Thu Dec 12 00:48:36 UTC 2024  I: starting to build unicycler/trixie/amd64 on jenkins on '2024-12-12 00:48'
Thu Dec 12 00:48:36 UTC 2024  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/40341/console.log
Thu Dec 12 00:48:36 UTC 2024  I: Downloading source for trixie/unicycler=0.5.1+dfsg-1.1
--2024-12-12 00:48:36--  http://deb.debian.org/debian/pool/main/u/unicycler/unicycler_0.5.1%2bdfsg-1.1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2523 (2.5K) [text/prs.lines.tag]
Saving to: ‘unicycler_0.5.1+dfsg-1.1.dsc’

     0K ..                                                    100%  346M=0s

2024-12-12 00:48:36 (346 MB/s) - ‘unicycler_0.5.1+dfsg-1.1.dsc’ saved [2523/2523]

Thu Dec 12 00:48:36 UTC 2024  I: unicycler_0.5.1+dfsg-1.1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: unicycler
Binary: unicycler, unicycler-data
Architecture: any all
Version: 0.5.1+dfsg-1.1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Liubov Chuprikova <chuprikovalv@gmail.com>
Homepage: https://github.com/rrwick/Unicycler
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/unicycler
Vcs-Git: https://salsa.debian.org/med-team/unicycler.git
Testsuite: autopkgtest
Testsuite-Triggers: @builddeps@
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, default-jdk <!nocheck>, bcftools, bowtie2 <!nocheck>, miniasm, ncbi-blast+ <!nocheck>, pilon <!nocheck>, racon, samtools <!nocheck>, spades (>= 3.14), libseqan2-dev, zlib1g-dev
Package-List:
 unicycler deb science optional arch=any
 unicycler-data deb science optional arch=all
Checksums-Sha1:
 74c2faf619e98fc0db52308548185114eb302ede 14771244 unicycler_0.5.1+dfsg.orig.tar.xz
 ea66c0d1d5a67fcdf02d8634ae0191ba3387de4c 12780 unicycler_0.5.1+dfsg-1.1.debian.tar.xz
Checksums-Sha256:
 e4ff9b7bb236d3c1b43e97318f09d781428f7ae917b06dfe505c0d8da3ffad69 14771244 unicycler_0.5.1+dfsg.orig.tar.xz
 4c7902cbee396da2281cb40d701f5763bbdc2b97bbd428b0568e531fcaed20b6 12780 unicycler_0.5.1+dfsg-1.1.debian.tar.xz
Files:
 22bef237ad14fd5fa44602f232e75a20 14771244 unicycler_0.5.1+dfsg.orig.tar.xz
 f5013a2caf0f3758605515e0930ca472 12780 unicycler_0.5.1+dfsg-1.1.debian.tar.xz
Dgit: 2f73c1dc5f16c92edb458c67273ab5193d67e12d debian archive/debian/0.5.1+dfsg-1.1 https://git.dgit.debian.org/unicycler

