0s autopkgtest [01:27:02]: starting date and time: 2025-03-16 01:27:02+0000 0s autopkgtest [01:27:02]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:27:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r5p5ktgc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade python-pauvre --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-5.secgroup --name adt-plucky-arm64-python-pauvre-20250316-012702-juju-7f2275-prod-proposed-migration-environment-2-55463627-2c5d-41c4-8acf-65f1f2f4f730 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 162s autopkgtest [01:29:44]: testbed dpkg architecture: arm64 162s autopkgtest [01:29:44]: testbed apt version: 2.9.33 163s autopkgtest [01:29:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 163s autopkgtest [01:29:45]: testbed release detected to be: None 164s autopkgtest [01:29:46]: updating testbed package index (apt update) 165s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 165s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 165s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 165s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 165s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 166s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 166s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 166s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [72.2 kB] 166s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1816 B] 166s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 166s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [316 kB] 166s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [13.9 kB] 166s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [16.8 kB] 166s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 166s Fetched 972 kB in 1s (701 kB/s) 167s Reading package lists... 168s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Calculating upgrade... 170s Calculating upgrade... 171s The following packages will be upgraded: 171s pinentry-curses python3-jinja2 strace 172s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 647 kB of archives. 172s After this operation, 11.3 kB of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 172s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 173s Fetched 647 kB in 1s (605 kB/s) 174s (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 ... 117701 files and directories currently installed.) 174s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 174s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 174s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 174s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 174s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 174s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 174s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 174s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 174s Setting up strace (6.13+ds-1ubuntu1) ... 174s Processing triggers for man-db (2.13.0-1) ... 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Solving dependencies... 177s The following packages will be REMOVED: 177s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 177s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 177s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 177s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 177s 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. 177s After this operation, 267 MB disk space will be freed. 177s (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 ... 117701 files and directories currently installed.) 177s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 177s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 177s Removing libpython3.12t64:arm64 (3.12.9-1) ... 177s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 177s Removing libnsl2:arm64 (1.3.0-3build3) ... 177s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 178s Removing libunwind8:arm64 (1.6.2-3.1) ... 178s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 178s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 180s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 180s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 180s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 180s /etc/kernel/postrm.d/initramfs-tools: 180s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 181s /etc/kernel/postrm.d/zz-flash-kernel: 181s flash-kernel: Kernel 6.11.0-8-generic has been removed. 181s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 181s /etc/kernel/postrm.d/zz-update-grub: 181s Sourcing file `/etc/default/grub' 181s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 181s Generating grub configuration file ... 181s Found linux image: /boot/vmlinuz-6.14.0-10-generic 181s Found initrd image: /boot/initrd.img-6.14.0-10-generic 182s Warning: os-prober will not be executed to detect other bootable partitions. 182s Systems on them will not be added to the GRUB boot configuration. 182s Check GRUB_DISABLE_OS_PROBER documentation entry. 182s Adding boot menu entry for UEFI Firmware Settings ... 182s done 182s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 182s Processing triggers for libc-bin (2.41-1ubuntu1) ... 182s (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 ... 81650 files and directories currently installed.) 182s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 182s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 182s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 183s autopkgtest [01:30:05]: upgrading testbed (apt dist-upgrade and autopurge) 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 184s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 185s Starting 2 pkgProblemResolver with broken count: 0 185s Done 186s Entering ResolveByKeep 186s 187s Calculating upgrade... 