0s autopkgtest [15:18:10]: starting date and time: 2024-03-23 15:18:10+0000 0s autopkgtest [15:18:10]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:18:10]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p5wg_48a/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade gasic --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-14.secgroup --name adt-noble-ppc64el-gasic-20240323-151810-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 176s autopkgtest [15:21:06]: testbed dpkg architecture: ppc64el 177s autopkgtest [15:21:07]: testbed apt version: 2.7.12 177s autopkgtest [15:21:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 178s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 178s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 178s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 178s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 178s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 178s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [659 kB] 178s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 178s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 178s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 178s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4248 kB] 179s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 179s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [60.8 kB] 179s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 182s Fetched 9623 kB in 2s (4044 kB/s) 182s Reading package lists... 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 185s Calculating upgrade... 185s The following packages will be REMOVED: 185s libssl3 185s The following NEW packages will be installed: 185s libssl3t64 185s The following packages have been kept back: 185s curl 185s The following packages will be upgraded: 185s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales openssl 185s python3-markupsafe 185s 8 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 185s Need to get 12.1 MB of archives. 185s After this operation, 10.2 kB of additional disk space will be used. 185s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6 ppc64el 2.39-0ubuntu6 [3274 kB] 186s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-bin ppc64el 2.39-0ubuntu6 [751 kB] 186s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB] 186s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB] 186s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libbsd0 ppc64el 0.12.1-1 [56.9 kB] 186s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el locales all 2.39-0ubuntu6 [4232 kB] 186s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 186s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-markupsafe ppc64el 2.1.5-1build1 [13.2 kB] 186s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el cloud-init all 24.1.2-0ubuntu1 [597 kB] 186s Preconfiguring packages ... 187s Fetched 12.1 MB in 1s (11.3 MB/s) 187s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 187s Preparing to unpack .../libc6_2.39-0ubuntu6_ppc64el.deb ... 187s Unpacking libc6:ppc64el (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 187s Setting up libc6:ppc64el (2.39-0ubuntu6) ... 188s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 188s Preparing to unpack .../libc-bin_2.39-0ubuntu6_ppc64el.deb ... 188s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 188s Setting up libc-bin (2.39-0ubuntu6) ... 188s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 188s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ... 188s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 188s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: 188s wget depends on libssl3 (>= 3.0.0). 188s tnftp depends on libssl3 (>= 3.0.0). 188s tcpdump depends on libssl3 (>= 3.0.0). 188s systemd-resolved depends on libssl3 (>= 3.0.0). 188s systemd depends on libssl3 (>= 3.0.0). 188s sudo depends on libssl3 (>= 3.0.0). 188s rsync depends on libssl3 (>= 3.0.0). 188s python3-cryptography depends on libssl3 (>= 3.0.0). 188s openssh-server depends on libssl3 (>= 3.0.10). 188s openssh-client depends on libssl3 (>= 3.0.10). 188s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 188s libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0). 188s libssh-4:ppc64el depends on libssl3 (>= 3.0.0). 188s libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0). 188s libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0). 188s libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0). 188s libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0). 188s libnvme1 depends on libssl3 (>= 3.0.0). 188s libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0). 188s libkmod2:ppc64el depends on libssl3 (>= 3.0.0). 188s libfido2-1:ppc64el depends on libssl3 (>= 3.0.0). 188s libcurl4:ppc64el depends on libssl3 (>= 3.0.0). 188s libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0). 188s kmod depends on libssl3 (>= 3.0.0). 188s dhcpcd-base depends on libssl3 (>= 3.0.0). 188s bind9-libs:ppc64el depends on libssl3 (>= 3.0.0). 188s 188s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70157 files and directories currently installed.) 188s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ... 188s Selecting previously unselected package libssl3t64:ppc64el. 188s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70146 files and directories currently installed.) 188s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ... 188s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 188s Preparing to unpack .../1-libbsd0_0.12.1-1_ppc64el.deb ... 188s Unpacking libbsd0:ppc64el (0.12.1-1) over (0.11.8-1) ... 188s Preparing to unpack .../2-locales_2.39-0ubuntu6_all.deb ... 188s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 188s Preparing to unpack .../3-fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 188s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 188s Preparing to unpack .../4-python3-markupsafe_2.1.5-1build1_ppc64el.deb ... 188s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 188s Preparing to unpack .../5-cloud-init_24.1.2-0ubuntu1_all.deb ... 188s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 189s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 189s Setting up cloud-init (24.1.2-0ubuntu1) ... 190s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ... 190s Setting up locales (2.39-0ubuntu6) ... 190s Generating locales (this might take a while)... 192s en_US.UTF-8... done 192s Generation complete. 192s Setting up python3-markupsafe (2.1.5-1build1) ... 192s Setting up openssl (3.0.13-0ubuntu2) ... 192s Setting up libbsd0:ppc64el (0.12.1-1) ... 192s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 192s Processing triggers for man-db (2.12.0-3) ... 193s Processing triggers for libc-bin (2.39-0ubuntu6) ... 193s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 194s sh: Attempting to set up Debian/Ubuntu apt sources automatically 194s sh: Distribution appears to be Ubuntu 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s eatmydata is already the newest version (131-1). 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 196s dbus is already the newest version (1.14.10-4ubuntu1). 196s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s rng-tools-debian is already the newest version (2.4). 196s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s The following packages will be REMOVED: 196s cloud-init* python3-configobj* python3-debconf* 196s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 196s After this operation, 3256 kB disk space will be freed. 196s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 70158 files and directories currently installed.) 196s Removing cloud-init (24.1.2-0ubuntu1) ... 197s Removing python3-configobj (5.0.8-3) ... 197s Removing python3-debconf (1.5.86) ... 197s Processing triggers for man-db (2.12.0-3) ... 198s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69769 files and directories currently installed.) 198s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 198s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 198s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 198s invoke-rc.d: policy-rc.d denied execution of try-restart. 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 199s linux-generic is already the newest version (6.8.0-11.11+1). 