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Thu Dec 12 00:48:36 UTC 2024  I: Checking whether the package is not for us
Thu Dec 12 00:48:36 UTC 2024  I: Starting 1st build on remote node ionos15-amd64.debian.net.
Thu Dec 12 00:48:36 UTC 2024  I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Thu Dec 12 00:53:40 UTC 2024  I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Jan 13 19:11:36 -12 2026
I: pbuilder-time-stamp: 1768374696
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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_0.5.1+dfsg-1.1.dsc]
I: copying [./unicycler_0.5.1+dfsg.orig.tar.xz]
I: copying [./unicycler_0.5.1+dfsg-1.1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sun Dec  8 22:47:16 2024 
gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv:                issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./unicycler_0.5.1+dfsg-1.1.dsc: no acceptable signature found
dpkg-source: info: extracting unicycler in unicycler-0.5.1+dfsg
dpkg-source: info: unpacking unicycler_0.5.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking unicycler_0.5.1+dfsg-1.1.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
dpkg-source: info: applying leftover-syntax-warnings.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3138382/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='amd64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='amd64'
  IFS=' 	
  '
  INVOCATION_ID='87be05e9a653462290016c5f74bc14ec'
  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='3138382'
  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/r-b-build.9JZqdmtR/pbuilderrc_0og5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9JZqdmtR/b1 --logfile b1/build.log unicycler_0.5.1+dfsg-1.1.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://213.165.73.152:3128'
I: uname -a
  Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3138382/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 <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, python3-setuptools, default-jdk, bcftools, bowtie2, miniasm, ncbi-blast+, pilon, racon, samtools, spades (>= 3.14), 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 ... 19965 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however:
  Package dh-sequence-python3 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 (>= 3.14); 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:
  adwaita-icon-theme{a} at-spi2-common{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} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{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{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} java-wrappers{a} libapache-pom-java{a} libapparmor1{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbamtools2.5.2{a} libbrotli1{a} libcairo-gobject2{a} libcairo2{a} libcloudproviders0{a} libcolord2{a} libcom-err2{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl3t64-gnutls{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libedlib1{a} libelf1t64{a} libepoxy0{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk-3-0t64{a} libgtk-3-common{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libhtsjdk-java{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm19{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmjson-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngs-java{a} libngs-jni{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnlopt0{a} libnsl2{a} libnspr4{a} libnss3{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqan2-dev{a} libsharpyuv0{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libspoa7.0.0{a} libssh2-1t64{a} libssw0{a} libsystemd-shared{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libvulkan1{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{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-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml2{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libyaml-0-2{a} libz3-4{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} miniasm{a} ncbi-blast+{a} ncbi-data{a} ncbi-vdb-data{a} netbase{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openssl{a} pilon{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-joblib{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} racon{a} readline-common{a} samtools{a} scala-library{a} sensible-utils{a} shared-mime-info{a} spades{a} systemd{a} systemd-sysv{a} tzdata{a} unzip{a} x11-common{a} xkb-data{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf at-spi2-core chrony curl fonts-dejavu-extra krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgtk-3-bin libkmod2 libldap-common libltdl-dev libmail-sendmail-perl libnss-systemd librsvg2-common libsasl2-modules libxt-dev linux-sysctl-defaults lynx mesa-vulkan-drivers minimap ntpsec openntpd psmisc publicsuffix python3-gffutils python3-matplotlib python3-numpy python3-psutil python3-pytest python3-simplejson rampler systemd-cryptsetup systemd-timesyncd wget xdg-user-dirs 
0 packages upgraded, 265 newly installed, 0 to remove and 0 not upgraded.
Need to get 293 MB of archives. After unpacking 950 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-1+b3 [42.1 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 257~rc3-1 [2136 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 257~rc3-1 [3608 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 257~rc3-1 [59.5 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.15.90-1 [176 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.15.90-1 [77.9 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.15.90-1 [50.2 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.15.90-1 [156 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.15.90-1 [51.3 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.15.90-1 [69.6 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 22 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-1 [677 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B]
Get: 32 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 257~rc3-1 [291 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.16.7+ds-1 [50.2 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.54.0-1 [170 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB]
Get: 72 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 bamtools amd64 2.5.2+dfsg-6+b1 [207 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 bcftools amd64 1.20-2 [760 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 bowtie2 amd64 2.5.4-1 [1510 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 bwa amd64 0.7.18-1 [212 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.15.90-1 [50.1 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b3 [41.9 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b3 [32.6 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b3 [28.8 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 101 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 102 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B]
Get: 109 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.36-1 [110 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.106-1 [1392 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.0-3 [55.8 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [41.8 MB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-15 [112 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-15 [44.1 kB]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-15 [48.1 kB]
Get: 141 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B]
Get: 156 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.2-1+b1 [37.6 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b2 [16.0 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b2 [111 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b1 [36.3 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB]
Get: 165 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.2.8-1 [38.0 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB]
Get: 173 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB]
Get: 177 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB]
Get: 178 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B]
Get: 179 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB]
Get: 180 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB]
Get: 181 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB]
Get: 182 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB]
Get: 183 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB]
Get: 184 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB]
Get: 185 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 186 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.5-1 [26.0 MB]
Get: 187 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 188 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB]
Get: 189 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.2.8-1 [9185 kB]
Get: 190 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB]
Get: 191 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB]
Get: 192 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.2.8-1 [42.8 kB]
Get: 193 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.2.8-1 [43.9 kB]
Get: 194 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.2.8-1 [154 kB]
Get: 195 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB]
Get: 196 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB]
Get: 197 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.12-1 [21.0 kB]
Get: 198 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.12-1+b1 [371 kB]
Get: 199 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB]
Get: 200 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB]
Get: 201 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b2 [25.9 kB]
Get: 202 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [205 kB]
Get: 203 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B]
Get: 204 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk-headless amd64 21.0.5+11-1 [82.8 MB]
Get: 205 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B]
Get: 206 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jdk amd64 21.0.5+11-1 [3360 kB]
Get: 207 http://deb.debian.org/debian trixie/main amd64 default-jdk amd64 2:1.21-76 [1076 B]
Get: 208 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 209 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get: 210 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 211 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 212 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 213 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 214 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 215 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB]
Get: 216 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 217 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 218 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.2.0-1 [731 kB]
Get: 219 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB]
Get: 220 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 221 http://deb.debian.org/debian trixie/main amd64 java-wrappers all 0.5 [8848 B]
Get: 222 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B]
Get: 223 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 224 http://deb.debian.org/debian trixie/main amd64 libcommons-codec-java all 1.17.1-1 [303 kB]
Get: 225 http://deb.debian.org/debian trixie/main amd64 libcommons-io-java all 2.17.0-1 [488 kB]
Get: 226 http://deb.debian.org/debian trixie/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB]
Get: 227 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get: 228 http://deb.debian.org/debian trixie/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 229 http://deb.debian.org/debian trixie/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 230 http://deb.debian.org/debian trixie/main amd64 libedlib1 amd64 1.2.7-6+b2 [18.1 kB]
Get: 231 http://deb.debian.org/debian trixie/main amd64 libmjson-java all 1.4.0-3 [60.4 kB]
Get: 232 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB]
Get: 233 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB]
Get: 234 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB]
Get: 235 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB]
Get: 236 http://deb.debian.org/debian trixie/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB]
Get: 237 http://deb.debian.org/debian trixie/main amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7 [157 kB]
Get: 238 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.9+dfsg-7 [25.6 kB]
Get: 239 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.9+dfsg-7 [112 kB]
Get: 240 http://deb.debian.org/debian trixie/main amd64 librhino-java all 1.7.14-2.1 [1357 kB]
Get: 241 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB]
Get: 242 http://deb.debian.org/debian trixie/main amd64 libsnappy-jni amd64 1.1.10.7-1 [6492 B]
Get: 243 http://deb.debian.org/debian trixie/main amd64 libsnappy-java all 1.1.10.7-1 [87.6 kB]
Get: 244 http://deb.debian.org/debian trixie/main amd64 libhtsjdk-java all 4.1.0+dfsg-2 [1833 kB]
Get: 245 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB]
Get: 246 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB]
Get: 247 http://deb.debian.org/debian trixie/main amd64 libnlopt0 amd64 2.7.1-6+b1 [178 kB]
Get: 248 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get: 249 http://deb.debian.org/debian trixie/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB]
Get: 250 http://deb.debian.org/debian trixie/main amd64 libssw0 amd64 1.1-15+b1 [21.8 kB]
Get: 251 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB]
Get: 252 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB]
Get: 253 http://deb.debian.org/debian trixie/main amd64 miniasm amd64 0.3+dfsg-4 [29.9 kB]
Get: 254 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB]
Get: 255 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB]
Get: 256 http://deb.debian.org/debian trixie/main amd64 scala-library all 2.11.12-5 [9588 kB]
Get: 257 http://deb.debian.org/debian trixie/main amd64 pilon all 1.24-3 [497 kB]
Get: 258 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B]
Get: 259 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-5 [216 kB]
Get: 260 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 261 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB]
Get: 262 http://deb.debian.org/debian trixie/main amd64 racon amd64 1.5.0-3 [3115 kB]
Get: 263 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB]
Get: 264 http://deb.debian.org/debian trixie/main amd64 spades amd64 3.15.5+dfsg-7 [9020 kB]
Get: 265 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Fetched 293 MB in 4s (80.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libapparmor1:amd64 (3.1.7-1+b3) ...
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Setting up systemd (257~rc3-1) ...
Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'.

Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'.

Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'.

Initializing machine ID from random generator.

Creating group 'systemd-journal' with GID 999.

Creating group 'systemd-network' with GID 998.

Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998.

/usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring.