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s Solving dependencies... 192s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s autopkgtest [01:30:14]: rebooting testbed after setup commands that affected boot 215s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 222s autopkgtest [01:30:44]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 225s autopkgtest [01:30:47]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pauvre 227s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pauvre 0.2.3-4 (dsc) [2485 B] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pauvre 0.2.3-4 (tar) [61.9 kB] 227s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pauvre 0.2.3-4 (diff) [8548 B] 227s gpgv: Signature made Thu Nov 7 22:55:52 2024 UTC 227s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 227s gpgv: issuer "emollier@debian.org" 227s gpgv: Can't check signature: No public key 227s dpkg-source: warning: cannot verify inline signature for ./python-pauvre_0.2.3-4.dsc: no acceptable signature found 228s autopkgtest [01:30:50]: testing package python-pauvre version 0.2.3-4 228s autopkgtest [01:30:50]: build not needed 228s autopkgtest [01:30:50]: test run-unit-test: preparing testbed 229s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s Starting pkgProblemResolver with broken count: 0 229s Starting 2 pkgProblemResolver with broken count: 0 229s Done 231s The following NEW packages will be installed: 231s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 231s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 231s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 231s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 231s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 231s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 231s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 231s python-matplotlib-data python3-biopython python3-brotli python3-cairo 231s python3-contourpy python3-cycler python3-dateutil python3-decorator 231s python3-fonttools python3-freetype python3-fs python3-joblib 231s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 231s python3-mpmath python3-nanoget-examples python3-numpy python3-numpy-dev 231s python3-packaging python3-pandas python3-pandas-lib python3-pauvre 231s python3-pil python3-pil.imagetk python3-platformdirs python3-pytz 231s python3-reportlab python3-rlpycairo python3-scipy python3-sklearn 231s python3-sklearn-lib python3-sympy python3-threadpoolctl python3-tk 231s python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13-tk 231s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 231s xfonts-utils xml-core 231s 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 126 MB of archives. 231s After this operation, 425 MB of additional disk space will be used. 231s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 232s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 232s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 232s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 233s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 233s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 233s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 233s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 233s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 233s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 233s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 233s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 234s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 234s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 235s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 235s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 235s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 235s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 235s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 235s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 235s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 235s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 235s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 235s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 235s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 235s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 235s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 235s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 235s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 235s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 235s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 235s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 235s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 235s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 235s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 235s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 235s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 235s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 235s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 235s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 235s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 235s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 235s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 235s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 235s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 235s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 235s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 235s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 236s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 236s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 236s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-2 [106 kB] 236s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 