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 199s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 199s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 199s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 202s Reading package lists... 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s Calculating upgrade... 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s autopkgtest [15:21:33]: rebooting testbed after setup commands that affected boot 364s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 371s autopkgtest [15:24:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 373s autopkgtest [15:24:23]: @@@@@@@@@@@@@@@@@@@@ apt-source gasic 376s Get:1 http://ftpmaster.internal/ubuntu noble/universe gasic 0.0.r19-8 (dsc) [2112 B] 376s Get:2 http://ftpmaster.internal/ubuntu noble/universe gasic 0.0.r19-8 (tar) [12.4 kB] 376s Get:3 http://ftpmaster.internal/ubuntu noble/universe gasic 0.0.r19-8 (diff) [7305 kB] 376s gpgv: Signature made Thu Dec 29 18:00:34 2022 UTC 376s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 376s gpgv: issuer "tille@debian.org" 376s gpgv: Can't check signature: No public key 376s dpkg-source: warning: cannot verify inline signature for ./gasic_0.0.r19-8.dsc: no acceptable signature found 376s autopkgtest [15:24:26]: testing package gasic version 0.0.r19-8 377s autopkgtest [15:24:27]: build not needed 377s autopkgtest [15:24:27]: test run-unit-test: preparing testbed 383s Reading package lists... 384s Building dependency tree... 384s Reading state information... 384s Starting pkgProblemResolver with broken count: 0 384s Starting 2 pkgProblemResolver with broken count: 0 384s Done 384s The following additional packages will be installed: 384s blt bowtie bowtie2 bwa fontconfig-config fonts-dejavu-core 384s fonts-dejavu-extra fonts-dejavu-mono fonts-lyx fonts-urw-base35 gasic 384s gasic-examples libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 384s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 384s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 384s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 384s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 384s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 384s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 384s python3-brotli python3-cairo python3-contourpy python3-cycler 384s python3-dateutil python3-decorator python3-fonttools python3-freetype 384s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 384s python3-mpmath python3-numpy python3-packaging python3-pil 384s python3-pil.imagetk python3-pysam python3-reportlab python3-rlpycairo 384s python3-scipy python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 384s seqan-apps sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 384s xfonts-encodings xfonts-utils xml-core 384s Suggested packages: 384s blt-demo bowtie-examples bowtie2-examples samtools fonts-freefont-otf 384s | fonts-freefont-ttf fonts-texgyre libjs-jquery-ui-docs liblcms2-utils 384s tcl8.6 tk8.6 clustalo clustalw dialign dssp emboss fasttree mafft muscle3 384s phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib 384s python3-psycopg2 raxml t-coffee wise python-cycler-doc python-lxml-doc 384s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 384s inkscape ipython3 librsvg2-common python3-cairocffi python3-gi-cairo 384s python3-gobject python3-pyqt5 python3-sip python3-tornado 384s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 384s gfortran python3-dev python3-pytest python-pil-doc pdf-viewer 384s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 384s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 384s cwltool | cwl-runner sgml-base-doc debhelper 384s Recommended packages: 384s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 384s python3-cssselect python3-html5lib python3-olefile g++ | c++-compiler 384s isympy-common 384s The following NEW packages will be installed: 384s autopkgtest-satdep blt bowtie bowtie2 bwa fontconfig-config 384s fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono fonts-lyx 384s fonts-urw-base35 gasic gasic-examples libblas3 libcairo2 libdeflate0 384s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 384s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 384s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 384s liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 libsharpyuv0 384s libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 384s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 384s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 384s python3-cairo python3-contourpy python3-cycler python3-dateutil 384s python3-decorator python3-fonttools python3-freetype python3-fs 384s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 384s python3-mpmath python3-numpy python3-packaging python3-pil 384s python3-pil.imagetk python3-pysam python3-reportlab python3-rlpycairo 384s python3-scipy python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 384s seqan-apps sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 384s xfonts-encodings xfonts-utils xml-core 384s 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. 384s Need to get 116 MB/116 MB of archives. 384s After this operation, 524 MB of additional disk space will be used. 384s Get:1 /tmp/autopkgtest.ANOheq/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 384s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] 384s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 385s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 385s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 386s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB] 386s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 386s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 386s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB] 386s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 388s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 388s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 388s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 388s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 388s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 388s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.14-1 [944 kB] 388s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7 [778 kB] 388s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el blt ppc64el 2.5.3+dfsg-7 [4832 B] 388s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el bwa ppc64el 0.7.17-7 [214 kB] 388s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-extra all 2.37-8 [1947 kB] 388s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el fonts-lyx all 2.4.0~RC3-1 [170 kB] 388s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 388s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 388s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 388s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 388s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 389s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 389s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 389s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tk ppc64el 3.11.5-1 [116 kB] 389s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pil.imagetk ppc64el 10.2.0-1 [10.1 kB] 389s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 389s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libimagequant0 ppc64el 2.18.0-1 [42.5 kB] 389s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 389s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 389s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB] 389s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libopenjp2-7 ppc64el 2.5.0-2 [233 kB] 389s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 389s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 390s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libraqm0 ppc64el 0.10.1-1 [18.9 kB] 390s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 390s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 390s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 390s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 390s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 390s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 390s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4 [14.4 kB] 390s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4 [31.2 kB] 390s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pil ppc64el 10.2.0-1 [526 kB] 390s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 