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Setting up libexpat1:amd64 (2.6.4-1) ...
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Selecting previously unselected package media-types.
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Unpacking netbase (6.4) ...
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Selecting previously unselected package libkrb5support0:amd64.
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Selecting previously unselected package libgssapi-krb5-2:amd64.
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Selecting previously unselected package libtirpc3t64:amd64.
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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Setting up python3-minimal (3.12.6-1) ...
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Selecting previously unselected package libproc2-0:amd64.
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
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Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
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Unpacking file (1:5.45-3+b1) ...
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Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libjsoncpp26:amd64 (1.9.6-3) ...
Setting up libapache-pom-java (33-2) ...
Setting up libavahi-common-data:amd64 (0.8-15) ...
Setting up libncurses6:amd64 (6.5-2+b1) ...
Setting up libdbus-1-3:amd64 (1.15.90-1) ...
Setting up libfribidi0:amd64 (1.0.15-1) ...
Setting up libproc2-0:amd64 (2:4.0.4-6) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libspoa7.0.0:amd64 (4.1.4-2+b1) ...
Setting up libpng16-16t64:amd64 (1.6.44-2) ...
Setting up autopoint (0.22.5-2) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libpcsclite1:amd64 (2.3.0-3) ...
Setting up libsensors5:amd64 (1:3.6.0-10+b1) ...
Setting up libk5crypto3:amd64 (1.21.3-3) ...
Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6+b1) ...
Setting up libglapi-mesa:amd64 (24.2.8-1) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ...
Setting up libvulkan1:amd64 (1.3.296.0-1) ...
Setting up autoconf (2.72-3) ...
Setting up libnghttp3-9:amd64 (1.6.0-2) ...
Setting up libwebp7:amd64 (1.4.0-0.1+b1) ...
Setting up libxcb-dri2-0:amd64 (1.17.0-2+b1) ...
Setting up libgif7:amd64 (5.2.2-1+b1) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libedlib1:amd64 (1.2.7-6+b2) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libxshmfence1:amd64 (1.3-1+b2) ...
Setting up at-spi2-common (2.54.0-1) ...
Setting up libtiff6:amd64 (4.5.1+git230720-5) ...
Setting up bamtools (2.5.2+dfsg-6+b1) ...
Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ...
Setting up dbus-session-bus-common (1.15.90-1) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up procps (2:4.0.4-6) ...
Setting up libx11-6:amd64 (2:1.8.10-2) ...
Setting up ncbi-vdb-data (3.0.9+dfsg-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up libngtcp2-16:amd64 (1.9.1-1) ...
Setting up libkrb5-3:amd64 (1.21.3-3) ...
Setting up libwayland-egl1:amd64 (1.23.0-1+b1) ...
Setting up libmbedcrypto16:amd64 (3.6.2-3) ...
Setting up libssh2-1t64:amd64 (1.11.1-1) ...
Setting up dbus-system-bus-common (1.15.90-1) ...
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
Setting up openssl (3.3.2-2) ...
Setting up libdrm-common (2.4.123-1) ...
Setting up libsnappy-jni (1.1.10.7-1) ...
Setting up libxcomposite1:amd64 (1:0.4.6-1) ...
Setting up libssw0:amd64 (1.1-15+b1) ...
Setting up readline-common (8.2-5) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up dbus-bin (1.15.90-1) ...
Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ...
Setting up libxkbcommon0:amd64 (1.6.0-1+b2) ...
Setting up libwayland-client0:amd64 (1.23.0-1+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ...
Setting up libllvm19:amd64 (1:19.1.5-1) ...
Setting up libx11-xcb1:amd64 (2:1.8.10-2) ...
Setting up gettext (0.22.5-2) ...
Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ...
Setting up java-wrappers (0.5) ...
Setting up libatk1.0-0t64:amd64 (2.54.0-1) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ...
Setting up libtool (2.4.7-8) ...
Setting up fontconfig-config (2.15.0-1.1+b1) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-15) ...
Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ...
Setting up libcommons-logging-java (1.3.0-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b2) ...
Setting up libnss3:amd64 (2:3.106-1) ...
Setting up dbus-daemon (1.15.90-1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ...
Setting up libcolord2:amd64 (1.4.7-1+b2) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libdconf1:amd64 (0.40.0-4+b3) ...
Setting up dh-autoreconf (20) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:amd64 (0.1.29-2+b1) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libmbedx509-7:amd64 (3.6.2-3) ...
Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ...
Setting up libxfixes3:amd64 (1:6.0.0-2+b2) ...
Setting up dbus (1.15.90-1) ...
Running in chroot, ignoring request.

invoke-rc.d: policy-rc.d denied execution of start.
Setting up shared-mime-info (2.4-5+b1) ...
Setting up libxinerama1:amd64 (2:1.1.4-3+b2) ...
Setting up racon (1.5.0-3) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ...
Setting up libxrandr2:amd64 (2:1.5.4-1+b1) ...
Setting up libmbedtls21:amd64 (3.6.2-3) ...
Setting up libreadline8t64:amd64 (8.2-5) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up libdrm2:amd64 (2.4.123-1) ...
Setting up groff-base (1.23.0-6) ...
Setting up libwayland-cursor0:amd64 (1.23.0-1+b1) ...
Setting up libpam-systemd:amd64 (257~rc3-1) ...
Setting up libharfbuzz0b:amd64 (10.0.1-1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ...
Setting up libsnappy-java (1.1.10.7-1) ...
Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libcommons-codec-java (1.17.1-1) ...
Setting up libavahi-client3:amd64 (0.8-15) ...
Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ...
Setting up gtk-update-icon-cache (4.16.7+ds-1) ...
Setting up fontconfig (2.15.0-1.1+b1) ...
Regenerating fonts cache... done.
Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxi6:amd64 (2:1.8.2-1) ...
Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ...
Setting up libcommons-io-java (2.17.0-1) ...
Setting up libdrm-radeon1:amd64 (2.4.123-1) ...
Setting up libxtst6:amd64 (2:1.2.3-1.1+b2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxcursor1:amd64 (1:1.2.2-1+b1) ...
Setting up libpango-1.0-0:amd64 (1.55.0+ds-3) ...
Setting up libdrm-intel1:amd64 (2.4.123-1) ...
Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'.