236s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 236s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 236s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 236s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build2 [122 kB] 236s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 236s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 236s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 236s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 236s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 236s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 236s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 236s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 236s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 236s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 236s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 236s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 236s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 236s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 237s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 237s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 238s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 239s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 239s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 239s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build3 [360 kB] 239s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 240s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 240s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-3 [205 kB] 240s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 240s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 240s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 243s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nanoget-examples all 1.19.3-1 [26.2 MB] 246s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 246s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 246s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8build1 [4586 kB] 246s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 247s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 247s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 247s Get:90 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 247s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pauvre all 0.2.3-4 [52.7 kB] 248s Fetched 126 MB in 16s (7700 kB/s) 248s Selecting previously unselected package python3-numpy-dev:arm64. 248s (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 ... 81647 files and directories currently installed.) 248s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 248s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 248s Selecting previously unselected package libblas3:arm64. 248s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 248s Unpacking libblas3:arm64 (3.12.1-2) ... 248s Selecting previously unselected package libgfortran5:arm64. 248s Preparing to unpack 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Selecting previously unselected package fonts-dejavu-core. 249s Preparing to unpack .../08-fonts-dejavu-core_2.37-8_all.deb ... 249s Unpacking fonts-dejavu-core (2.37-8) ... 249s Selecting previously unselected package libfontenc1:arm64. 249s Preparing to unpack .../09-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 249s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 249s Selecting previously unselected package x11-common. 249s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu3_all.deb ... 249s Unpacking x11-common (1:7.7+23ubuntu3) ... 249s Selecting previously unselected package xfonts-encodings. 249s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 249s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 249s Selecting previously unselected package xfonts-utils. 249s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7_arm64.deb ... 249s Unpacking xfonts-utils (1:7.7+7) ... 249s Selecting previously unselected package fonts-urw-base35. 249s Preparing to unpack .../13-fonts-urw-base35_20200910-8_all.deb ... 249s Unpacking fonts-urw-base35 (20200910-8) ... 249s Selecting previously unselected package fontconfig-config. 249s Preparing to unpack .../14-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 250s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 250s Selecting previously unselected package libfontconfig1:arm64. 250s Preparing to unpack .../15-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 250s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 250s Selecting previously unselected package libxrender1:arm64. 250s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 250s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 250s Selecting previously unselected package libxft2:arm64. 250s Preparing to unpack .../17-libxft2_2.3.6-1build1_arm64.deb ... 250s Unpacking libxft2:arm64 (2.3.6-1build1) ... 250s Selecting previously unselected package libxss1:arm64. 250s Preparing to unpack .../18-libxss1_1%3a1.2.3-1build3_arm64.deb ... 250s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 250s Selecting previously unselected package libtk8.6:arm64. 250s Preparing to unpack .../19-libtk8.6_8.6.16-1_arm64.deb ... 250s Unpacking libtk8.6:arm64 (8.6.16-1) ... 250s Selecting previously unselected package tk8.6-blt2.5. 250s Preparing to unpack .../20-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 250s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 250s Selecting previously unselected package blt. 250s Preparing to unpack .../21-blt_2.5.3+dfsg-8_arm64.deb ... 250s Unpacking blt (2.5.3+dfsg-8) ... 250s Selecting previously unselected package fonts-lyx. 250s Preparing to unpack .../22-fonts-lyx_2.4.3-1_all.deb ... 250s Unpacking fonts-lyx (2.4.3-1) ... 