I: pbuilder: network access will be disabled during build
I: Current time: Sat Mar  8 06:08:02 -12 2025
I: pbuilder-time-stamp: 1741457282
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: using eatmydata during job
I: Copying source file
I: copying [iva_1.0.11+ds-6.dsc]
I: copying [./iva_1.0.11+ds.orig.tar.xz]
I: copying [./iva_1.0.11+ds-6.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-6.dsc: unsupported subcommand
dpkg-source: info: extracting iva in iva-1.0.11+ds
dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz
dpkg-source: info: unpacking iva_1.0.11+ds-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-multithreaded-test.patch
dpkg-source: info: applying perl-shebang.patch
dpkg-source: info: applying samtools1.10
dpkg-source: info: applying disable-ram-test.patch
dpkg-source: info: applying python3.12.patch
dpkg-source: info: applying syntax-warning.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/31052/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='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  INVOCATION_ID='d59ac2b50fdf4a95acbeb20a41fb9056'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  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='31052'
  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.kbi2XxIm/pbuilderrc_fU7R --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.kbi2XxIm/b1 --logfile b1/build.log iva_1.0.11+ds-6.dsc'
  SUDO_GID='112'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://46.16.76.132:3128'
I: uname -a
  Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/31052/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: i386
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, libssl-dev, bioperl, fastaq, kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19787 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 libssl-dev; however:
  Package libssl-dev is not installed.
 pbuilder-satisfydepends-dummy depends on bioperl; however:
  Package bioperl is not installed.
 pbuilder-satisfydepends-dummy depends on fastaq; however:
  Package fastaq is not installed.
 pbuilder-satisfydepends-dummy depends on kmc; however:
  Package kmc is not installed.
 pbuilder-satisfydepends-dummy depends on help2man; however:
  Package help2man is not installed.
 pbuilder-satisfydepends-dummy depends on mummer; however:
  Package mummer is not installed.
 pbuilder-satisfydepends-dummy depends on python3; however:
  Package python3 is not installed.
 pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
  Package python3-setuptools is not installed.
 pbuilder-satisfydepends-dummy depends on python3-packaging; however:
  Package python3-packaging is not installed.
 pbuilder-satisfydepends-dummy depends on python3-numpy; however:
  Package python3-numpy is not installed.
 pbuilder-satisfydepends-dummy depends on python3-networkx; however:
  Package python3-networkx is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pysam; however:
  Package python3-pysam is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pytest; however:
  Package python3-pytest is not installed.
 pbuilder-satisfydepends-dummy depends on samtools; however:
  Package samtools is not installed.
 pbuilder-satisfydepends-dummy depends on smalt; however:
  Package smalt is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk-headless; however:
  Package default-jdk-headless is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk-headless{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} java-common{a} kmc{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbambamc0{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libio-string-perl{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnspr4{a} libnss3{a} libp11-kit0{a} libpcsclite1{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1t64{a} libssl-dev{a} libsub-uplevel-perl{a} libtasn1-6{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} mummer{a} netbase{a} openjdk-21-jdk-headless{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} smalt{a} tzdata{a} 
The following packages are RECOMMENDED but will NOT be installed:
  bioperl-run curl krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libasound2t64 libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libcups2t64 libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libfontconfig1 libfreetype6 libgd-perl libgpm2 libgraph-perl libgraphviz-perl libharfbuzz0b libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk publicsuffix python3-gdal python3-matplotlib python3-pydot python3-pygments python3-pygraphviz python3-scipy python3-yaml wget 
0 packages upgraded, 133 newly installed, 0 to remove and 0 not upgraded.
Need to get 201 MB of archives. After unpacking 627 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libsigsegv2 i386 2.14-1+b2 [34.6 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 gawk i386 1:5.2.1-2+b1 [680 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.2-1 [27.1 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 media-types all 12.0.0 [28.9 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.2-1 [10.0 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.2-1 [28.1 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 python3-numpy-dev i386 1:2.2.3+ds-2+b1 [145 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.1-2 [150 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-17 [735 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.1-2 [2198 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:2.2.3+ds-2+b1 [5060 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 openssl i386 3.4.1-1 [1432 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20241223 [164 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-5 [96.5 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-7 [301 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libio-string-perl all 1.08-4 [12.1 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 libdata-stag-perl all 0.14-3 [448 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get: 44 http://deb.debian.org/debian trixie/main i386 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libexception-class-perl all 1.45-1 [34.6 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 libtest-deep-perl all 1.204-1 [52.9 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 libcapture-tiny-perl all 0.50-1 [24.6 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 libalgorithm-diff-perl all 1.201-1 [43.3 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 libtext-diff-perl all 1.45-2 [27.2 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 libtest-differences-perl all 0.71-1 [17.9 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libsub-uplevel-perl all 0.2800-3 [14.0 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libtest-exception-perl all 0.43-3 [16.9 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 libtest-warn-perl all 0.37-2 [14.5 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 libtest-most-perl all 0.38-1 [25.1 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 bioperl all 1.7.8-1 [246 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 ca-certificates-java all 20240118 [11.6 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 63 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 java-common all 0.76 [6776 B]