Setting up libcairo2:amd64 (1.18.2-2) ...
Setting up dbus-user-session (1.15.90-1) ...
Setting up adwaita-icon-theme (47.0-2) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ...
Setting up libnsl2:amd64 (1.3.0-3+b3) ...
Setting up libhts3t64:amd64 (1.20+ds-2) ...
Setting up libcairo-gobject2:amd64 (1.18.2-2) ...
Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ...
Setting up libcups2t64:amd64 (2.4.10-2) ...
Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ...
Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ...
Setting up mesa-libgallium:amd64 (24.2.8-1) ...
Setting up libngs-jni:amd64 (3.0.9+dfsg-7) ...
Setting up libpython3.12-stdlib:amd64 (3.12.8-1) ...
Setting up libcommons-compress-java (1.27.1-2) ...
Setting up libgbm1:amd64 (24.2.8-1) ...
Setting up python3.12 (3.12.8-1) ...
Setting up libgl1-mesa-dri:amd64 (24.2.8-1) ...
Setting up bcftools (1.20-2) ...
Setting up debhelper (13.20) ...
Setting up dconf-service (0.40.0-4+b3) ...
Setting up samtools (1.20-3) ...
Setting up libngs-java:amd64 (3.0.9+dfsg-7) ...
Setting up libhtsjdk-java (4.1.0+dfsg-2) ...
Setting up libpython3-stdlib:amd64 (3.12.6-1) ...
Setting up libglx-mesa0:amd64 (24.2.8-1) ...
Setting up libglx0:amd64 (1.7.0-1+b2) ...
Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b3) ...
Setting up python3 (3.12.6-1) ...
/usr/share/spades/spades_pipeline/support.py:531: SyntaxWarning: invalid escape sequence '\d'
  return [atoi(c) for c in re.split("(\d+)", text)]
Setting up python3-zipp (3.21.0-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up bowtie2 (2.5.4-1) ...
Setting up ncbi-blast+ (2.16.0+ds-6+b1) ...
Setting up python3-packaging (24.2-1) ...
Setting up libgl1:amd64 (1.7.0-1+b2) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up libgtk-3-common (3.24.43-4) ...
Setting up python3-more-itertools (10.5.0-1) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up python3-typeguard (4.4.1-1) ...
Setting up python3-all (3.12.6-1) ...
Setting up python3-yaml (6.0.2-1+b1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up libgtk-3-0t64:amd64 (3.24.43-4) ...
Setting up python3-pkg-resources (75.2.0-1) ...
Setting up python3-setuptools (75.2.0-1) ...
Setting up python3-joblib (1.3.2-5) ...
Setting up spades (3.15.5+dfsg-7) ...
Setting up dh-python (6.20241024) ...
Processing triggers for libc-bin (2.40-4) ...
Processing triggers for systemd (257~rc3-1) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ...
Setting up openjdk-21-jdk-headless:amd64 (21.0.5+11-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre-headless (2:1.21-76) ...
Setting up default-jre (2:1.21-76) ...
Setting up openjdk-21-jdk:amd64 (21.0.5+11-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jdk-headless (2:1.21-76) ...
Setting up pilon (1.24-3) ...
Setting up default-jdk (2:1.21-76) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20240118) ...
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
I: Building the package
I: Running cd /build/reproducible-path/unicycler-0.5.1+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_0.5.1+dfsg-1.1_source.changes
dpkg-buildpackage: info: source package unicycler
dpkg-buildpackage: info: source version 0.5.1+dfsg-1.1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
find . -name __pycache__ -type d | xargs rm -rf
make distclean
make[2]: Entering directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
Platform: Linux
Compiler: g++ 14.2.0
rm -f unicycler/src/minimap/sketch.o unicycler/src/minimap/sdust.o unicycler/src/minimap/kthread.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/index.o unicycler/src/minimap/bseq.o unicycler/src/semi_global_align.o unicycler/src/scoredalignment.o unicycler/src/miniasm_assembly.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/path_align.o unicycler/src/kmers.o unicycler/src/consensus_align.o unicycler/src/ref_seqs.o unicycler/src/start_end_align.o unicycler/src/overlap_align.o unicycler/src/minimap_align.o unicycler/src/string_functions.o unicycler/src/global_align.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sys.o unicycler/src/random_alignments.o
rm -f unicycler/cpp_functions.so
make[2]: Leaving directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
make
make[2]: Entering directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
Platform: Linux
Compiler: g++ 14.2.0
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/consensus_align.o unicycler/src/consensus_align.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o unicycler/src/random_alignments.o unicycler/src/random_alignments.cpp
g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/unicycler-0.5.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-soname,unicycler/cpp_functions.so -o unicycler/cpp_functions.so unicycler/src/minimap/sketch.o unicycler/src/minimap/sdust.o unicycler/src/minimap/kthread.o unicycler/src/minimap/map.o unicycler/src/minimap/misc.o unicycler/src/minimap/index.o unicycler/src/minimap/bseq.o unicycler/src/semi_global_align.o unicycler/src/scoredalignment.o unicycler/src/miniasm_assembly.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/path_align.o unicycler/src/kmers.o unicycler/src/consensus_align.o unicycler/src/ref_seqs.o unicycler/src/start_end_align.o unicycler/src/overlap_align.o unicycler/src/minimap_align.o unicycler/src/string_functions.o unicycler/src/global_align.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sys.o unicycler/src/random_alignments.o -Wl,-z,relro -Wl,-z,now -shared -lz
make[2]: Leaving directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
dh_auto_build
I: pybuild base:311: /usr/bin/python3 setup.py build 
running build
running build_py
creating /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/bridge_miniasm.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/read_ref.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/string_graph.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/path_finding.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/bridge_long_read_simple.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/version.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/assembly_graph_segment.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/misc.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/unicycler.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/minimap_alignment.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/bridge_common.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/assembly_graph_copy_depth.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/blast_func.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/bridge_loop_unroll.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/bridge_long_read.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/__init__.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/assembly_graph.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/settings.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/alignment.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/cpp_wrappers.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/bridge_spades_contig.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/spades_func.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/miniasm_assembly.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/log.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
copying unicycler/unicycler_align.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler
make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
   dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:308: cp -a unicycler-runner.py /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build; cp -a unicycler/cpp_functions.so /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler; cp -a sample_data /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build
I: pybuild base:311: cd /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build; python3.12 -m unittest discover -v 
test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_attributes) ... ok
test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_dead_end_count) ... ok
test_filter_by_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_filter_by_read_depth) ... ok
test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_forward_links) ... ok
test_get_all_gfa_link_lines (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_all_gfa_link_lines) ... ok
test_get_estimated_sequence_len (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_estimated_sequence_len) ... ok
test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_median_read_depth) ... ok
test_get_n_segment_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_n_segment_length) ... ok
test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_total_length) ... ok
test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_get_total_length_no_overlaps) ... ok
test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_links_match)
Tests that each segment's forward links match up with its reverse complement's reverse ... ok
test_load_paths (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_load_paths) ... ok
test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_normalise_read_depths) ... ok
test_remove_all_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_all_overlaps) ... ok
test_remove_segments (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_segments) ... ok
test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_remove_small_components) ... ok
test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_reverse_links) ... ok
test_save_specific_segments_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_specific_segments_to_fasta) ... ok
test_save_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_fasta) ... ok
test_save_to_fasta_length (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_fasta_length) ... ok
test_save_to_gfa (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_save_to_gfa)