390s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 390s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 390s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 390s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-cairo ppc64el 1.25.1-2 [162 kB] 390s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB] 390s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 390s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-reportlab all 4.1.0-1 [683 kB] 390s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] 390s Get:58 http://ftpmaster.internal/ubuntu noble/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 390s Get:59 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biopython ppc64el 1.81+dfsg-3 [1738 kB] 390s Get:60 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 390s Get:61 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhts3 ppc64el 1.18+ds-1 [553 kB] 390s Get:62 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pysam ppc64el 0.22.0+ds-1 [5037 kB] 390s Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 390s Get:64 http://ftpmaster.internal/ubuntu noble/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 390s Get:65 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 390s Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 390s Get:67 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-contourpy ppc64el 1.0.7-1build2 [300 kB] 390s Get:68 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cycler all 0.11.0-2 [8202 B] 390s Get:69 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-brotli ppc64el 1.1.0-2 [420 kB] 390s Get:70 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 390s Get:71 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-mpmath all 1.2.1-3 [421 kB] 390s Get:72 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-sympy all 1.12-7 [3966 kB] 390s Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 390s Get:74 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-fs all 2.4.16-3 [91.1 kB] 390s Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1 [192 kB] 390s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-lxml ppc64el 5.1.0-1 [2191 kB] 390s Get:77 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build2 [28.8 kB] 390s Get:78 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1 [368 kB] 390s Get:79 http://ftpmaster.internal/ubuntu noble/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 390s Get:80 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-fonttools ppc64el 4.46.0-1 [1746 kB] 391s Get:81 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-kiwisolver ppc64el 1.4.4-2 [55.8 kB] 391s Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] 391s Get:83 http://ftpmaster.internal/ubuntu noble/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6 [220 kB] 391s Get:84 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-matplotlib ppc64el 3.6.3-1ubuntu3 [7651 kB] 391s Get:85 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie ppc64el 1.3.1-3 [1698 kB] 391s Get:86 http://ftpmaster.internal/ubuntu noble/universe ppc64el bowtie2 ppc64el 2.5.2-1 [1367 kB] 391s Get:87 http://ftpmaster.internal/ubuntu noble/universe ppc64el seqan-apps ppc64el 2.4.0+dfsg-16 [12.7 MB] 391s Get:88 http://ftpmaster.internal/ubuntu noble/universe ppc64el gasic all 0.0.r19-8 [21.1 kB] 391s Get:89 http://ftpmaster.internal/ubuntu noble/universe ppc64el gasic-examples all 0.0.r19-8 [7270 kB] 392s Fetched 116 MB in 7s (16.4 MB/s) 392s Selecting previously unselected package sgml-base. 392s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 69714 files and directories currently installed.) 392s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 392s Unpacking sgml-base (1.31) ... 392s Selecting previously unselected package libtcl8.6:ppc64el. 392s Preparing to unpack .../01-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 392s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 392s Selecting previously unselected package fonts-dejavu-mono. 392s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 392s Unpacking fonts-dejavu-mono (2.37-8) ... 392s Selecting previously unselected package fonts-dejavu-core. 392s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 392s Unpacking fonts-dejavu-core (2.37-8) ... 392s Selecting previously unselected package libfontenc1:ppc64el. 392s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1_ppc64el.deb ... 392s Unpacking libfontenc1:ppc64el (1:1.1.8-1) ... 392s Selecting previously unselected package x11-common. 392s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ... 392s Unpacking x11-common (1:7.7+23ubuntu2) ... 392s Selecting previously unselected package xfonts-encodings. 392s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 392s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 392s Selecting previously unselected package xfonts-utils. 392s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_ppc64el.deb ... 392s Unpacking xfonts-utils (1:7.7+6build2) ... 392s Selecting previously unselected package fonts-urw-base35. 392s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 392s Unpacking fonts-urw-base35 (20200910-8) ... 392s Selecting previously unselected package fontconfig-config. 392s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 392s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 392s Selecting previously unselected package libfontconfig1:ppc64el. 392s Preparing to unpack .../10-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 392s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 392s Selecting previously unselected package libxrender1:ppc64el. 392s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 392s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 392s Selecting previously unselected package libxft2:ppc64el. 392s Preparing to unpack .../12-libxft2_2.3.6-1_ppc64el.deb ... 392s Unpacking libxft2:ppc64el (2.3.6-1) ... 392s Selecting previously unselected package libxss1:ppc64el. 392s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 392s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 392s Selecting previously unselected package libtk8.6:ppc64el. 392s Preparing to unpack .../14-libtk8.6_8.6.14-1_ppc64el.deb ... 392s Unpacking libtk8.6:ppc64el (8.6.14-1) ... 392s Selecting previously unselected package tk8.6-blt2.5. 392s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7_ppc64el.deb ... 392s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 392s Selecting previously unselected package blt. 392s Preparing to unpack .../16-blt_2.5.3+dfsg-7_ppc64el.deb ... 392s Unpacking blt (2.5.3+dfsg-7) ... 392s Selecting previously unselected package bwa. 392s Preparing to unpack .../17-bwa_0.7.17-7_ppc64el.deb ... 392s Unpacking bwa (0.7.17-7) ... 392s Selecting previously unselected package fonts-dejavu-extra. 392s Preparing to unpack .../18-fonts-dejavu-extra_2.37-8_all.deb ... 392s Unpacking fonts-dejavu-extra (2.37-8) ... 392s Selecting previously unselected package fonts-lyx. 392s Preparing to unpack .../19-fonts-lyx_2.4.0~RC3-1_all.deb ... 392s Unpacking fonts-lyx (2.4.0~RC3-1) ... 393s Selecting previously unselected package python3-decorator. 393s Preparing to unpack .../20-python3-decorator_5.1.1-5_all.deb ... 393s Unpacking python3-decorator (5.1.1-5) ... 393s Selecting previously unselected package libblas3:ppc64el. 393s Preparing to unpack .../21-libblas3_3.12.0-3_ppc64el.deb ... 393s Unpacking libblas3:ppc64el (3.12.0-3) ... 393s Selecting previously unselected package libgfortran5:ppc64el. 393s Preparing to unpack .../22-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 393s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 393s Selecting previously unselected package liblapack3:ppc64el. 393s Preparing to unpack .../23-liblapack3_3.12.0-3_ppc64el.deb ... 393s Unpacking liblapack3:ppc64el (3.12.0-3) ... 393s Selecting previously unselected package python3-numpy. 393s Preparing to unpack .../24-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 393s Unpacking python3-numpy (1:1.24.2-2) ... 393s Selecting previously unselected package liblbfgsb0:ppc64el. 393s Preparing to unpack .../25-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 393s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 393s Selecting previously unselected package python3-scipy. 393s Preparing to unpack .../26-python3-scipy_1.11.4-6_ppc64el.deb ... 393s Unpacking python3-scipy (1.11.4-6) ... 