Get: 73 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.16-2 [171 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3.1 [170 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 libnspr4 i386 2:4.36-1 [119 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 libnss3 i386 2:3.108-1 [1505 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libpcsclite1 i386 2.3.1-1 [57.3 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 openjdk-21-jre-headless i386 21.0.6+7-1 [43.2 MB]
Get: 79 http://deb.debian.org/debian trixie/main i386 default-jre-headless i386 2:1.21-76 [3192 B]
Get: 80 http://deb.debian.org/debian trixie/main i386 openjdk-21-jdk-headless i386 21.0.6+7-1 [85.3 MB]
Get: 81 http://deb.debian.org/debian trixie/main i386 default-jdk-headless i386 2:1.21-76 [1124 B]
Get: 82 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.1-1 [8276 B]
Get: 88 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 91 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 92 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.8.0-1 [724 kB]
Get: 93 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20250108 [113 kB]
Get: 94 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB]
Get: 95 http://deb.debian.org/debian trixie/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 96 http://deb.debian.org/debian trixie/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 97 http://deb.debian.org/debian trixie/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB]
Get: 98 http://deb.debian.org/debian trixie/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB]
Get: 99 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 100 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 101 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 102 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 103 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 104 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 105 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-9 [20.8 kB]
Get: 106 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-9 [61.2 kB]
Get: 107 http://deb.debian.org/debian trixie/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 108 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 109 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.8.0-1 [78.7 kB]
Get: 110 http://deb.debian.org/debian trixie/main i386 libngtcp2-16 i386 1.11.0-1 [163 kB]
Get: 111 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls8 i386 1.11.0-1 [29.9 kB]
Get: 112 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 113 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 114 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 115 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.12.1-3 [411 kB]
Get: 116 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 117 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.1-2 [70.9 kB]
Get: 118 http://deb.debian.org/debian trixie/main i386 libhts3t64 i386 1.21+ds-1 [506 kB]
Get: 119 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.5+20250216-1 [112 kB]
Get: 120 http://deb.debian.org/debian trixie/main i386 samtools i386 1.21-1 [700 kB]
Get: 121 http://deb.debian.org/debian trixie/main i386 fastaq all 3.17.0-9 [47.8 kB]
Get: 122 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB]
Get: 123 http://deb.debian.org/debian trixie/main i386 kmc i386 3.2.4+dfsg-1+b2 [1096 kB]
Get: 124 http://deb.debian.org/debian trixie/main i386 libbambamc0 i386 0.0.50-6+b2 [43.7 kB]
Get: 125 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.4.1-1 [2837 kB]
Get: 126 http://deb.debian.org/debian trixie/main i386 mummer i386 3.23+dfsg-8 [669 kB]
Get: 127 http://deb.debian.org/debian trixie/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 128 http://deb.debian.org/debian trixie/main i386 python3-networkx all 3.2.1-5 [13.0 MB]
Get: 129 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.2-1 [55.3 kB]
Get: 130 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 131 http://deb.debian.org/debian trixie/main i386 python3-pysam i386 0.23.0+ds-1+b1 [3665 kB]
Get: 132 http://deb.debian.org/debian trixie/main i386 python3-pytest all 8.3.4-1 [250 kB]
Get: 133 http://deb.debian.org/debian trixie/main i386 smalt i386 0.7.6-13 [127 kB]
Fetched 201 MB in 3s (68.1 MB/s)
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Setting up java-common (0.76) ...
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Setting up gawk (1:5.2.1-2+b1) ...
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Setting up libbrotli1:i386 (1.1.0-2+b7) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up libnghttp2-14:i386 (1.64.0-1) ...
Setting up libdeflate0:i386 (1.23-1+b1) ...
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Setting up m4 (1.4.19-7) ...
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Setting up file (1:5.45-3+b1) ...
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Setting up libkrb5support0:i386 (1.21.3-4) ...
Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-9) ...
Setting up tzdata (2025a-2) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Sat Mar  8 18:08:46 UTC 2025.
Universal Time is now:  Sat Mar  8 18:08:46 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

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Setting up libblas3:i386 (3.12.1-2) ...
update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode
Setting up libclass-data-inheritable-perl (0.10-1) ...
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Setting up libssl-dev:i386 (3.4.1-1) ...
Setting up python3-numpy-dev:i386 (1:2.2.3+ds-2+b1) ...
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Setting up libpcsclite1:i386 (2.3.1-1) ...
Setting up libk5crypto3:i386 (1.21.3-4) ...
Setting up libsasl2-2:i386 (2.1.28+dfsg1-9) ...
Setting up libgfortran5:i386 (14.2.0-17) ...
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Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up libldap2:i386 (2.6.9+dfsg-1) ...
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Setting up libpython3-stdlib:i386 (3.13.2-1) ...
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Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
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Setting up python3-numpy (1:2.2.3+ds-2+b1) ...
Setting up python3-pluggy (1.5.0-1) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libgnutls30t64:i386 (3.8.9-2) ...
Setting up python3-more-itertools (10.6.0-1) ...
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Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up openjdk-21-jre-headless:i386 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up python3-jaraco.context (6.0.1-1) ...
Setting up libtest-most-perl (0.38-1) ...
Setting up python3-pytest (8.3.4-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3-typeguard (4.4.2-1) ...
Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up python3-jaraco.text (4.0.0-1) ...
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Setting up bioperl (1.7.8-1) ...
Setting up python3-setuptools (75.8.0-1) ...
Setting up libcurl3t64-gnutls:i386 (8.12.1-3) ...
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Setting up python3-networkx (3.2.1-5) ...