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.TestAssemblyGraphFunctions1.test_segments) ... ok
test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_sequence) ... ok
test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions1.test_total_dead_end_count) ... ok
test_add_link_1 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_add_link_1) ... ok
test_add_link_2 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_add_link_2) ... ok
test_all_segments_below_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_all_segments_below_depth) ... ok
test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_attributes) ... ok
test_bad_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_bad_overlaps) ... ok
test_dead_end_change_if_deleted (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_change_if_deleted) ... ok
test_dead_end_change_if_path_deleted (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_change_if_path_deleted) ... ok
test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_dead_end_count) ... ok
test_filter_homopolymer_loops (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_filter_homopolymer_loops) ... ok
test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_forward_links) ... ok
test_get_connected_components_and_remove_link (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_connected_components_and_remove_link) ... ok
test_get_connected_segments (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_connected_segments) ... ok
test_get_exclusive_inputs (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_exclusive_inputs) ... ok
test_get_exclusive_outputs (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_exclusive_outputs) ... ok
test_get_mean_path_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_mean_path_depth) ... ok
test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_median_read_depth) ... ok
test_get_next_available_seg_number (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_next_available_seg_number) ... ok
test_get_path_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_path_sequence) ... ok
test_get_simple_path (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_simple_path) ... ok
test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_total_length) ... ok
test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_get_total_length_no_overlaps) ... ok
test_lead_exclusively_from (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_lead_exclusively_from) ... ok
test_lead_exclusively_to (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_lead_exclusively_to) ... ok
test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_links_match)
Tests that each segment's forward links match up with its reverse complement's reverse ... ok
test_merge_all_possible (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_all_possible) ... ok
test_merge_simple_path_1 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_1) ... ok
test_merge_simple_path_2 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_2) ... ok
test_merge_simple_path_3 (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_merge_simple_path_3) ... ok
test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_normalise_read_depths) ... ok
test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_remove_small_components) ... ok
test_remove_small_dead_ends (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_remove_small_dead_ends) ... ok
test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_reverse_links) ... ok
test_segments (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_segments) ... ok
test_seq_from_signed_seg_num (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_seq_from_signed_seg_num) ... ok
test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_sequence) ... ok
test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctions2.test_total_dead_end_count) ... ok
test_expand_repeats_1 (test.test_assembly_graph.TestExpandRepeats.test_expand_repeats_1)
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.test_expand_repeats_2)
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.test_expand_repeats_3)
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.test_expand_repeats_4)
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.test_expand_repeats_5)
Tests that paths through the graph are unchanged by the repeat expansion. ... ok
test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_graph) ... ok
test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_1)
Tests that segment 9638 has been removed. ... ok
test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_10)
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.test_remove_zero_length_segs_11)
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.test_remove_zero_length_segs_2)
Tests that segment 5849 has been removed. ... ok
test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_3)
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.test_remove_zero_length_segs_4)
Tests that both segments 8851 and 8852 have been removed. ... ok
test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_5)
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.test_remove_zero_length_segs_6)
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.test_remove_zero_length_segs_7)
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.test_remove_zero_length_segs_8)
Tests that segment 1 has been removed (it's isolated and unconnected). ... ok
test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments.test_remove_zero_length_segs_9)
Tests that segment 8232 has been removed. ... ok
test_graph (test.test_assembly_graph.TestRepairMultiwayJunction.test_graph) ... ok
test_repair_multi_way_junctions_1 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_1) ... ok
test_repair_multi_way_junctions_2 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_2) ... ok
test_repair_multi_way_junctions_3 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_3) ... ok
test_repair_multi_way_junctions_4 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_4) ... ok
test_repair_multi_way_junctions_5 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_5) ... ok
test_repair_multi_way_junctions_6 (test.test_assembly_graph.TestRepairMultiwayJunction.test_repair_multi_way_junctions_6) ... ok
test_merge_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_1)
Tests a particular part of the graph with merging and splitting. ... ok
test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_split_1)
Tests a particular part of the graph with merging and splitting. ... ok
test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_merge_split_2)
Tests a particular part of the graph with merging and splitting. ... ok
test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth.test_single_copy_segments_1)
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.test_single_copy_segments_2)
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.test_random_seq_no_start_gene) ... ok
test_random_seq_with_exact_gene_forward_strand (test.test_blast_func.TestBlastFunc.test_random_seq_with_exact_gene_forward_strand) ... ok
test_random_seq_with_exact_gene_reverse_strand (test.test_blast_func.TestBlastFunc.test_random_seq_with_exact_gene_reverse_strand) ... ok
test_1bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_1bp_deletion) ... ok
test_1bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_1bp_insertion) ... ok
test_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_deletion) ... ok
test_2bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_insertion) ... ok
test_2bp_insertion_and_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_2bp_insertion_and_2bp_deletion) ... ok
test_long_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_long_perfect_alignment) ... ok
test_one_mismatch (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_one_mismatch) ... ok
test_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_perfect_alignment) ... ok
test_random_seqs (test.test_cpp_wrappers.TestFullyGlobalAlignment.test_random_seqs)
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.test_shift_big_band)
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.test_shift_small_band)
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.test_consensus_different_qualities) ... ok
test_consensus_with_all (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_all) ... ok
test_consensus_with_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_deletions) ... ok
test_consensus_with_deletions_and_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_deletions_and_insertions) ... ok
test_consensus_with_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_insertions) ... ok
test_consensus_with_subs (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_consensus_with_subs) ... ok
test_start_end_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_deletions) ... ok
test_start_end_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_insertions) ... ok
test_start_end_insertions_and_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_start_end_insertions_and_deletions) ... ok
test_two_way_consensus (test.test_cpp_wrappers.TestMultipleSequenceAlignment.test_two_way_consensus) ... ok
test_makeblastdb_not_found (test.test_dependencies.TestDependencies.test_makeblastdb_not_found) ... ok
test_no_rotate (test.test_dependencies.TestDependencies.test_no_rotate) ... ok
test_spades_not_found (test.test_dependencies.TestDependencies.test_spades_not_found) ... ok
test_tblastn_not_found (test.test_dependencies.TestDependencies.test_tblastn_not_found) ... ok
test_verbosity_1 (test.test_dependencies.TestDependencies.test_verbosity_1) ... ok
test_verbosity_2 (test.test_dependencies.TestDependencies.test_verbosity_2) ... ok
test_basic_options (test.test_help_text.TestBasicHelpText.test_basic_options) ... ok