394s Selecting previously unselected package python3-tk:ppc64el. 394s Preparing to unpack .../27-python3-tk_3.11.5-1_ppc64el.deb ... 394s Unpacking python3-tk:ppc64el (3.11.5-1) ... 394s Selecting previously unselected package python3-pil.imagetk:ppc64el. 394s Preparing to unpack .../28-python3-pil.imagetk_10.2.0-1_ppc64el.deb ... 394s Unpacking python3-pil.imagetk:ppc64el (10.2.0-1) ... 394s Selecting previously unselected package libgomp1:ppc64el. 394s Preparing to unpack .../29-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 394s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 394s Selecting previously unselected package libimagequant0:ppc64el. 394s Preparing to unpack .../30-libimagequant0_2.18.0-1_ppc64el.deb ... 394s Unpacking libimagequant0:ppc64el (2.18.0-1) ... 394s Selecting previously unselected package libjpeg-turbo8:ppc64el. 394s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 394s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 394s Selecting previously unselected package libjpeg8:ppc64el. 394s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 394s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 394s Selecting previously unselected package liblcms2-2:ppc64el. 394s Preparing to unpack .../33-liblcms2-2_2.14-2_ppc64el.deb ... 394s Unpacking liblcms2-2:ppc64el (2.14-2) ... 394s Selecting previously unselected package libopenjp2-7:ppc64el. 394s Preparing to unpack .../34-libopenjp2-7_2.5.0-2_ppc64el.deb ... 394s Unpacking libopenjp2-7:ppc64el (2.5.0-2) ... 394s Selecting previously unselected package libgraphite2-3:ppc64el. 394s Preparing to unpack .../35-libgraphite2-3_1.3.14-2_ppc64el.deb ... 394s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 394s Selecting previously unselected package libharfbuzz0b:ppc64el. 394s Preparing to unpack .../36-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 394s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 394s Selecting previously unselected package libraqm0:ppc64el. 394s Preparing to unpack .../37-libraqm0_0.10.1-1_ppc64el.deb ... 394s Unpacking libraqm0:ppc64el (0.10.1-1) ... 394s Selecting previously unselected package libdeflate0:ppc64el. 394s Preparing to unpack .../38-libdeflate0_1.19-1_ppc64el.deb ... 394s Unpacking libdeflate0:ppc64el (1.19-1) ... 394s Selecting previously unselected package libjbig0:ppc64el. 394s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 394s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 394s Selecting previously unselected package liblerc4:ppc64el. 394s Preparing to unpack .../40-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 394s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 394s Selecting previously unselected package libsharpyuv0:ppc64el. 394s Preparing to unpack .../41-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 394s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 394s Selecting previously unselected package libwebp7:ppc64el. 394s Preparing to unpack .../42-libwebp7_1.3.2-0.4_ppc64el.deb ... 394s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 394s Selecting previously unselected package libtiff6:ppc64el. 394s Preparing to unpack .../43-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 394s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 394s Selecting previously unselected package libwebpdemux2:ppc64el. 394s Preparing to unpack .../44-libwebpdemux2_1.3.2-0.4_ppc64el.deb ... 394s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4) ... 394s Selecting previously unselected package libwebpmux3:ppc64el. 394s Preparing to unpack .../45-libwebpmux3_1.3.2-0.4_ppc64el.deb ... 394s Unpacking libwebpmux3:ppc64el (1.3.2-0.4) ... 394s Selecting previously unselected package python3-pil:ppc64el. 394s Preparing to unpack .../46-python3-pil_10.2.0-1_ppc64el.deb ... 394s Unpacking python3-pil:ppc64el (10.2.0-1) ... 394s Selecting previously unselected package libpixman-1-0:ppc64el. 394s Preparing to unpack .../47-libpixman-1-0_0.42.2-1_ppc64el.deb ... 394s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 394s Selecting previously unselected package libxcb-render0:ppc64el. 394s Preparing to unpack .../48-libxcb-render0_1.15-1_ppc64el.deb ... 394s Unpacking libxcb-render0:ppc64el (1.15-1) ... 394s Selecting previously unselected package libxcb-shm0:ppc64el. 394s Preparing to unpack .../49-libxcb-shm0_1.15-1_ppc64el.deb ... 394s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 394s Selecting previously unselected package libcairo2:ppc64el. 394s Preparing to unpack .../50-libcairo2_1.18.0-1_ppc64el.deb ... 394s Unpacking libcairo2:ppc64el (1.18.0-1) ... 394s Selecting previously unselected package python3-cairo. 394s Preparing to unpack .../51-python3-cairo_1.25.1-2_ppc64el.deb ... 394s Unpacking python3-cairo (1.25.1-2) ... 394s Selecting previously unselected package python3-freetype. 394s Preparing to unpack .../52-python3-freetype_2.4.0-1_all.deb ... 394s Unpacking python3-freetype (2.4.0-1) ... 394s Selecting previously unselected package python3-rlpycairo. 394s Preparing to unpack .../53-python3-rlpycairo_0.3.0-3_all.deb ... 394s Unpacking python3-rlpycairo (0.3.0-3) ... 394s Selecting previously unselected package python3-reportlab. 394s Preparing to unpack .../54-python3-reportlab_4.1.0-1_all.deb ... 394s Unpacking python3-reportlab (4.1.0-1) ... 394s Selecting previously unselected package xml-core. 394s Preparing to unpack .../55-xml-core_0.19_all.deb ... 394s Unpacking xml-core (0.19) ... 394s Selecting previously unselected package w3c-sgml-lib. 394s Preparing to unpack .../56-w3c-sgml-lib_1.3-3_all.deb ... 394s Unpacking w3c-sgml-lib (1.3-3) ... 395s Selecting previously unselected package python3-biopython. 395s Preparing to unpack .../57-python3-biopython_1.81+dfsg-3_ppc64el.deb ... 395s Unpacking python3-biopython (1.81+dfsg-3) ... 395s Selecting previously unselected package libhtscodecs2:ppc64el. 395s Preparing to unpack .../58-libhtscodecs2_1.6.0-1_ppc64el.deb ... 395s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 395s Selecting previously unselected package libhts3:ppc64el. 395s Preparing to unpack .../59-libhts3_1.18+ds-1_ppc64el.deb ... 395s Unpacking libhts3:ppc64el (1.18+ds-1) ... 395s Selecting previously unselected package python3-pysam. 395s Preparing to unpack .../60-python3-pysam_0.22.0+ds-1_ppc64el.deb ... 395s Unpacking python3-pysam (0.22.0+ds-1) ... 395s Selecting previously unselected package libjs-jquery. 395s Preparing to unpack .../61-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 395s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 395s Selecting previously unselected package libjs-jquery-ui. 395s Preparing to unpack .../62-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 395s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 395s Selecting previously unselected package python-matplotlib-data. 395s Preparing to unpack .../63-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 395s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 395s Selecting previously unselected package python3-dateutil. 395s Preparing to unpack .../64-python3-dateutil_2.8.2-3_all.deb ... 395s Unpacking python3-dateutil (2.8.2-3) ... 395s Selecting previously unselected package python3-contourpy. 395s Preparing to unpack .../65-python3-contourpy_1.0.7-1build2_ppc64el.deb ... 395s Unpacking python3-contourpy (1.0.7-1build2) ... 395s Selecting previously unselected package python3-cycler. 395s Preparing to unpack .../66-python3-cycler_0.11.0-2_all.deb ... 395s Unpacking python3-cycler (0.11.0-2) ... 395s Selecting previously unselected package python3-brotli. 395s Preparing to unpack .../67-python3-brotli_1.1.0-2_ppc64el.deb ... 395s Unpacking python3-brotli (1.1.0-2) ... 395s Selecting previously unselected package python3-ufolib2. 395s Preparing to unpack .../68-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 395s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 395s Selecting previously unselected package python3-mpmath. 395s Preparing to unpack .../69-python3-mpmath_1.2.1-3_all.deb ... 395s Unpacking python3-mpmath (1.2.1-3) ... 395s Selecting previously unselected package python3-sympy. 395s Preparing to unpack .../70-python3-sympy_1.12-7_all.deb ... 395s Unpacking python3-sympy (1.12-7) ... 396s Selecting previously unselected package python3-appdirs. 396s Preparing to unpack .../71-python3-appdirs_1.4.4-4_all.deb ... 396s Unpacking python3-appdirs (1.4.4-4) ... 