Setting up libhts3t64:i386 (1.21+ds-1) ...
Setting up dh-python (6.20250108) ...
Setting up python3-pysam (0.23.0+ds-1+b1) ...
Setting up samtools (1.21-1) ...
Setting up fastaq (3.17.0-9) ...
Processing triggers for libc-bin (2.40-7) ...
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
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Adding debian:Amazon_Root_CA_3.pem
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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
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Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
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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
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Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
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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
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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:SecureSign_Root_CA12.pem
Adding debian:SecureSign_Root_CA14.pem
Adding debian:SecureSign_Root_CA15.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: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_CYBER_Root_CA.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem
Adding debian:Telekom_Security_TLS_RSA_Root_2023.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-jdk-headless:i386 (21.0.6+7-1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-i386/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre-headless (2:1.21-76) ...
Setting up default-jdk-headless (2:1.21-76) ...
Processing triggers for ca-certificates (20241223) ...
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/iva-1.0.11+ds/ && 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  > ../iva_1.0.11+ds-6_source.changes
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.11+ds-6
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 i386
 debian/rules clean
dh clean --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds'
rm -rf .pybuild *.egg-info .pytest_cache build
rm -f iva/gage/*.class
rm -rf /build/reproducible-path/iva-1.0.11+ds/debian/man
find . -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds'
   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: python3.13 setup.py config 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
Checking dependencies found in path:
 OK	kmc
 OK	kmc_dump
 OK	nucmer
 OK	delta-filter
 OK	show-coords
 OK	samtools
 OK	smalt
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds'
chmod a-x /build/reproducible-path/iva-1.0.11+ds/iva/read_trim/adapters.fasta
chmod a+x /build/reproducible-path/iva-1.0.11+ds/iva/gage/getCorrectnessStats.sh
chmod a+x /build/reproducible-path/iva-1.0.11+ds/iva/ratt/main.ratt.pl
chmod a+x scripts/*
javac -verbose /build/reproducible-path/iva-1.0.11+ds/iva/gage/*.java
[parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats.java]]
[parsing completed 90ms]
[parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]]
[parsing completed 9ms]
[parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]]
[parsing completed 6ms]
[parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]]
[parsing completed 29ms]
[parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]]
[parsing completed 51ms]
[loading /modules/java.base/module-info.class]
[loading /modules/jdk.editpad/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
[loading /modules/jdk.attach/module-info.class]
[loading /modules/jdk.unsupported.desktop/module-info.class]
[loading /modules/java.sql/module-info.class]
[loading /modules/jdk.zipfs/module-info.class]
[loading /modules/java.sql.rowset/module-info.class]
[loading /modules/java.security.jgss/module-info.class]
[loading /modules/jdk.crypto.cryptoki/module-info.class]
[loading /modules/java.transaction.xa/module-info.class]
[loading /modules/java.instrument/module-info.class]
[loading /modules/java.smartcardio/module-info.class]
[loading /modules/jdk.jconsole/module-info.class]
[loading /modules/java.security.sasl/module-info.class]
[loading /modules/jdk.security.auth/module-info.class]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/java.logging/module-info.class]
[loading /modules/jdk.nio.mapmode/module-info.class]
[loading /modules/jdk.httpserver/module-info.class]
[loading /modules/jdk.xml.dom/module-info.class]
[loading /modules/jdk.internal.ed/module-info.class]
[loading /modules/jdk.jdwp.agent/module-info.class]
[loading /modules/jdk.management/module-info.class]
[loading /modules/jdk.incubator.vector/module-info.class]
[loading /modules/jdk.jfr/module-info.class]
[loading /modules/java.management.rmi/module-info.class]
[loading /modules/jdk.javadoc/module-info.class]
[loading /modules/jdk.jstatd/module-info.class]
[loading /modules/jdk.security.jgss/module-info.class]
[loading /modules/jdk.internal.opt/module-info.class]
[loading /modules/jdk.localedata/module-info.class]
[loading /modules/jdk.management.jfr/module-info.class]
[loading /modules/jdk.compiler/module-info.class]
[loading /modules/jdk.jlink/module-info.class]
[loading /modules/java.naming/module-info.class]
[loading /modules/java.desktop/module-info.class]
[loading /modules/java.datatransfer/module-info.class]
[loading /modules/jdk.jdi/module-info.class]
[loading /modules/jdk.jshell/module-info.class]
[loading /modules/jdk.jcmd/module-info.class]
[loading /modules/java.prefs/module-info.class]
[loading /modules/jdk.naming.dns/module-info.class]
[loading /modules/java.management/module-info.class]
[loading /modules/java.rmi/module-info.class]
[loading /modules/jdk.dynalink/module-info.class]
[loading /modules/jdk.jdeps/module-info.class]
[loading /modules/jdk.naming.rmi/module-info.class]
[loading /modules/jdk.net/module-info.class]
[loading /modules/jdk.random/module-info.class]
[loading /modules/jdk.charsets/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/jdk.jsobject/module-info.class]
[loading /modules/jdk.sctp/module-info.class]
[loading /modules/java.scripting/module-info.class]
[loading /modules/java.compiler/module-info.class]
[loading /modules/jdk.accessibility/module-info.class]
[loading /modules/jdk.internal.le/module-info.class]
[loading /modules/jdk.internal.jvmstat/module-info.class]
[loading /modules/jdk.unsupported/module-info.class]
[loading /modules/java.xml.crypto/module-info.class]
[loading /modules/jdk.hotspot.agent/module-info.class]
[loading /modules/jdk.management.agent/module-info.class]
[loading /modules/java.se/module-info.class]
[loading /modules/java.xml/module-info.class]
[loading /modules/jdk.jpackage/module-info.class]
[search path for source files: .]