test_extended_options (test.test_help_text.TestBasicHelpText.test_extended_options) ... ok
test_output (test.test_help_text.TestBasicHelpText.test_output) ... ok
test_return_code (test.test_help_text.TestBasicHelpText.test_return_code) ... ok
test_title (test.test_help_text.TestBasicHelpText.test_title) ... ok
test_error_message (test.test_help_text.TestEmptyCommand.test_error_message) ... ok
test_output (test.test_help_text.TestEmptyCommand.test_output) ... ok
test_return_code (test.test_help_text.TestEmptyCommand.test_return_code) ... ok
test_basic_options (test.test_help_text.TestExtendedHelpText.test_basic_options) ... ok
test_extended_options (test.test_help_text.TestExtendedHelpText.test_extended_options) ... ok
test_output (test.test_help_text.TestExtendedHelpText.test_output) ... ok
test_return_code (test.test_help_text.TestExtendedHelpText.test_return_code) ... ok
test_title (test.test_help_text.TestExtendedHelpText.test_title) ... ok
test_contig_placement_1 (test.test_miniasm_assembly.TestContigPlacement.test_contig_placement_1)
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.test_contig_placement_2)
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.test_contig_placement_3)
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.test_contig_placement_4)
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.test_add_line_breaks_to_sequence) ... ok
test_colour (test.test_misc.TestMiscFunctions.test_colour) ... ok
test_flip_number_order (test.test_misc.TestMiscFunctions.test_flip_number_order) ... ok
test_float_to_str (test.test_misc.TestMiscFunctions.test_float_to_str) ... ok
test_get_compression_type (test.test_misc.TestMiscFunctions.test_get_compression_type) ... ok
test_get_nice_header (test.test_misc.TestMiscFunctions.test_get_nice_header) ... ok
test_get_num_agreement (test.test_misc.TestMiscFunctions.test_get_num_agreement) ... ok
test_get_percentile (test.test_misc.TestMiscFunctions.test_get_percentile) ... ok
test_get_random_base (test.test_misc.TestMiscFunctions.test_get_random_base) ... ok
test_get_random_sequence (test.test_misc.TestMiscFunctions.test_get_random_sequence) ... ok
test_get_sequence_file_type (test.test_misc.TestMiscFunctions.test_get_sequence_file_type) ... ok
test_int_to_str (test.test_misc.TestMiscFunctions.test_int_to_str) ... ok
test_is_header_spades_format (test.test_misc.TestMiscFunctions.test_is_header_spades_format) ... ok
test_len_without_format (test.test_misc.TestMiscFunctions.test_len_without_format) ... ok
test_load_fasta (test.test_misc.TestMiscFunctions.test_load_fasta) ... ok
test_load_fasta_with_full_header (test.test_misc.TestMiscFunctions.test_load_fasta_with_full_header) ... ok
test_remove_formatting (test.test_misc.TestMiscFunctions.test_remove_formatting) ... ok
test_reverse_complement (test.test_misc.TestMiscFunctions.test_reverse_complement) ... ok
test_round_to_nearest_odd (test.test_misc.TestMiscFunctions.test_round_to_nearest_odd) ... ok
test_score_function (test.test_misc.TestMiscFunctions.test_score_function) ... ok
test_spades_version_parsing_1 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_1) ... ok
test_spades_version_parsing_2 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_2) ... ok
test_spades_version_parsing_3 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_3) ... ok
test_spades_version_parsing_4 (test.test_misc.TestMiscFunctions.test_spades_version_parsing_4) ... ok
test_spades_version_status_1 (test.test_misc.TestMiscFunctions.test_spades_version_status_1) ... ok
test_spades_version_status_10 (test.test_misc.TestMiscFunctions.test_spades_version_status_10) ... ok
test_spades_version_status_11 (test.test_misc.TestMiscFunctions.test_spades_version_status_11) ... ok
test_spades_version_status_12 (test.test_misc.TestMiscFunctions.test_spades_version_status_12) ... ok
test_spades_version_status_13 (test.test_misc.TestMiscFunctions.test_spades_version_status_13) ... ok
test_spades_version_status_14 (test.test_misc.TestMiscFunctions.test_spades_version_status_14) ... ok
test_spades_version_status_2 (test.test_misc.TestMiscFunctions.test_spades_version_status_2) ... ok
test_spades_version_status_3 (test.test_misc.TestMiscFunctions.test_spades_version_status_3) ... ok
test_spades_version_status_4 (test.test_misc.TestMiscFunctions.test_spades_version_status_4) ... ok
test_spades_version_status_5 (test.test_misc.TestMiscFunctions.test_spades_version_status_5) ... ok
test_spades_version_status_6 (test.test_misc.TestMiscFunctions.test_spades_version_status_6) ... ok
test_spades_version_status_7 (test.test_misc.TestMiscFunctions.test_spades_version_status_7) ... ok
test_spades_version_status_8 (test.test_misc.TestMiscFunctions.test_spades_version_status_8) ... ok
test_spades_version_status_9 (test.test_misc.TestMiscFunctions.test_spades_version_status_9) ... ok
test_strip_read_extensions_capitals (test.test_misc.TestMiscFunctions.test_strip_read_extensions_capitals) ... ok
test_strip_read_extensions_fa (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fa) ... ok
test_strip_read_extensions_fasta (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fasta) ... ok
test_strip_read_extensions_fastq (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fastq) ... ok
test_strip_read_extensions_fastq_extra_dots (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fastq_extra_dots) ... ok
test_strip_read_extensions_fna (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fna) ... ok
test_strip_read_extensions_fq (test.test_misc.TestMiscFunctions.test_strip_read_extensions_fq) ... ok
test_strip_read_extensions_other_fasta (test.test_misc.TestMiscFunctions.test_strip_read_extensions_other_fasta) ... ok
test_weighted_average (test.test_misc.TestMiscFunctions.test_weighted_average) ... ok
test_weighted_average_list (test.test_misc.TestMiscFunctions.test_weighted_average_list) ... ok
test_absolute_paths (test.test_options.TestUnicyclerOptions.test_absolute_paths) ... ok
test_defaults (test.test_options.TestUnicyclerOptions.test_defaults) ... ok
test_modes (test.test_options.TestUnicyclerOptions.test_modes) ... ok
test_relative_paths (test.test_options.TestUnicyclerOptions.test_relative_paths) ... ok
test_long_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_long_contained_read) ... ok
test_medium_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_medium_contained_read) ... ok
test_short_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments.test_short_contained_read) ... ok
test_end_to_end (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_end_to_end) ... ok
test_read_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_1) ... ok
test_read_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_2) ... ok
test_read_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_contained_3) ... ok
test_read_end_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_end_overlap) ... ok
test_read_start_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_read_start_overlap) ... ok
test_ref_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_1) ... ok
test_ref_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_2) ... ok
test_ref_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments.test_ref_contained_3) ... ok
test_tough_alignment_0 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_0)
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.test_tough_alignment_1)
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.test_tough_alignment_10)
This is a very low quality read. ... ok
test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_11)
Repeats at one end of the read. ... ok
test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_12)
Repeats at one end of the read. ... ok
test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_13)
This read caused a crash before I added the getMaxSeedChainGapArea function in ... ok
test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_14)
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.test_tough_alignment_15)
This read should hit the same reference twice, even at low sensitivities. ... ok
test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_2)
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.test_tough_alignment_3)
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.test_tough_alignment_4)
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.test_tough_alignment_5) ... ok
test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments.test_tough_alignment_6)
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.test_tough_alignment_7)
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.test_tough_alignment_8)
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.test_tough_alignment_9)
This is a very low quality read. ... ok
test_bad_fastq_1 (test.test_spades_func.TestSPAdesFunc.test_bad_fastq_1) ... ok
test_bad_fastq_2 (test.test_spades_func.TestSPAdesFunc.test_bad_fastq_2) ... ok
test_build_spades_command_1 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_1) ... ok
test_build_spades_command_2 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_2) ... ok
test_build_spades_command_3 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_3) ... ok
test_build_spades_command_4 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_4) ... ok
test_build_spades_command_5 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_5) ... ok
test_build_spades_command_6 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_6) ... ok
test_build_spades_command_7 (test.test_spades_func.TestSPAdesFunc.test_build_spades_command_7) ... ok
test_get_read_count_1 (test.test_spades_func.TestSPAdesFunc.test_get_read_count_1) ... ok
test_get_read_count_2 (test.test_spades_func.TestSPAdesFunc.test_get_read_count_2) ... ok
test_get_read_lengths_1 (test.test_spades_func.TestSPAdesFunc.test_get_read_lengths_1) ... ok
test_get_read_lengths_2 (test.test_spades_func.TestSPAdesFunc.test_get_read_lengths_2) ... ok

