3ebad42f40 6888380 debug optional unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb 0b450b7aa796d0535d98cce019f6fc56 11930 science optional unicycler_0.4.8+dfsg-2_amd64.buildinfo 5ec700ebab7e2c744800cbe90070196a 885140 science optional unicycler_0.4.8+dfsg-2_amd64.deb Sun Jan 16 19:53:22 UTC 2022 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/unicycler_0.4.8+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/unicycler_0.4.8+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/unicycler_0.4.8+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/b1/unicycler_0.4.8+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.8aMf6IrMFH/b2/unicycler_0.4.8+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.984s) 0.984s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.337s) 0.336s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jan 16 19:55:43 UTC 2022 I: found no differences in the changes files, and a .buildinfo file also exists. Sun Jan 16 19:55:43 UTC 2022 I: unicycler from bullseye built successfully and reproducibly on amd64. Sun Jan 16 19:55:51 UTC 2022 I: Submitting .buildinfo files to external archives: Sun Jan 16 19:55:52 UTC 2022 I: Submitting 16K b1/unicycler_0.4.8+dfsg-2_amd64.buildinfo.asc Sun Jan 16 19:56:04 UTC 2022 I: Submitting 16K b2/unicycler_0.4.8+dfsg-2_amd64.buildinfo.asc Sun Jan 16 19:56:15 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jan 16 19:56:15 UTC 2022 I: Done submitting .buildinfo files. Sun Jan 16 19:56:15 UTC 2022 I: Removing signed unicycler_0.4.8+dfsg-2_amd64.buildinfo.asc files: removed './b1/unicycler_0.4.8+dfsg-2_amd64.buildinfo.asc' removed './b2/unicycler_0.4.8+dfsg-2_amd64.buildinfo.asc'