396s Selecting previously unselected package python3-fs. 396s Preparing to unpack .../72-python3-fs_2.4.16-3_all.deb ... 396s Unpacking python3-fs (2.4.16-3) ... 396s Selecting previously unselected package libxslt1.1:ppc64el. 396s Preparing to unpack .../73-libxslt1.1_1.1.39-0exp1_ppc64el.deb ... 396s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1) ... 396s Selecting previously unselected package python3-lxml:ppc64el. 396s Preparing to unpack .../74-python3-lxml_5.1.0-1_ppc64el.deb ... 396s Unpacking python3-lxml:ppc64el (5.1.0-1) ... 396s Selecting previously unselected package python3-lz4. 396s Preparing to unpack .../75-python3-lz4_4.0.2+dfsg-1build2_ppc64el.deb ... 396s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 396s Selecting previously unselected package python3-unicodedata2. 396s Preparing to unpack .../76-python3-unicodedata2_15.1.0+ds-1_ppc64el.deb ... 396s Unpacking python3-unicodedata2 (15.1.0+ds-1) ... 396s Selecting previously unselected package unicode-data. 396s Preparing to unpack .../77-unicode-data_15.1.0-1_all.deb ... 396s Unpacking unicode-data (15.1.0-1) ... 396s Selecting previously unselected package python3-fonttools. 396s Preparing to unpack .../78-python3-fonttools_4.46.0-1_ppc64el.deb ... 396s Unpacking python3-fonttools (4.46.0-1) ... 396s Selecting previously unselected package python3-kiwisolver. 396s Preparing to unpack .../79-python3-kiwisolver_1.4.4-2_ppc64el.deb ... 396s Unpacking python3-kiwisolver (1.4.4-2) ... 396s Selecting previously unselected package python3-packaging. 396s Preparing to unpack .../80-python3-packaging_23.2-1_all.deb ... 396s Unpacking python3-packaging (23.2-1) ... 396s Selecting previously unselected package libqhull-r8.0:ppc64el. 396s Preparing to unpack .../81-libqhull-r8.0_2020.2-6_ppc64el.deb ... 396s Unpacking libqhull-r8.0:ppc64el (2020.2-6) ... 396s Selecting previously unselected package python3-matplotlib. 396s Preparing to unpack .../82-python3-matplotlib_3.6.3-1ubuntu3_ppc64el.deb ... 396s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 397s Selecting previously unselected package bowtie. 397s Preparing to unpack .../83-bowtie_1.3.1-3_ppc64el.deb ... 397s Unpacking bowtie (1.3.1-3) ... 397s Selecting previously unselected package bowtie2. 397s Preparing to unpack .../84-bowtie2_2.5.2-1_ppc64el.deb ... 397s Unpacking bowtie2 (2.5.2-1) ... 397s Selecting previously unselected package seqan-apps. 397s Preparing to unpack .../85-seqan-apps_2.4.0+dfsg-16_ppc64el.deb ... 397s Unpacking seqan-apps (2.4.0+dfsg-16) ... 397s Selecting previously unselected package gasic. 397s Preparing to unpack .../86-gasic_0.0.r19-8_all.deb ... 397s Unpacking gasic (0.0.r19-8) ... 397s Selecting previously unselected package gasic-examples. 397s Preparing to unpack .../87-gasic-examples_0.0.r19-8_all.deb ... 397s Unpacking gasic-examples (0.0.r19-8) ... 397s Selecting previously unselected package autopkgtest-satdep. 397s Preparing to unpack .../88-1-autopkgtest-satdep.deb ... 397s Unpacking autopkgtest-satdep (0) ... 397s Setting up libhtscodecs2:ppc64el (1.6.0-1) ... 397s Setting up libgraphite2-3:ppc64el (1.3.14-2) ... 397s Setting up liblcms2-2:ppc64el (2.14-2) ... 397s Setting up libpixman-1-0:ppc64el (0.42.2-1) ... 397s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 397s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 397s Setting up bowtie (1.3.1-3) ... 397s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 397s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 397s Setting up libxcb-render0:ppc64el (1.15-1) ... 397s Setting up bwa (0.7.17-7) ... 397s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 397s Setting up fonts-lyx (2.4.0~RC3-1) ... 397s Setting up gasic-examples (0.0.r19-8) ... 397s Setting up x11-common (1:7.7+23ubuntu2) ... 398s Setting up libdeflate0:ppc64el (1.19-1) ... 398s Setting up libqhull-r8.0:ppc64el (2020.2-6) ... 398s Setting up libxcb-shm0:ppc64el (1.15-1) ... 398s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 398s Setting up python3-freetype (2.4.0-1) ... 398s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 398s Setting up bowtie2 (2.5.2-1) ... 398s Setting up unicode-data (15.1.0-1) ... 398s Setting up python3-decorator (5.1.1-5) ... 398s Setting up libfontenc1:ppc64el (1:1.1.8-1) ... 398s Setting up libblas3:ppc64el (3.12.0-3) ... 398s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 398s Setting up python3-packaging (23.2-1) ... 398s Setting up python3-brotli (1.1.0-2) ... 398s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 398s Setting up python3-cycler (0.11.0-2) ... 399s Setting up libimagequant0:ppc64el (2.18.0-1) ... 399s Setting up seqan-apps (2.4.0+dfsg-16) ... 399s Setting up fonts-dejavu-mono (2.37-8) ... 399s Setting up python3-kiwisolver (1.4.4-2) ... 399s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 399s Setting up fonts-dejavu-core (2.37-8) ... 399s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 399s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 399s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 399s Setting up fonts-dejavu-extra (2.37-8) ... 399s Setting up libxslt1.1:ppc64el (1.1.39-0exp1) ... 399s Setting up libopenjp2-7:ppc64el (2.5.0-2) ... 399s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 399s Setting up python3-dateutil (2.8.2-3) ... 399s Setting up sgml-base (1.31) ... 399s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 399s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 399s Setting up python3-mpmath (1.2.1-3) ... 399s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 399s Setting up libwebpmux3:ppc64el (1.3.2-0.4) ... 399s Setting up python3-appdirs (1.4.4-4) ... 400s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 400s Setting up python3-sympy (1.12-7) ... 405s Setting up liblapack3:ppc64el (3.12.0-3) ... 405s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 405s Setting up libhts3:ppc64el (1.18+ds-1) ... 405s Setting up python3-pysam (0.22.0+ds-1) ... 405s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 406s Setting up libwebpdemux2:ppc64el (1.3.2-0.4) ... 406s Setting up xfonts-utils (1:7.7+6build2) ... 406s Setting up python3-fs (2.4.16-3) ... 406s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 406s Setting up libraqm0:ppc64el (0.10.1-1) ... 406s Setting up python3-numpy (1:1.24.2-2) ... 408s Setting up python3-lxml:ppc64el (5.1.0-1) ... 408s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 408s Setting up xml-core (0.19) ... 408s Setting up python3-contourpy (1.0.7-1build2) ... 408s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 408s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 408s Setting up libxft2:ppc64el (2.3.6-1) ... 408s Setting up python3-scipy (1.11.4-6) ... 412s Setting up libtk8.6:ppc64el (8.6.14-1) ... 412s Setting up fonts-urw-base35 (20200910-8) ... 412s Setting up libcairo2:ppc64el (1.18.0-1) ... 412s Setting up python3-pil:ppc64el (10.2.0-1) ... 412s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 412s Setting up python3-cairo (1.25.1-2) ... 412s Setting up blt (2.5.3+dfsg-7) ... 412s Setting up python3-tk:ppc64el (3.11.5-1) ... 412s Setting up python3-pil.imagetk:ppc64el (10.2.0-1) ... 413s Setting up python3-rlpycairo (0.3.0-3) ... 413s Setting up python3-reportlab (4.1.0-1) ... 413s Setting up python3-fonttools (4.46.0-1) ... 414s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 415s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 416s Processing triggers for libc-bin (2.39-0ubuntu6) ... 416s Processing triggers for man-db (2.12.0-3) ... 417s Processing triggers for sgml-base (1.31) ... 417s Setting up w3c-sgml-lib (1.3-3) ... 445s Setting up python3-biopython (1.81+dfsg-3) ... 446s Setting up gasic (0.0.r19-8) ... 446s Setting up autopkgtest-satdep (0) ... 449s (Reading database ... 79276 files and directories currently installed.) 449s Removing autopkgtest-satdep (0) ... 450s autopkgtest [15:25:40]: test run-unit-test: [----------------------- 450s [bwa_index] Pack FASTA... Test 0: Create Genome Indices 450s 0.00 sec 450s [bwa_index] Construct BWT for the packed sequence... 450s [bwa_index] 0.00 seconds elapse. 450s [bwa_index] Update BWT... 0.00 sec 450s [bwa_index] Pack forward-only FASTA... 0.00 sec 450s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 450s [main] Version: 0.7.17-r1188 450s [main] CMD: bwa index dwv.fasta 450s [main] Real time: 0.015 sec; CPU: 0.005 sec 450s [bwa_index] Pack FASTA... 