[search path for class files: /usr/lib/jvm/java-21-openjdk-i386/lib/modules,.]
[loading /modules/java.base/java/io/BufferedReader.class]
[loading /modules/java.base/java/io/FileInputStream.class]
[loading /modules/java.base/java/io/InputStreamReader.class]
[loading /modules/java.base/java/text/DecimalFormat.class]
[loading /modules/java.base/java/text/NumberFormat.class]
[loading /modules/java.base/java/util/ArrayList.class]
[loading /modules/java.base/java/util/Arrays.class]
[loading /modules/java.base/java/util/HashMap.class]
[loading /modules/java.base/java/lang/Object.class]
[loading /modules/java.base/java/lang/String.class]
[loading /modules/java.base/java/lang/Integer.class]
[loading /modules/java.base/java/lang/Exception.class]
[loading /modules/java.base/java/lang/StringBuffer.class]
[loading /modules/java.management/java/lang/management/ManagementFactory.class]
[loading /modules/java.management/java/lang/management/MemoryMXBean.class]
[loading /modules/java.base/java/io/File.class]
[loading /modules/java.base/java/io/FileReader.class]
[loading /modules/java.base/java/lang/Boolean.class]
[loading /modules/java.base/java/lang/Enum.class]
[loading /modules/java.base/java/lang/constant/Constable.class]
[loading /modules/java.base/java/lang/Comparable.class]
[loading /modules/java.base/java/io/Serializable.class]
[loading /modules/java.base/java/util/Collections.class]
[loading /modules/java.base/java/lang/Deprecated.class]
[loading /modules/java.base/java/lang/annotation/Retention.class]
[loading /modules/java.base/java/lang/annotation/RetentionPolicy.class]
[loading /modules/java.base/java/lang/annotation/Target.class]
[loading /modules/java.base/java/lang/annotation/ElementType.class]
[checking GetFastaStats]
[loading /modules/java.base/java/lang/AutoCloseable.class]
[loading /modules/java.base/java/util/Map.class]
[loading /modules/java.base/java/lang/Throwable.class]
[loading /modules/java.base/java/lang/CharSequence.class]
[loading /modules/java.base/java/lang/constant/ConstantDesc.class]
[loading /modules/java.base/java/io/Reader.class]
[loading /modules/java.base/java/lang/Readable.class]
[loading /modules/java.base/java/io/Closeable.class]
[loading /modules/java.base/java/lang/Number.class]
[loading /modules/java.base/java/lang/Cloneable.class]
[loading /modules/java.base/java/util/AbstractMap.class]
[loading /modules/java.base/java/lang/Appendable.class]
[loading /modules/java.base/java/lang/AbstractStringBuilder.class]
[loading /modules/java.base/java/lang/Byte.class]
[loading /modules/java.base/java/lang/Character.class]
[loading /modules/java.base/java/lang/Short.class]
[loading /modules/java.base/java/lang/Long.class]
[loading /modules/java.base/java/lang/Float.class]
[loading /modules/java.base/java/lang/Double.class]
[loading /modules/java.base/java/lang/Void.class]
[loading /modules/java.base/java/io/FileDescriptor.class]
[loading /modules/java.base/java/lang/System.class]
[loading /modules/java.base/java/io/PrintStream.class]
[loading /modules/java.base/java/io/FilterOutputStream.class]
[loading /modules/java.base/java/io/OutputStream.class]
[loading /modules/java.base/java/io/Flushable.class]
[loading /modules/java.base/java/util/Set.class]
[loading /modules/java.base/java/lang/Iterable.class]
[loading /modules/java.base/java/util/Collection.class]
[loading /modules/java.base/java/util/Iterator.class]
[loading /modules/java.base/java/lang/Math.class]
[loading /modules/java.base/java/util/List.class]
[loading /modules/java.base/java/util/SequencedCollection.class]
[loading /modules/java.base/java/util/RandomAccess.class]
[loading /modules/java.base/java/util/AbstractList.class]
[loading /modules/java.base/java/util/AbstractCollection.class]
[loading /modules/java.base/java/util/function/IntFunction.class]
[loading /modules/java.base/java/util/Comparator.class]
[loading /modules/java.base/java/text/Format.class]
[loading /modules/java.base/java/lang/Error.class]
[loading /modules/java.base/java/lang/RuntimeException.class]
[loading /modules/java.base/java/io/IOException.class]
[loading /modules/java.base/java/lang/NumberFormatException.class]
[loading /modules/java.base/java/lang/IllegalArgumentException.class]
[loading /modules/java.base/java/io/FileNotFoundException.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats$ContigAt.class]
[loading /modules/java.base/java/lang/invoke/StringConcatFactory.class]
[loading /modules/java.base/jdk/internal/javac/PreviewFeature.class]
[loading /modules/java.base/jdk/internal/javac/PreviewFeature$Feature.class]
[loading /modules/java.base/jdk/internal/javac/PreviewFeature$JEP.class]
[loading /modules/java.base/java/lang/invoke/MethodHandles.class]
[loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class]
[loading /modules/java.base/java/lang/invoke/MethodType.class]
[loading /modules/java.base/java/io/InputStream.class]
[loading /modules/java.base/java/lang/invoke/CallSite.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats.class]
[checking SizeFasta]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.class]
[checking SplitFastaByLetter]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.class]
[checking Utils]
[loading /modules/java.base/java/util/Optional.class]
[loading /modules/java.base/java/lang/Enum$EnumDesc.class]