----------------------------------------------------------------------
Ran 229 tests in 43.727s

OK
I: pybuild pybuild:334: rm /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler-runner.py; rm -r /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/sample_data; rm -r /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/__pycache__
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
dh_auto_install --destdir=debian/unicycler
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler 
running install
/build/reproducible-path/unicycler-0.5.1+dfsg/setup.py:86: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  install.initialize_options(self)
running build
running build_py
running install_lib
creating /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages
creating /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_miniasm.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/cpp_functions.so -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/read_ref.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/string_graph.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/path_finding.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/version.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/assembly_graph_segment.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/misc.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/unicycler.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/minimap_alignment.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_common.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/blast_func.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_long_read.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/__init__.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/assembly_graph.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/settings.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/alignment.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/cpp_wrappers.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/bridge_spades_contig.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/spades_func.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/miniasm_assembly.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/log.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
copying /build/reproducible-path/unicycler-0.5.1+dfsg/.pybuild/cpython3_3.12_unicycler/build/unicycler/unicycler_align.py -> /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/read_ref.py to read_ref.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/string_graph.py to string_graph.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/path_finding.py to path_finding.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/version.py to version.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/misc.py to misc.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/unicycler.py to unicycler.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/blast_func.py to blast_func.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/__init__.py to __init__.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/settings.py to settings.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/alignment.py to alignment.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/spades_func.py to spades_func.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/log.py to log.cpython-312.pyc
byte-compiling /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-312.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'
adding license file 'LICENSE'
writing manifest file 'unicycler.egg-info/SOURCES.txt'
Copying unicycler.egg-info to /build/reproducible-path/unicycler-0.5.1+dfsg/debian/unicycler/usr/lib/python3.12/dist-packages/unicycler-0.5.1.egg-info
Skipping SOURCES.txt
running install_scripts
Installing unicycler script to /build/reproducible-path/unicycler-0.5.1+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/reproducible-path/unicycler-0.5.1+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/reproducible-path/unicycler-0.5.1+dfsg'
dh_python3 --no-ext-rename
make[1]: Leaving directory '/build/reproducible-path/unicycler-0.5.1+dfsg'
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
   dh_strip_nondeterminism -O--buildsystem=pybuild
   dh_compress -O--buildsystem=pybuild
   dh_fixperms -O--buildsystem=pybuild
   dh_missing -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -O--buildsystem=pybuild
   dh_gencontrol -O--buildsystem=pybuild
   dh_md5sums -O--buildsystem=pybuild
   dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'unicycler' in '../unicycler_0.5.1+dfsg-1.1_amd64.deb'.
dpkg-deb: building package 'unicycler-dbgsym' in '../unicycler-dbgsym_0.5.1+dfsg-1.1_amd64.deb'.
dpkg-deb: building package 'unicycler-data' in '../unicycler-data_0.5.1+dfsg-1.1_all.deb'.
 dpkg-genbuildinfo --build=binary -O../unicycler_0.5.1+dfsg-1.1_amd64.buildinfo
 dpkg-genchanges --build=binary -O../unicycler_0.5.1+dfsg-1.1_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/3138382 and its subdirectories
I: Current time: Tue Jan 13 19:16:37 -12 2026
I: pbuilder-time-stamp: 1768374997
Thu Dec 12 00:53:41 UTC 2024  I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Thu Dec 12 00:53:41 UTC 2024  I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Thu Dec 12 01:00:51 UTC 2024  I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Thu Dec 12 01:00:52 UTC 2024  I: unicycler_0.5.1+dfsg-1.1_amd64.changes:
Format: 1.8
Date: Sun, 08 Dec 2024 22:50:24 +0100
Source: unicycler
Binary: unicycler unicycler-data unicycler-dbgsym
Architecture: all amd64
Version: 0.5.1+dfsg-1.1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
 unicycler  - hybrid assembly pipeline for bacterial genomes
 unicycler-data - hybrid assembly pipeline for bacterial genomes (data package)
Closes: 1048635 1087157
Changes:
 unicycler (0.5.1+dfsg-1.1) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Michael R. Crusoe ]
   * salsa ci: skip i386
 .
   [ Étienne Mollier ]
   * spades.patch: unfuzz hunk with offset.
   * d/clean: new: remove leftover .pybuild and egg info. (Closes: #1048635)
   * leftover-syntax-warnings.patch: fix remaining SyntaxWarnings.
     (Closes: #1087157)
   * d/patches/*: normalize last-update timestamp.
Checksums-Sha1:
 288836db33ae763ab551967309bac3c378072c82 12043080 unicycler-data_0.5.1+dfsg-1.1_all.deb
 5e0c2f74be67ed054de471b04efffb9d2a4ea993 7239508 unicycler-dbgsym_0.5.1+dfsg-1.1_amd64.deb
 7bdaf742fca906dd1c1eac8f2cf3385ae1c436fd 13042 unicycler_0.5.1+dfsg-1.1_amd64.buildinfo
 5b1ed6f023454f53fc7f0e04eedd1391e36ac009 897716 unicycler_0.5.1+dfsg-1.1_amd64.deb
Checksums-Sha256:
 d1d446911a154d979aa8dab8bd4ed09e5e86039a1bc47972f4881d364f64adde 12043080 unicycler-data_0.5.1+dfsg-1.1_all.deb
 107c5d3b49e576825e732ae0cb898bd874cca63ee3869f66b231f0d9868d83bd 7239508 unicycler-dbgsym_0.5.1+dfsg-1.1_amd64.deb
 ee81b827664e64e2a6bbad334700bb866b66c36011e427acab03dcbc02c09f1c 13042 unicycler_0.5.1+dfsg-1.1_amd64.buildinfo
 f9be5d5bb022f9762050c399dbf7b0cf2dd70e883775f40171670c4f68f8a47d 897716 unicycler_0.5.1+dfsg-1.1_amd64.deb
Files:
 7125dcc65af067375cb5c4646aead871 12043080 science optional unicycler-data_0.5.1+dfsg-1.1_all.deb
 e30b1702579e56464160df406e1f48bc 7239508 debug optional unicycler-dbgsym_0.5.1+dfsg-1.1_amd64.deb
 6a0bb0066208ed32dc919ef55ababa0f 13042 science optional unicycler_0.5.1+dfsg-1.1_amd64.buildinfo
 7debe725ce3e52da0762dd9a88bf2e44 897716 science optional unicycler_0.5.1+dfsg-1.1_amd64.deb
Thu Dec 12 01:00:53 UTC 2024  I: diffoscope 284 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_12-40341.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9JZqdmtR/unicycler_0.5.1+dfsg-1.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9JZqdmtR/unicycler_0.5.1+dfsg-1.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9JZqdmtR/unicycler_0.5.1+dfsg-1.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9JZqdmtR/b1/unicycler_0.5.1+dfsg-1.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9JZqdmtR/b2/unicycler_0.5.1+dfsg-1.1_amd64.changes