0.00 sec 450s [bwa_index] Construct BWT for the packed sequence... 450s [bwa_index] 0.00 seconds elapse. 450s [bwa_index] Update BWT... 0.00 sec 450s [bwa_index] Pack forward-only FASTA... 0.00 sec 450s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 450s [main] Version: 0.7.17-r1188 450s [main] CMD: bwa index vdv1.fasta 450s [main] Real time: 0.012 sec; CPU: 0.005 sec 450s [bwa_index] Pack FASTA... 0.00 sec 450s [bwa_index] Construct BWT for the packed sequence... 450s [bwa_index] 0.00 seconds elapse. 450s [bwa_index] Update BWT... Passed 450s 450s Test 1: run_mappers 450s 0.00 sec 450s [bwa_index] Pack forward-only FASTA... 0.00 sec 450s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 450s [main] Version: 0.7.17-r1188 450s [main] CMD: bwa index vdv1dwv9.fasta 450s [main] Real time: 0.015 sec; CPU: 0.005 sec 450s [bwa_index] Pack FASTA... 0.00 sec 450s [bwa_index] Construct BWT for the packed sequence... 450s [bwa_index] 0.00 seconds elapse. 450s [bwa_index] Update BWT... 0.00 sec 450s [bwa_index] Pack forward-only FASTA... 0.00 sec 450s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 450s [main] Version: 0.7.17-r1188 450s [main] CMD: bwa index vdv1dwv5.fasta 450s [main] Real time: 0.011 sec; CPU: 0.005 sec 450s [bwa_aln] 17bp reads: max_diff = 2 450s [bwa_aln] 38bp reads: max_diff = 3 450s [bwa_aln] 64bp reads: max_diff = 4 450s [bwa_aln] 93bp reads: max_diff = 5 450s [bwa_aln] 124bp reads: max_diff = 6 450s [bwa_aln] 157bp reads: max_diff = 7 450s [bwa_aln] 190bp reads: max_diff = 8 450s [bwa_aln] 225bp reads: max_diff = 9 452s [bwa_aln_core] calculate SA coordinate... 1.10 sec 452s [bwa_aln_core] write to the disk... 0.00 sec 452s [bwa_aln_core] 100000 sequences have been processed. 452s [main] Version: 0.7.17-r1188 452s [main] CMD: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq 452s [main] Real time: 1.202 sec; CPU: 1.189 sec 452s [bwa_aln_core] convert to sequence coordinate... 0.12 sec 452s [bwa_aln_core] refine gapped alignments... 0.03 sec 452s [bwa_aln_core] print alignments... 0.11 sec 452s [bwa_aln_core] 100000 sequences have been processed. 452s [main] Version: 0.7.17-r1188 452s [main] CMD: bwa samse ./genomes/dwv.fasta /tmp/res.sai reads/SRR059298_subset.fastq 452s [main] Real time: 0.372 sec; CPU: 0.348 sec 452s [bwa_aln] 17bp reads: max_diff = 2 452s [bwa_aln] 38bp reads: max_diff = 3 452s [bwa_aln] 64bp reads: max_diff = 4 452s [bwa_aln] 93bp reads: max_diff = 5 452s [bwa_aln] 124bp reads: max_diff = 6 452s [bwa_aln] 157bp reads: max_diff = 7 452s [bwa_aln] 190bp reads: max_diff = 8 452s [bwa_aln] 225bp reads: max_diff = 9 453s [bwa_aln_core] calculate SA coordinate... 0.85 sec 453s [bwa_aln_core] write to the disk... 0.01 sec 453s [bwa_aln_core] 100000 sequences have been processed. 453s [main] Version: 0.7.17-r1188 453s [main] CMD: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq 453s [main] Real time: 0.938 sec; CPU: 0.935 sec 453s [bwa_aln_core] convert to sequence coordinate... 0.06 sec 453s [bwa_aln_core] refine gapped alignments... 0.02 sec 453s [bwa_aln_core] print alignments... 0.08 sec 453s [bwa_aln_core] 100000 sequences have been processed. 453s [main] Version: 0.7.17-r1188 453s [main] CMD: bwa samse ./genomes/vdv1.fasta /tmp/res.sai reads/SRR059298_subset.fastq 453s [main] Real time: 0.259 sec; CPU: 0.248 sec 453s [bwa_aln] 17bp reads: max_diff = 2 453s [bwa_aln] 38bp reads: max_diff = 3 453s [bwa_aln] 64bp reads: max_diff = 4 453s [bwa_aln] 93bp reads: max_diff = 5 453s [bwa_aln] 124bp reads: max_diff = 6 453s [bwa_aln] 157bp reads: max_diff = 7 453s [bwa_aln] 190bp reads: max_diff = 8 453s [bwa_aln] 225bp reads: max_diff = 9 454s [bwa_aln_core] calculate SA coordinate... 1.40 sec 454s [bwa_aln_core] write to the disk... 0.01 sec 454s [bwa_aln_core] 100000 sequences have been processed. 454s [main] Version: 0.7.17-r1188 455s [main] CMD: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq 455s [main] Real time: 1.490 sec; CPU: 1.486 sec 455s [bwa_aln_core] convert to sequence coordinate... 0.16 sec 455s [bwa_aln_core] refine gapped alignments... 0.03 sec 455s [bwa_aln_core] print alignments... 0.13 sec 455s [bwa_aln_core] 100000 sequences have been processed. 455s [main] Version: 0.7.17-r1188 455s [main] CMD: bwa samse ./genomes/vdv1dwv5.fasta /tmp/res.sai reads/SRR059298_subset.fastq 455s [main] Real time: 0.421 sec; CPU: 0.409 sec 455s [bwa_aln] 17bp reads: max_diff = 2 455s [bwa_aln] 38bp reads: max_diff = 3 455s [bwa_aln] 64bp reads: max_diff = 4 455s [bwa_aln] 93bp reads: max_diff = 5 455s [bwa_aln] 124bp reads: max_diff = 6 455s [bwa_aln] 157bp reads: max_diff = 7 455s [bwa_aln] 190bp reads: max_diff = 8 455s [bwa_aln] 225bp reads: max_diff = 9 456s [bwa_aln_core] calculate SA coordinate... 1.26 sec 456s [bwa_aln_core] write to the disk... 0.00 sec 456s [bwa_aln_core] 100000 sequences have been processed. 456s [main] Version: 0.7.17-r1188 456s [main] CMD: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq 456s [main] Real time: 1.340 sec; CPU: 1.337 sec 456s [bwa_aln_core] convert to sequence coordinate... 0.12 sec 456s [bwa_aln_core] refine gapped alignments... 0.03 sec 457s [bwa_aln_core] print alignments... 0.11 sec 457s [bwa_aln_core] 100000 sequences have been processed. 457s [main] Version: 0.7.17-r1188 457s [main] CMD: bwa samse ./genomes/vdv1dwv9.fasta /tmp/res.sai reads/SRR059298_subset.fastq 457s [main] Real time: 0.363 sec; CPU: 0.352 sec 457s --- mapping reads with bwa to ./genomes/dwv.fasta 457s Executing: bwa aln ./genomes/dwv.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 457s --- mapping reads with bwa to ./genomes/vdv1.fasta 457s Executing: bwa aln ./genomes/vdv1.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 457s --- mapping reads with bwa to ./genomes/vdv1dwv5.fasta 457s Executing: bwa aln ./genomes/vdv1dwv5.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 457s --- mapping reads with bwa to ./genomes/vdv1dwv9.fasta 457s Executing: bwa aln ./genomes/vdv1dwv9.fasta reads/SRR059298_subset.fastq > /tmp/res.sai 457s 457s Mapping done. 457s 457s Passed 457s 457s Test 2: create_matrix 457s MASON SIMULATOR 457s =============== 457s 457s ____INITIALIZING______________________________________________________________ 457s 457s Opening reference and variants file ... OK 457s Initializing fragment-to-contig distribution ... OK 457s Initializing simulation threads ... OK 457s Opening output file ./SAM/dwv.fastq ... OK 457s 457s ____READ SIMULATION___________________________________________________________ 457s 457s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 457s 457s Simulating Reads: 457s gi|71480055|ref|NC_004830.2| (allele 1) .. (10000 fragments) OK 457s Done simulating reads. 457s 457s Joining temporary files ... OK 457s rm: cannot remove './SAM/dwv.fastq.sam': No such file or directory 457s MASON SIMULATOR 457s =============== 457s 457s ____INITIALIZING______________________________________________________________ 457s 457s Opening reference and variants file ... OK 457s Initializing fragment-to-contig distribution ... OK 457s Initializing simulation threads ... OK 457s Opening output file ./SAM/vdv1.fastq ... OK 457s 457s ____READ SIMULATION___________________________________________________________ 457s 457s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 457s 457s Simulating Reads: 457s gi|56121875|ref|NC_006494.1| (allele 1) .. (10000 fragments) OK 457s Done simulating reads. 457s 457s Joining temporary files ... OK 457s rm: cannot remove './SAM/vdv1.fastq.sam': No such file or directory 457s MASON SIMULATOR 457s =============== 457s 457s ____INITIALIZING______________________________________________________________ 457s 457s Opening reference and variants file ... OK 457s Initializing fragment-to-contig distribution ... OK 457s Initializing simulation threads ... OK 457s Opening output file ./SAM/vdv1dwv5.fastq ... OK 457s 457s ____READ SIMULATION___________________________________________________________ 457s 457s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 457s 457s Simulating Reads: 457s gi|301070167|gb|HM067437.1| (allele 1) .. (10000 fragments) OK 457s Done simulating reads. 