[loading /modules/java.base/java/lang/constant/DynamicConstantDesc.class]
[loading /modules/java.base/java/lang/CloneNotSupportedException.class]
[loading /modules/java.base/java/lang/Class.class]
[loading /modules/java.base/java/net/URI.class]
[loading /modules/java.base/java/lang/Process.class]
[loading /modules/java.base/java/lang/Runtime.class]
[loading /modules/java.base/java/lang/StringBuilder.class]
[loading /modules/java.base/java/lang/reflect/GenericDeclaration.class]
[loading /modules/java.base/java/lang/reflect/AnnotatedElement.class]
[loading /modules/java.base/java/lang/reflect/Type.class]
[loading /modules/java.base/java/lang/invoke/TypeDescriptor.class]
[loading /modules/java.base/java/lang/invoke/TypeDescriptor$OfField.class]
[loading /modules/java.base/java/lang/AssertionError.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils$Pair.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils$Translate.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils$ToProtein.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.class]
[checking getScaffoldStats]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats$Scaffold.class]
[wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.class]
[total 1459ms]
Note: /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
dh_auto_build --
I: pybuild base:311: /usr/bin/python3 setup.py build 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
Checking dependencies found in path:
 OK	kmc
 OK	kmc_dump
 OK	nucmer
 OK	delta-filter
 OK	show-coords
 OK	samtools
 OK	smalt
running build
running build_py
creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
copying iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva
creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
copying iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt
creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/read_trim
creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
copying iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
copying iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data
running build_scripts
creating build/scripts-3.13
copying and adjusting scripts/iva_qc -> build/scripts-3.13
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.13
copying and adjusting scripts/iva -> build/scripts-3.13
changing mode of build/scripts-3.13/iva_qc from 644 to 755
changing mode of build/scripts-3.13/iva_qc_make_db from 644 to 755
changing mode of build/scripts-3.13/iva from 644 to 755
make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds'
python3 -m pytest --verbose
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3
cachedir: .pytest_cache
rootdir: /build/reproducible-path/iva-1.0.11+ds
plugins: typeguard-4.4.2
collecting ... collected 160 items

iva/tests/assembly_test.py::TestAssembly::test_contig_contained_in_nucmer_hits PASSED [  0%]
iva/tests/assembly_test.py::TestAssembly::test_contig_names_size_order PASSED [  1%]
iva/tests/assembly_test.py::TestAssembly::test_contig_worth_extending PASSED [  1%]
iva/tests/assembly_test.py::TestAssembly::test_coords_to_new_contig PASSED [  2%]
iva/tests/assembly_test.py::TestAssembly::test_extend_contigs_with_bam PASSED [  3%]
iva/tests/assembly_test.py::TestAssembly::test_get_contig_order_by_orfs PASSED [  3%]
iva/tests/assembly_test.py::TestAssembly::test_get_ref_length PASSED     [  4%]
iva/tests/assembly_test.py::TestAssembly::test_get_ref_length_sam_pair PASSED [  5%]
iva/tests/assembly_test.py::TestAssembly::test_get_unmapped_pairs PASSED [  5%]
iva/tests/assembly_test.py::TestAssembly::test_good_intervals_from_strand_coverage PASSED [  6%]
iva/tests/assembly_test.py::TestAssembly::test_init_and_write PASSED     [  6%]
iva/tests/assembly_test.py::TestAssembly::test_map_reads PASSED          [  7%]
iva/tests/assembly_test.py::TestAssembly::test_merge_overlapping_contigs PASSED [  8%]
iva/tests/assembly_test.py::TestAssembly::test_read_pair_extend PASSED   [  8%]
iva/tests/assembly_test.py::TestAssembly::test_remove_contained_contigs PASSED [  9%]
iva/tests/assembly_test.py::TestAssembly::test_remove_contig PASSED      [ 10%]
iva/tests/assembly_test.py::TestAssembly::test_remove_contig_from_nucmer_hits PASSED [ 10%]
iva/tests/assembly_test.py::TestAssembly::test_subcontigs_from_strand_bias PASSED [ 11%]
iva/tests/assembly_test.py::TestAssembly::test_trim_contig_for_strand_bias PASSED [ 11%]
iva/tests/assembly_test.py::TestAssembly::test_trim_contigs PASSED       [ 12%]
iva/tests/assembly_test.py::TestAssembly::test_trim_strand_biased_ends PASSED [ 13%]
iva/tests/assembly_test.py::TestAssembly::test_worth_extending PASSED    [ 13%]
iva/tests/contig_test.py::TestContig::test_add_left_kmer PASSED          [ 14%]
iva/tests/contig_test.py::TestContig::test_add_right_kmer PASSED         [ 15%]
iva/tests/contig_test.py::TestContig::test_extend PASSED                 [ 15%]
iva/tests/contig_test.py::TestContig::test_init PASSED                   [ 16%]
iva/tests/contig_test.py::TestContig::test_len PASSED                    [ 16%]
iva/tests/contig_trim_test.py::TestContigTrim::test_coverage_to_trimmed_coords PASSED [ 17%]
iva/tests/contig_trim_test.py::TestContigTrim::test_trim_ends PASSED     [ 18%]
iva/tests/contig_trim_test.py::TestContigTrim::test_trim_primers_and_adapters PASSED [ 18%]
iva/tests/edge_test.py::TestEdge::test_change_hit_coords_with_intersection PASSED [ 19%]