250s Selecting previously unselected package libpixman-1-0:arm64. 250s Preparing to unpack .../23-libpixman-1-0_0.44.0-3_arm64.deb ... 250s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 250s Selecting previously unselected package libxcb-render0:arm64. 250s Preparing to unpack .../24-libxcb-render0_1.17.0-2_arm64.deb ... 250s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 250s Selecting previously unselected package libxcb-shm0:arm64. 250s Preparing to unpack .../25-libxcb-shm0_1.17.0-2_arm64.deb ... 250s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 250s Selecting previously unselected package libcairo2:arm64. 250s Preparing to unpack .../26-libcairo2_1.18.2-2_arm64.deb ... 250s Unpacking libcairo2:arm64 (1.18.2-2) ... 250s Selecting previously unselected package libdeflate0:arm64. 250s Preparing to unpack .../27-libdeflate0_1.23-1_arm64.deb ... 250s Unpacking libdeflate0:arm64 (1.23-1) ... 250s Selecting previously unselected package libgomp1:arm64. 250s Preparing to unpack .../28-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 250s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 250s Selecting previously unselected package libgraphite2-3:arm64. 250s Preparing to unpack .../29-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 250s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 250s Selecting previously unselected package libharfbuzz0b:arm64. 250s Preparing to unpack .../30-libharfbuzz0b_10.2.0-1_arm64.deb ... 250s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 250s Selecting previously unselected package libimagequant0:arm64. 250s Preparing to unpack .../31-libimagequant0_2.18.0-1build1_arm64.deb ... 250s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 250s Selecting previously unselected package libjpeg-turbo8:arm64. 250s Preparing to unpack .../32-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 250s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 250s Selecting previously unselected package libjpeg8:arm64. 250s Preparing to unpack .../33-libjpeg8_8c-2ubuntu11_arm64.deb ... 250s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 251s Selecting previously unselected package libjs-jquery. 251s Preparing to unpack .../34-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 251s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 251s Selecting previously unselected package libjs-jquery-ui. 251s Preparing to unpack .../35-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 251s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 251s Selecting previously unselected package liblbfgsb0:arm64. 251s Preparing to unpack .../36-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 251s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 251s Selecting previously unselected package liblcms2-2:arm64. 251s Preparing to unpack .../37-liblcms2-2_2.16-2_arm64.deb ... 251s Unpacking liblcms2-2:arm64 (2.16-2) ... 251s Selecting previously unselected package liblerc4:arm64. 251s Preparing to unpack .../38-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 251s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 251s Selecting previously unselected package libqhull-r8.0:arm64. 251s Preparing to unpack .../39-libqhull-r8.0_2020.2-6build1_arm64.deb ... 251s 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package libwebpdemux2:arm64. 251s Preparing to unpack .../45-libwebpdemux2_1.5.0-0.1_arm64.deb ... 251s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 251s Selecting previously unselected package libwebpmux3:arm64. 251s Preparing to unpack .../46-libwebpmux3_1.5.0-0.1_arm64.deb ... 251s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 251s Selecting previously unselected package libxslt1.1:arm64. 251s Preparing to unpack .../47-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 251s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 251s Selecting previously unselected package python-matplotlib-data. 251s Preparing to unpack .../48-python-matplotlib-data_3.8.3-7build1_all.deb ... 251s Unpacking python-matplotlib-data (3.8.3-7build1) ... 251s Selecting previously unselected package python3.12-tk. 251s Preparing to unpack .../49-python3.12-tk_3.12.9-1_arm64.deb ... 251s Unpacking python3.12-tk (3.12.9-1) ... 251s Selecting previously unselected package python3.13-tk. 251s Preparing to unpack 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python3-cairo (1.26.1-2build2) ... 252s Selecting previously unselected package python3-freetype. 252s Preparing to unpack .../56-python3-freetype_2.5.1-1_all.deb ... 252s Unpacking python3-freetype (2.5.1-1) ... 252s Selecting previously unselected package python3-rlpycairo. 252s Preparing to unpack .../57-python3-rlpycairo_0.3.0-3_all.deb ... 252s Unpacking python3-rlpycairo (0.3.0-3) ... 252s Selecting previously unselected package python3-reportlab. 252s Preparing to unpack .../58-python3-reportlab_4.3.1-1_all.deb ... 252s Unpacking python3-reportlab (4.3.1-1) ... 252s Selecting previously unselected package xml-core. 252s Preparing to unpack .../59-xml-core_0.19_all.deb ... 252s Unpacking xml-core (0.19) ... 252s Selecting previously unselected package w3c-sgml-lib. 252s Preparing to unpack .../60-w3c-sgml-lib_1.3-3_all.deb ... 252s Unpacking w3c-sgml-lib (1.3-3) ... 252s Selecting previously unselected package python3-biopython. 252s Preparing to unpack .../61-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 252s Unpacking python3-biopython (1.85+dfsg-2build1) ... 252s Selecting previously unselected package python3-brotli. 252s Preparing to unpack .../62-python3-brotli_1.1.0-2build4_arm64.deb ... 252s Unpacking python3-brotli (1.1.0-2build4) ... 252s Selecting previously unselected package python3-contourpy. 252s Preparing to unpack .../63-python3-contourpy_1.3.1-1build1_arm64.deb ... 