457s 457s Joining temporary files ... OK 457s rm: cannot remove './SAM/vdv1dwv5.fastq.sam': No such file or directory 457s MASON SIMULATOR 457s =============== 457s 457s ____INITIALIZING______________________________________________________________ 457s 457s Opening reference and variants file ... OK 457s Initializing fragment-to-contig distribution ... OK 457s Initializing simulation threads ... OK 457s Opening output file ./SAM/vdv1dwv9.fastq ... OK 457s 457s ____READ SIMULATION___________________________________________________________ 457s 457s Distributing fragments to 1 contigs (1 haplotypes each) ... OK 457s 457s Simulating Reads: 457s gi|301070169|gb|HM067438.1| (allele 1) .. (10000 fragments) OK 457s Done simulating reads. 457s 457s Joining temporary files ... OK 457s rm: cannot remove './SAM/vdv1dwv9.fastq.sam': No such file or directory 457s [bwa_aln] 17bp reads: max_diff = 2 457s [bwa_aln] 38bp reads: max_diff = 3 457s [bwa_aln] 64bp reads: max_diff = 4 457s [bwa_aln] 93bp reads: max_diff = 5 457s [bwa_aln] 124bp reads: max_diff = 6 457s [bwa_aln] 157bp reads: max_diff = 7 457s [bwa_aln] 190bp reads: max_diff = 8 457s [bwa_aln] 225bp reads: max_diff = 9 457s [bwa_aln_core] calculate SA coordinate... 0.14 sec 457s [bwa_aln_core] write to the disk... 0.00 sec 457s [bwa_aln_core] 10000 sequences have been processed. 457s [main] Version: 0.7.17-r1188 457s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq 457s [main] Real time: 0.154 sec; CPU: 0.152 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 458s [bwa_aln_core] refine gapped alignments... 0.01 sec 458s [bwa_aln_core] print alignments... 0.02 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/dwv.fastq 458s [main] Real time: 0.056 sec; CPU: 0.054 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.05 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq 458s [main] Real time: 0.057 sec; CPU: 0.055 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/dwv.fastq 458s [main] Real time: 0.016 sec; CPU: 0.014 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.09 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq 458s [main] Real time: 0.102 sec; CPU: 0.100 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.01 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/dwv.fastq 458s [main] Real time: 0.032 sec; CPU: 0.030 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.09 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq 458s [main] Real time: 0.100 sec; CPU: 0.098 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.01 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/dwv.fastq 458s [main] Real time: 0.031 sec; CPU: 0.029 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.05 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq 458s [main] Real time: 0.058 sec; CPU: 0.056 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.00 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1.fastq 458s [main] Real time: 0.016 sec; CPU: 0.013 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.14 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq 458s [main] Real time: 0.154 sec; CPU: 0.152 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.02 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1.fastq 458s [main] Real time: 0.052 sec; CPU: 0.049 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.10 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq 458s [main] Real time: 0.111 sec; CPU: 0.109 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.01 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1.fastq 458s [main] Real time: 0.035 sec; CPU: 0.033 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 458s [bwa_aln_core] calculate SA coordinate... 0.10 sec 458s [bwa_aln_core] write to the disk... 0.00 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq 458s [main] Real time: 0.113 sec; CPU: 0.111 sec 458s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 458s [bwa_aln_core] refine gapped alignments... 0.00 sec 458s [bwa_aln_core] print alignments... 0.01 sec 458s [bwa_aln_core] 10000 sequences have been processed. 458s [main] Version: 0.7.17-r1188 458s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1.fastq 458s [main] Real time: 0.036 sec; CPU: 0.034 sec 458s [bwa_aln] 17bp reads: max_diff = 2 458s [bwa_aln] 38bp reads: max_diff = 3 458s [bwa_aln] 64bp reads: max_diff = 4 458s [bwa_aln] 93bp reads: max_diff = 5 458s [bwa_aln] 124bp reads: max_diff = 6 458s [bwa_aln] 157bp reads: max_diff = 7 458s [bwa_aln] 190bp reads: max_diff = 8 458s [bwa_aln] 225bp reads: max_diff = 9 459s [bwa_aln_core] calculate SA coordinate... 0.10 sec 459s [bwa_aln_core] write to the disk... 0.00 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.104 sec; CPU: 0.102 sec 459s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 459s [bwa_aln_core] refine gapped alignments... 0.00 sec 459s [bwa_aln_core] print alignments... 0.01 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.033 sec; CPU: 0.031 sec 459s [bwa_aln] 17bp reads: max_diff = 2 459s [bwa_aln] 38bp reads: max_diff = 3 459s [bwa_aln] 64bp reads: max_diff = 4 459s [bwa_aln] 93bp reads: max_diff = 5 459s [bwa_aln] 124bp reads: max_diff = 6 459s [bwa_aln] 157bp reads: max_diff = 7 459s [bwa_aln] 190bp reads: max_diff = 8 459s [bwa_aln] 225bp reads: max_diff = 9 459s [bwa_aln_core] calculate SA coordinate... 0.10 sec 459s [bwa_aln_core] write to the disk... 0.00 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.113 sec; CPU: 0.111 sec 459s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 459s [bwa_aln_core] refine gapped alignments... 0.00 sec 459s [bwa_aln_core] print alignments... 0.01 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.035 sec; CPU: 0.033 sec 459s [bwa_aln] 17bp reads: max_diff = 2 459s [bwa_aln] 38bp reads: max_diff = 3 459s [bwa_aln] 64bp reads: max_diff = 4 459s [bwa_aln] 93bp reads: max_diff = 5 459s [bwa_aln] 124bp reads: max_diff = 6 459s [bwa_aln] 157bp reads: max_diff = 7 459s [bwa_aln] 190bp reads: max_diff = 8 459s [bwa_aln] 225bp reads: max_diff = 9 459s [bwa_aln_core] calculate SA coordinate... 0.14 sec 459s [bwa_aln_core] write to the disk... 0.00 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.153 sec; CPU: 0.152 sec 459s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 459s [bwa_aln_core] refine gapped alignments... 0.00 sec 459s [bwa_aln_core] print alignments... 0.02 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.054 sec; CPU: 0.050 sec 459s [bwa_aln] 17bp reads: max_diff = 2 459s [bwa_aln] 38bp reads: max_diff = 3 459s [bwa_aln] 64bp reads: max_diff = 4 459s [bwa_aln] 93bp reads: max_diff = 5 459s [bwa_aln] 124bp reads: max_diff = 6 459s [bwa_aln] 157bp reads: max_diff = 7 459s [bwa_aln] 190bp reads: max_diff = 8 459s [bwa_aln] 225bp reads: max_diff = 9 459s [bwa_aln_core] calculate SA coordinate... 0.13 sec 459s [bwa_aln_core] write to the disk... 0.00 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.142 sec; CPU: 0.140 sec 459s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 459s [bwa_aln_core] refine gapped alignments... 0.00 sec 459s [bwa_aln_core] print alignments... 0.01 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv5.fastq 459s [main] Real time: 0.046 sec; CPU: 0.043 sec 459s [bwa_aln] 17bp reads: max_diff = 2 459s [bwa_aln] 38bp reads: max_diff = 3 459s [bwa_aln] 64bp reads: max_diff = 4 459s [bwa_aln] 93bp reads: max_diff = 5 459s [bwa_aln] 124bp reads: max_diff = 6 459s [bwa_aln] 157bp reads: max_diff = 7 459s [bwa_aln] 190bp reads: max_diff = 8 459s [bwa_aln] 225bp reads: max_diff = 9 459s [bwa_aln_core] calculate SA coordinate... 0.09 sec 459s [bwa_aln_core] write to the disk... 0.00 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq 459s [main] Real time: 0.104 sec; CPU: 0.102 sec 459s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 459s [bwa_aln_core] refine gapped alignments... 0.00 sec 459s [bwa_aln_core] print alignments... 0.01 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa samse genomes/dwv.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 459s [main] Real time: 0.033 sec; CPU: 0.031 sec 459s [bwa_aln] 17bp reads: max_diff = 2 459s [bwa_aln] 38bp reads: max_diff = 3 459s [bwa_aln] 64bp reads: max_diff = 4 459s [bwa_aln] 93bp reads: max_diff = 5 459s [bwa_aln] 124bp reads: max_diff = 6 459s [bwa_aln] 157bp reads: max_diff = 7 459s [bwa_aln] 190bp reads: max_diff = 8 459s [bwa_aln] 225bp reads: max_diff = 9 459s [bwa_aln_core] calculate SA coordinate... 0.11 sec 459s [bwa_aln_core] write to the disk... 0.00 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq 459s [main] Real time: 0.114 sec; CPU: 0.112 sec 459s [bwa_aln_core] convert to sequence coordinate... 