iva/tests/edge_test.py::TestEdge::test_make_contig_first PASSED          [ 20%]
iva/tests/edge_test.py::TestEdge::test_make_contig_forwards PASSED       [ 20%]
iva/tests/edge_test.py::TestEdge::test_merge_into PASSED                 [ 21%]
iva/tests/edge_test.py::TestEdge::test_open_end PASSED                   [ 21%]
iva/tests/edge_test.py::TestEdge::test_reverse PASSED                    [ 22%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir PASSED      [ 23%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_unzipped PASSED [ 23%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_zipped PASSED [ 24%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file PASSED     [ 25%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_unzipped PASSED [ 25%]
iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_zipped PASSED [ 26%]
iva/tests/egg_extract_test.py::TestEggExtract::test_init_and_write PASSED [ 26%]
iva/tests/external_progs_test.py::TestExternalProgs::test_blastn_version PASSED [ 27%]
iva/tests/external_progs_test.py::TestExternalProgs::test_delta_filter_in_path PASSED [ 28%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_in_path PASSED [ 28%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_version PASSED [ 29%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_in_path PASSED [ 30%]
iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_version PASSED [ 30%]
iva/tests/external_progs_test.py::TestExternalProgs::test_makeblastdb_version PASSED [ 31%]
iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_in_path PASSED [ 31%]
iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED [ 32%]
iva/tests/external_progs_test.py::TestExternalProgs::test_r_version PASSED [ 33%]
iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_in_path PASSED [ 33%]
iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 34%]
iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_version PASSED [ 35%]
iva/tests/external_progs_test.py::TestExternalProgs::test_show_coords_in_path PASSED [ 35%]
iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_in_path PASSED [ 36%]
iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_version PASSED [ 36%]
iva/tests/graph_test.py::TestGraph::test_add_and_get_edges PASSED        [ 37%]
iva/tests/graph_test.py::TestGraph::test_connected_components PASSED     [ 38%]
iva/tests/graph_test.py::TestGraph::test_degree PASSED                   [ 38%]
iva/tests/graph_test.py::TestGraph::test_edges_are_consistent PASSED     [ 39%]
iva/tests/graph_test.py::TestGraph::test_find_simple_path PASSED         [ 40%]
iva/tests/graph_test.py::TestGraph::test_get_nodes PASSED                [ 40%]
iva/tests/graph_test.py::TestGraph::test_merged_coords_from_simple_nonredundant_path PASSED [ 41%]
iva/tests/graph_test.py::TestGraph::test_node_to_coords PASSED           [ 41%]
iva/tests/graph_test.py::TestGraph::test_remove_middle_node PASSED       [ 42%]
iva/tests/graph_test.py::TestGraph::test_remove_node PASSED              [ 43%]
iva/tests/graph_test.py::TestGraph::test_remove_redundant_nodes_from_simple_path PASSED [ 43%]
iva/tests/graph_test.py::TestGraph::test_simple_path_is_consistent PASSED [ 44%]
iva/tests/kcount_test.py::TestKcount::test_counts_file_to_fasta PASSED   [ 45%]
iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fa PASSED         [ 45%]
iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fq PASSED         [ 46%]
iva/tests/kcount_test.py::TestKcount::test_kmc_to_kmer_counts PASSED     [ 46%]
iva/tests/kcount_test.py::TestKcount::test_median PASSED                 [ 47%]
iva/tests/kmers_test.py::TestKmers::test_append PASSED                   [ 48%]
iva/tests/kmers_test.py::TestKmers::test_commonest_kmers PASSED          [ 48%]
iva/tests/kmers_test.py::TestKmers::test_extend PASSED                   [ 49%]
iva/tests/kmers_test.py::TestKmers::test_extension PASSED                [ 50%]
iva/tests/kmers_test.py::TestKmers::test_init PASSED                     [ 50%]
iva/tests/kmers_test.py::TestKmers::test_kmer_dict PASSED                [ 51%]
iva/tests/kraken_test.py::TestKraken::test_append_to_file PASSED         [ 51%]
iva/tests/kraken_test.py::TestKraken::test_count_cds_from_embl PASSED    [ 52%]
iva/tests/kraken_test.py::TestKraken::test_genbank_to_taxon_and_gi PASSED [ 53%]
iva/tests/kraken_test.py::TestKraken::test_get_most_common_species_dir PASSED [ 53%]
iva/tests/kraken_test.py::TestKraken::test_get_parent_taxons PASSED      [ 54%]
iva/tests/kraken_test.py::TestKraken::test_load_extra_ref_info PASSED    [ 55%]
iva/tests/kraken_test.py::TestKraken::test_replace_fasta_header PASSED   [ 55%]
iva/tests/kraken_test.py::TestKraken::test_species_to_dir PASSED         [ 56%]
iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files PASSED [ 56%]
iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files_region PASSED [ 57%]
iva/tests/mapping_test.py::TestMapping::test_bam_file_to_region_fasta PASSED [ 58%]
iva/tests/mapping_test.py::TestMapping::test_bam_to_fasta PASSED         [ 58%]
iva/tests/mapping_test.py::TestMapping::test_can_extend PASSED           [ 59%]
iva/tests/mapping_test.py::TestMapping::test_consensus_base PASSED       [ 60%]
iva/tests/mapping_test.py::TestMapping::test_consensus_base_both_strands PASSED [ 60%]