## close_archive (total time: 0.000s)
       0.000s     20 calls    diffoscope.comparators.xz.XzContainer
       0.000s     10 calls    diffoscope.comparators.deb.DebContainer
       0.000s     14 calls    diffoscope.comparators.tar.TarContainer
       0.000s      6 calls    diffoscope.comparators.deb.DebTarContainer

## command (total time: 441.576s)
     215.758s    937 calls    readelf
     205.233s    110 calls    diff
      17.861s    143 calls    objdump
       1.395s      2 calls    objcopy
       1.033s     20 calls    xz
       0.250s     22 calls    strings
       0.022s      2 calls    cmp
       0.022s      2 calls    cmp (external)
       0.002s     18 calls    cmp (internal)

## compare_files (cumulative) (total time: 1480.410s)
     281.345s      1 call     abc.DotChangesFile
     281.236s      2 calls    abc.DebFile
     281.083s      4 calls    abc.XzFile
     280.290s      2 calls    abc.DebDataTarFile
     279.487s      2 calls    abc.ElfFile
      73.550s     10 calls    diffoscope.comparators.elf.ElfCodeSection
       1.701s      3 calls    diffoscope.comparators.elf.ElfStringSection
       1.518s     33 calls    diffoscope.comparators.elf.ElfSection
       0.118s      2 calls    abc.TarFile
       0.035s      2 calls    abc.TextFile
       0.025s      1 call     diffoscope.comparators.elf.MonkeyPatchedElfSection
       0.022s      2 calls    abc.Md5sumsFile

## container_extract (total time: 1.299s)
       1.034s     20 calls    diffoscope.comparators.xz.XzContainer
       0.140s     24 calls    diffoscope.comparators.deb.DebContainer
       0.102s     90 calls    diffoscope.comparators.deb.DebTarContainer
       0.023s     22 calls    diffoscope.comparators.tar.TarContainer

## diff (total time: 40.908s)
      40.908s   2053 calls    linediff

## has_same_content_as (total time: 0.026s)
       0.020s      3 calls    abc.DebFile
       0.003s      2 calls    abc.DebDataTarFile
       0.001s      6 calls    abc.TextFile
       0.001s      4 calls    abc.Md5sumsFile
       0.000s      4 calls    abc.XzFile
       0.000s      2 calls    abc.TarFile
       0.000s     33 calls    diffoscope.comparators.elf.ElfSection
       0.000s      1 call     diffoscope.comparators.utils.libarchive.LibarchiveSymlink
       0.000s      1 call     abc.DotChangesFile
       0.000s      2 calls    abc.ElfFile
       0.000s     10 calls    diffoscope.comparators.elf.ElfCodeSection
       0.000s      3 calls    diffoscope.comparators.elf.ElfStringSection
       0.000s      1 call     diffoscope.comparators.elf.MonkeyPatchedElfSection

## main (total time: 465.267s)
     465.266s      2 calls    outputs
       0.001s      1 call     cleanup

## open_archive (total time: 0.000s)
       0.000s     20 calls    diffoscope.comparators.xz.XzContainer
       0.000s     14 calls    diffoscope.comparators.tar.TarContainer
       0.000s     10 calls    diffoscope.comparators.deb.DebContainer
       0.000s      6 calls    diffoscope.comparators.deb.DebTarContainer

## output (total time: 183.398s)
     164.084s      1 call     html
      11.447s      1 call     text
       7.867s      1 call     json

## recognizes (total time: 1.215s)
       0.477s    900 calls    diffoscope.comparators.utils.archive.ArchiveMember
       0.383s   1904 calls    diffoscope.comparators.utils.libarchive.LibarchiveMember
       0.194s     12 calls    diffoscope.comparators.binary.FilesystemFile
       0.161s    324 calls    diffoscope.comparators.debian.DebControlMember

## specialize (total time: 0.261s)
       0.261s     72 calls    specialize
Finished with result: success
Main processes terminated with: code=exited/status=1
Service runtime: 7min 45.613s
CPU time consumed: 8min 41.745s
Thu Dec 12 01:08:43 UTC 2024  W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate.
Thu Dec 12 01:08:43 UTC 2024  E: unicycler failed to build reproducibly in trixie on amd64.
Thu Dec 12 01:13:03 UTC 2024  I: Submitting .buildinfo files to external archives:
Thu Dec 12 01:13:03 UTC 2024  I: Submitting 16K	b1/unicycler_0.5.1+dfsg-1.1_amd64.buildinfo.asc
Thu Dec 12 01:13:04 UTC 2024  I: Submitting 16K	b2/unicycler_0.5.1+dfsg-1.1_amd64.buildinfo.asc
Thu Dec 12 01:13:05 UTC 2024  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Dec 12 01:13:05 UTC 2024  I: Done submitting .buildinfo files.
Thu Dec 12 01:13:05 UTC 2024  I: Removing signed unicycler_0.5.1+dfsg-1.1_amd64.buildinfo.asc files:
removed './b1/unicycler_0.5.1+dfsg-1.1_amd64.buildinfo.asc'
removed './b2/unicycler_0.5.1+dfsg-1.1_amd64.buildinfo.asc'