0.01 sec 459s [bwa_aln_core] refine gapped alignments... 0.00 sec 459s [bwa_aln_core] print alignments... 0.01 sec 459s [bwa_aln_core] 10000 sequences have been processed. 459s [main] Version: 0.7.17-r1188 459s [main] CMD: bwa samse genomes/vdv1.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 459s [main] Real time: 0.037 sec; CPU: 0.034 sec 459s [bwa_aln] 17bp reads: max_diff = 2 459s [bwa_aln] 38bp reads: max_diff = 3 459s [bwa_aln] 64bp reads: max_diff = 4 459s [bwa_aln] 93bp reads: max_diff = 5 459s [bwa_aln] 124bp reads: max_diff = 6 459s [bwa_aln] 157bp reads: max_diff = 7 459s [bwa_aln] 190bp reads: max_diff = 8 459s [bwa_aln] 225bp reads: max_diff = 9 460s [bwa_aln_core] calculate SA coordinate... 0.13 sec 460s [bwa_aln_core] write to the disk... 0.00 sec 460s [bwa_aln_core] 10000 sequences have been processed. 460s [main] Version: 0.7.17-r1188 460s [main] CMD: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq 460s [main] Real time: 0.140 sec; CPU: 0.139 sec 460s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 460s [bwa_aln_core] refine gapped alignments... 0.00 sec 460s [bwa_aln_core] print alignments... 0.01 sec 460s [bwa_aln_core] 10000 sequences have been processed. 460s [main] Version: 0.7.17-r1188 460s [main] CMD: bwa samse genomes/vdv1dwv5.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 460s [main] Real time: 0.045 sec; CPU: 0.043 sec 460s [bwa_aln] 17bp reads: max_diff = 2 460s [bwa_aln] 38bp reads: max_diff = 3 460s [bwa_aln] 64bp reads: max_diff = 4 460s [bwa_aln] 93bp reads: max_diff = 5 460s [bwa_aln] 124bp reads: max_diff = 6 460s [bwa_aln] 157bp reads: max_diff = 7 460s [bwa_aln] 190bp reads: max_diff = 8 460s [bwa_aln] 225bp reads: max_diff = 9 460s [bwa_aln_core] calculate SA coordinate... 0.15 sec 460s [bwa_aln_core] write to the disk... 0.00 sec 460s [bwa_aln_core] 10000 sequences have been processed. 460s [main] Version: 0.7.17-r1188 460s [main] CMD: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq 460s [main] Real time: 0.154 sec; CPU: 0.152 sec 460s [bwa_aln_core] convert to sequence coordinate... 0.02 sec 460s [bwa_aln_core] refine gapped alignments... 0.00 sec 460s [bwa_aln_core] print alignments... 0.02 sec 460s [bwa_aln_core] 10000 sequences have been processed. 460s [main] Version: 0.7.17-r1188 460s [main] CMD: bwa samse genomes/vdv1dwv9.fasta /tmp/res.sai ./SAM/vdv1dwv9.fastq 460s [main] Real time: 0.052 sec; CPU: 0.049 sec 460s 460s --- Simulating reads for each reference genome with mason_illumina 460s 460s Original command with mason from SeQan 1 was 460s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/dwv.fastq genomes/dwv.fasta 460s Please verify that the following call of mason_simulator fits your needs. If not 460s please use 460s reportbug gasic 460s to propose enhancements. 460s 460s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/dwv.fastq -ir genomes/dwv.fasta 460s Original command with mason from SeQan 1 was 460s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1.fastq genomes/vdv1.fasta 460s Please verify that the following call of mason_simulator fits your needs. If not 460s please use 460s reportbug gasic 460s to propose enhancements. 460s 460s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1.fastq -ir genomes/vdv1.fasta 460s Original command with mason from SeQan 1 was 460s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv5.fastq genomes/vdv1dwv5.fasta 460s Please verify that the following call of mason_simulator fits your needs. If not 460s please use 460s reportbug gasic 460s to propose enhancements. 460s 460s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv5.fastq -ir genomes/vdv1dwv5.fasta 460s Original command with mason from SeQan 1 was 460s mason illumina -N 10000 -hi 0 -hs 0 -n 72 -sq -o ./SAM/vdv1dwv9.fastq genomes/vdv1dwv9.fasta 460s Please verify that the following call of mason_simulator fits your needs. If not 460s please use 460s reportbug gasic 460s to propose enhancements. 460s 460s Executing: /usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o ./SAM/vdv1dwv9.fastq -ir genomes/vdv1dwv9.fasta 460s 460s --- Mapping simulated reads to reference genomes with bwa 460s 460s Executing: bwa aln genomes/dwv.fasta ./SAM/dwv.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1.fasta ./SAM/dwv.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/dwv.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/dwv.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv5.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/dwv.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv5.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 460s Executing: bwa aln genomes/vdv1dwv9.fasta ./SAM/vdv1dwv9.fastq > /tmp/res.sai 460s 460s --- Parsing SAM files 460s 461s SAM file 1 of 16 SAM file 2 of 16 SAM file 3 of 16 SAM file 4 of 16 SAM file 5 of 16 SAM file 6 of 16 SAM file 7 of 16 SAM file 8 of 16 SAM file 9 of 16 SAM file 10 of 16 SAM file 11 of 16 SAM file 12 of 16 SAM file 13 of 16 SAM file 14 of 16 SAM file 15 of 16 SAM file 16 of 16 461s 461s Matrix creation done 461s 461s Wrote similarity matrix to ./similarity_matrix.npy 461s Passed 461s 461s Test 3: correct_abundances 461s 461s --- GASiC correction 461s 461s found 100000 reads 461s 461s --- Analyzing SAM files 461s 461s SAM file 1 of 4 SAM file 2 of 4 SAM file 3 of 4 SAM file 4 of 4 461s 461s --- Bootstrapping abundances 461s 469s bootstrapping 1 of 100 bootstrapping 2 of 100 bootstrapping 3 of 100 bootstrapping 4 of 100 bootstrapping 5 of 100 bootstrapping 6 of 100 bootstrapping 7 of 100 bootstrapping 8 of 100 bootstrapping 9 of 100 bootstrapping 10 of 100 bootstrapping 11 of 100 bootstrapping 12 of 100 bootstrapping 13 of 100 bootstrapping 14 of 100 bootstrapping 15 of 100 bootstrapping 16 of 100 bootstrapping 17 of 100 bootstrapping 18 of 100 bootstrapping 19 of 100 bootstrapping 20 of 100 bootstrapping 21 of 100 bootstrapping 22 of 100 bootstrapping 23 of 100 bootstrapping 24 of 100 bootstrapping 25 of 100 bootstrapping 26 of 100 bootstrapping 27 of 100 bootstrapping 28 of 100 bootstrapping 29 of 100 bootstrapping 30 of 100 bootstrapping 31 of 100 bootstrapping 32 of 100 bootstrapping 33 of 100 bootstrapping 34 of 100 bootstrapping 35 of 100 bootstrapping 36 of 100 bootstrapping 37 of 100 bootstrapping 38 of 100 bootstrapping 39 of 100 bootstrapping 40 of 100 bootstrapping 41 of 100 bootstrapping 42 of 100 bootstrapping 43 of 100 bootstrapping 44 of 100 bootstrapping 45 of 100 bootstrapping 46 of 100 bootstrapping 47 of 100 bootstrapping 48 of 100 bootstrapping 49 of 100 bootstrapping 50 of 100 bootstrapping 51 of 100 bootstrapping 52 of 100 bootstrapping 53 of 100 bootstrapping 54 of 100 bootstrapping 55 of 100 bootstrapping 56 of 100 bootstrapping 57 of 100 bootstrapping 58 of 100 bootstrapping 59 of 100 bootstrapping 60 of 100 bootstrapping 61 of 100 bootstrapping 62 of 100 bootstrapping 63 of 100 bootstrapping 64 of 100 bootstrapping 65 of 100 bootstrapping 66 of 100 bootstrapping 67 of 100 bootstrapping 68 of 100 bootstrapping 69 of 100 bootstrapping 70 of 100 bootstrapping 71 of 100 bootstrapping 72 of 100 bootstrapping 73 of 100 bootstrapping 74 of 100 bootstrapping 75 of 100 bootstrapping 76 of 100 bootstrapping 77 of 100 bootstrapping 78 of 100 bootstrapping 79 of 100 bootstrapping 80 of 100 bootstrapping 81 of 100 bootstrapping 82 of 100 bootstrapping 83 of 100 bootstrapping 84 of 100 bootstrapping 85 of 100 bootstrapping 86 of 100 bootstrapping 87 of 100 bootstrapping 88 of 100 bootstrapping 89 of 100 bootstrapping 90 of 100 bootstrapping 91 of 100 bootstrapping 92 of 100 bootstrapping 93 of 100 bootstrapping 94 of 100 bootstrapping 95 of 100 bootstrapping 96 of 100 bootstrapping 97 of 100 bootstrapping 98 of 100 bootstrapping 99 of 100 bootstrapping 100 of 100 469s 469s Done estimating abundances 469s 469s --- wrote results to results.txt 469s Passed 469s 469s Test 4: quality_check 471s Passed 471s 471s autopkgtest [15:26:01]: test run-unit-test: -----------------------] 472s run-unit-test PASS 472s autopkgtest [15:26:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 472s autopkgtest [15:26:02]: @@@@@@@@@@@@@@@@@@@@ summary 472s run-unit-test PASS 494s Creating nova instance adt-noble-ppc64el-gasic-20240323-151810-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240321.img (UUID 024d6af5-fcba-4a84-85f9-01f41e1878d6)...