iva/tests/mapping_test.py::TestMapping::test_find_incorrect_ref_bases PASSED [ 61%]
iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd PASSED [ 61%]
iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd_And_rev PASSED [ 62%]
iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_rev PASSED [ 63%]
iva/tests/mapping_test.py::TestMapping::test_get_pair_type PASSED        [ 63%]
iva/tests/mapping_test.py::TestMapping::test_get_ref_name PASSED         [ 64%]
iva/tests/mapping_test.py::TestMapping::test_map_reads PASSED            [ 65%]
iva/tests/mapping_test.py::TestMapping::test_map_reads_and_sort PASSED   [ 65%]
iva/tests/mapping_test.py::TestMapping::test_map_reads_wth_flag PASSED   [ 66%]
iva/tests/mapping_test.py::TestMapping::test_remove_indels PASSED        [ 66%]
iva/tests/mapping_test.py::TestMapping::test_sam_to_fasta PASSED         [ 67%]
iva/tests/mapping_test.py::TestMapping::test_smalt_in_path PASSED        [ 68%]
iva/tests/mapping_test.py::TestMapping::test_soft_clipped PASSED         [ 68%]
iva/tests/mapping_test.py::TestMapping::test_strip_mpileup_coverage_string PASSED [ 69%]
iva/tests/mapping_test.py::TestMapping::test_total_ref_length_from_bam PASSED [ 70%]
iva/tests/mummer_test.py::TestMummer::test_file_read PASSED              [ 70%]
iva/tests/mummer_test.py::TestMummer::test_is_at_ends PASSED             [ 71%]
iva/tests/mummer_test.py::TestMummer::test_is_self_hit PASSED            [ 71%]
iva/tests/mummer_test.py::TestMummer::test_on_same_strand PASSED         [ 72%]
iva/tests/mummer_test.py::TestMummer::test_qry_coords PASSED             [ 73%]
iva/tests/mummer_test.py::TestMummer::test_ref_coords PASSED             [ 73%]
iva/tests/mummer_test.py::TestMummer::test_run_nucmer PASSED             [ 74%]
iva/tests/mummer_test.py::TestMummer::test_sort PASSED                   [ 75%]
iva/tests/mummer_test.py::TestMummer::test_swap PASSED                   [ 75%]
iva/tests/mummer_test.py::TestMummer::test_to_graph_edge PASSED          [ 76%]
iva/tests/qc_external_test.py::TestQcExternal::test_run_gage PASSED      [ 76%]
iva/tests/qc_external_test.py::TestQcExternal::test_run_ratt PASSED      [ 77%]
iva/tests/qc_test.py::TestQc::test_calculate_cds_assembly_stats PASSED   [ 78%]
iva/tests/qc_test.py::TestQc::test_calculate_contig_placement PASSED     [ 78%]
iva/tests/qc_test.py::TestQc::test_calculate_ref_positions_covered_by_contigs PASSED [ 79%]
iva/tests/qc_test.py::TestQc::test_calculate_ref_read_coverage PASSED    [ 80%]
iva/tests/qc_test.py::TestQc::test_calculate_ref_read_region_coverage PASSED [ 80%]
iva/tests/qc_test.py::TestQc::test_calculate_refseq_assembly_stats PASSED [ 81%]
iva/tests/qc_test.py::TestQc::test_calculate_should_have_assembled PASSED [ 81%]
iva/tests/qc_test.py::TestQc::test_contig_placement_in_reference PASSED  [ 82%]
iva/tests/qc_test.py::TestQc::test_contigs_and_bases_that_hit_ref PASSED [ 83%]
iva/tests/qc_test.py::TestQc::test_cov_to_R_string PASSED                [ 83%]
iva/tests/qc_test.py::TestQc::test_coverage_list_to_low_cov_intervals PASSED [ 84%]
iva/tests/qc_test.py::TestQc::test_get_R_plot_contig_order_from_contig_placement PASSED [ 85%]
iva/tests/qc_test.py::TestQc::test_get_contig_hits_to_reference PASSED   [ 85%]
iva/tests/qc_test.py::TestQc::test_get_overlapping_qry_hits PASSED       [ 86%]
iva/tests/qc_test.py::TestQc::test_get_ref_cds_from_gff PASSED           [ 86%]
iva/tests/qc_test.py::TestQc::test_get_unique_and_repetitive_from_contig_hits PASSED [ 87%]
iva/tests/qc_test.py::TestQc::test_gff_and_fasta_to_cds PASSED           [ 88%]
iva/tests/qc_test.py::TestQc::test_has_orf PASSED                        [ 88%]
iva/tests/qc_test.py::TestQc::test_hash_nucmer_hits_by_ref PASSED        [ 89%]
iva/tests/qc_test.py::TestQc::test_ids_in_order_from_fai PASSED          [ 90%]
iva/tests/qc_test.py::TestQc::test_invert_list PASSED                    [ 90%]
iva/tests/qc_test.py::TestQc::test_map_cds_to_assembly PASSED            [ 91%]
iva/tests/qc_test.py::TestQc::test_mummer_coords_file_to_dict PASSED     [ 91%]
iva/tests/qc_test.py::TestQc::test_write_cds_seqs PASSED                 [ 92%]
iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_hit_ref PASSED    [ 93%]
iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_not_hit_ref PASSED [ 93%]
iva/tests/qc_test.py::TestQc::test_write_ref_coverage_to_files_for_R PASSED [ 94%]
iva/tests/read_trim_test.py::TestReadTrim::test_run_trimmomatic PASSED   [ 95%]
iva/tests/seed_test.py::TestSeed::test_extend PASSED                     [ 95%]
iva/tests/seed_test.py::TestSeed::test_extend_with_reads_as_single_end PASSED [ 96%]
iva/tests/seed_test.py::TestSeed::test_extension_from_read PASSED        [ 96%]
iva/tests/seed_test.py::TestSeed::test_extensions_from_reads_file PASSED [ 97%]
iva/tests/seed_test.py::TestSeed::test_init PASSED                       [ 98%]
iva/tests/seed_test.py::TestSeed::test_kmc_in_path PASSED                [ 98%]
iva/tests/seed_test.py::TestSeed::test_len PASSED                        [ 99%]
iva/tests/seed_test.py::TestSeed::test_write_fasta PASSED                [100%]

=============================== warnings summary ===============================
../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
  /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'}
    __version__ = Distribution().from_name('pyfastaq').version

iva/test_data_runner.py:20
  /build/reproducible-path/iva-1.0.11+ds/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py)
    class Tester:

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================= 160 passed, 2 warnings in 6.36s ========================
make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   dh_auto_install --destdir=debian/iva/ -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/iva-1.0.11+ds/debian/iva 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
Checking dependencies found in path:
 OK	kmc
 OK	kmc_dump
 OK	nucmer
 OK	delta-filter
 OK	show-coords
 OK	samtools
 OK	smalt
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: 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.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage
running build_scripts
running install_lib
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/gage
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/ratt
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_run_data
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/read_trim
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/read_trim
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.13_iva/build/iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/mummer.py to mummer.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/read_trim.py to read_trim.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/mapping.py to mapping.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/seed.py to seed.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/external_progs.py to external_progs.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/seed_processor.py to seed_processor.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/graph.py to graph.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/contig_trim.py to contig_trim.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/assembly.py to assembly.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/egg_extract.py to egg_extract.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/common.py to common.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/kcount.py to kcount.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/qc.py to qc.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/edge.py to edge.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/contig.py to contig.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/qc_external.py to qc_external.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/kraken.py to kraken.cpython-313.pyc
byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva/kmers.py to kmers.cpython-313.pyc
running install_egg_info
running egg_info
creating iva.egg-info
writing iva.egg-info/PKG-INFO
writing dependency_links to iva.egg-info/dependency_links.txt
writing requirements to iva.egg-info/requires.txt
writing top-level names to iva.egg-info/top_level.txt
writing manifest file 'iva.egg-info/SOURCES.txt'
reading manifest file 'iva.egg-info/SOURCES.txt'
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'iva.egg-info/SOURCES.txt'
Copying iva.egg-info to /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.13/dist-packages/iva-1.0.9.egg-info
Skipping SOURCES.txt
running install_scripts
creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.13/iva_qc -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.13/iva_qc_make_db -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.13/iva -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin
changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755
changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc_make_db to 755
changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva to 755
   dh_installdocs -O--buildsystem=pybuild
   dh_installchangelogs -O--buildsystem=pybuild
   debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds'
mkdir -p /build/reproducible-path/iva-1.0.11+ds/debian/man
PYTHONPATH=. help2man -N -o /build/reproducible-path/iva-1.0.11+ds/debian/man/iva.1 \
          -n 'iterative virus assembler' \
          --no-discard-stderr  ./scripts/iva
PYTHONPATH=. help2man -N -o /build/reproducible-path/iva-1.0.11+ds/debian/man/iva_qc.1 \
          -n 'compare an assembly to a reference' \
          --no-discard-stderr ./scripts/iva_qc
PYTHONPATH=. help2man -N -o /build/reproducible-path/iva-1.0.11+ds/debian/man/iva_qc_make_db.1 \
          -n 'make a database as input for iva_qc' \
          --no-discard-stderr  ./scripts/iva_qc_make_db
dh_installman --
make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds'
   dh_python3 -O--buildsystem=pybuild
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
   dh_strip_nondeterminism -O--buildsystem=pybuild
   dh_compress -O--buildsystem=pybuild
   dh_fixperms -O--buildsystem=pybuild
   dh_missing -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -O--buildsystem=pybuild
   dh_gencontrol -O--buildsystem=pybuild
   dh_md5sums -O--buildsystem=pybuild
   dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'iva' in '../iva_1.0.11+ds-6_i386.deb'.
 dpkg-genbuildinfo --build=binary -O../iva_1.0.11+ds-6_i386.buildinfo
 dpkg-genchanges --build=binary -O../iva_1.0.11+ds-6_i386.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/31052 and its subdirectories
I: Current time: Sat Mar  8 06:09:37 -12 2025
I: pbuilder-time-stamp: 1741457377