252s Unpacking python3-contourpy (1.3.1-1build1) ... 252s Selecting previously unselected package python3-cycler. 252s Preparing to unpack .../64-python3-cycler_0.12.1-1_all.deb ... 252s Unpacking python3-cycler (0.12.1-1) ... 252s Selecting previously unselected package python3-dateutil. 252s Preparing to unpack .../65-python3-dateutil_2.9.0-3_all.deb ... 252s Unpacking python3-dateutil (2.9.0-3) ... 252s Selecting previously unselected package python3-decorator. 252s Preparing to unpack .../66-python3-decorator_5.1.1-5_all.deb ... 252s Unpacking python3-decorator (5.1.1-5) ... 252s Selecting previously unselected package python3-platformdirs. 252s Preparing to unpack .../67-python3-platformdirs_4.3.6-1_all.deb ... 252s Unpacking python3-platformdirs (4.3.6-1) ... 252s Selecting previously unselected package python3-fs. 252s Preparing to unpack .../68-python3-fs_2.4.16-7_all.deb ... 252s Unpacking python3-fs (2.4.16-7) ... 252s Selecting previously unselected package python3-lxml:arm64. 252s Preparing to unpack .../69-python3-lxml_5.3.1-1build1_arm64.deb ... 252s Unpacking python3-lxml:arm64 (5.3.1-1build1) ... 252s Selecting previously unselected package python3-lz4. 252s Preparing to unpack .../70-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 252s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 253s Selecting previously unselected package python3-scipy. 253s Preparing to unpack .../71-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 253s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 253s Selecting previously unselected package python3-mpmath. 253s Preparing to unpack .../72-python3-mpmath_1.3.0-1_all.deb ... 253s Unpacking python3-mpmath (1.3.0-1) ... 253s Selecting previously unselected package python3-sympy. 253s Preparing to unpack .../73-python3-sympy_1.13.3-5_all.deb ... 253s Unpacking python3-sympy (1.13.3-5) ... 253s Selecting previously unselected package python3-ufolib2. 253s Preparing to unpack .../74-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 253s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 253s Selecting previously unselected package python3-unicodedata2. 253s Preparing to unpack .../75-python3-unicodedata2_15.1.0+ds-1build3_arm64.deb ... 253s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 253s Selecting previously unselected package unicode-data. 253s Preparing to unpack .../76-unicode-data_15.1.0-1_all.deb ... 253s Unpacking unicode-data (15.1.0-1) ... 254s Selecting previously unselected package python3-fonttools. 254s Preparing to unpack .../77-python3-fonttools_4.55.3-2build1_arm64.deb ... 254s Unpacking python3-fonttools (4.55.3-2build1) ... 254s Selecting previously unselected package python3-joblib. 254s Preparing to unpack .../78-python3-joblib_1.4.2-3_all.deb ... 254s Unpacking python3-joblib (1.4.2-3) ... 254s Selecting previously unselected package python3-kiwisolver. 254s Preparing to unpack .../79-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 254s Unpacking python3-kiwisolver (1.4.7-3build1) ... 254s Selecting previously unselected package python3-packaging. 254s Preparing to unpack .../80-python3-packaging_24.2-1_all.deb ... 254s Unpacking python3-packaging (24.2-1) ... 254s Selecting previously unselected package python3-matplotlib. 254s Preparing to unpack .../81-python3-matplotlib_3.8.3-7build1_arm64.deb ... 254s Unpacking python3-matplotlib (3.8.3-7build1) ... 254s Selecting previously unselected package python3-nanoget-examples. 254s Preparing to unpack .../82-python3-nanoget-examples_1.19.3-1_all.deb ... 254s Unpacking python3-nanoget-examples (1.19.3-1) ... 254s Selecting previously unselected package python3-pytz. 254s Preparing to unpack .../83-python3-pytz_2025.1-3_all.deb ... 254s Unpacking python3-pytz (2025.1-3) ... 254s Selecting previously unselected package python3-tz. 255s Preparing to unpack .../84-python3-tz_2025.1-3_all.deb ... 255s Unpacking python3-tz (2025.1-3) ... 255s Selecting previously unselected package python3-pandas-lib:arm64. 255s Preparing to unpack .../85-python3-pandas-lib_2.2.3+dfsg-8build1_arm64.deb ... 255s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 255s Selecting previously unselected package python3-pandas. 255s Preparing to unpack .../86-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 255s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 255s Selecting previously unselected package python3-threadpoolctl. 255s Preparing to unpack .../87-python3-threadpoolctl_3.1.0-1_all.deb ... 255s Unpacking python3-threadpoolctl (3.1.0-1) ... 255s Selecting previously unselected package python3-sklearn-lib:arm64. 255s Preparing to unpack .../88-python3-sklearn-lib_1.4.2+dfsg-8_arm64.deb ... 255s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 255s Selecting previously unselected package python3-sklearn. 255s Preparing to unpack .../89-python3-sklearn_1.4.2+dfsg-8_all.deb ... 255s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 255s Selecting previously unselected package python3-pauvre. 255s Preparing to unpack .../90-python3-pauvre_0.2.3-4_all.deb ... 255s Unpacking python3-pauvre (0.2.3-4) ... 255s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 255s Setting up liblcms2-2:arm64 (2.16-2) ... 255s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 255s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 255s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 255s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 255s Setting up python3-joblib (1.4.2-3) ... 256s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 256s Setting up libxcb-render0:arm64 (1.17.0-2) ... 256s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 256s Setting up fonts-lyx (2.4.3-1) ... 256s Setting up python3-threadpoolctl (3.1.0-1) ... 256s Setting up x11-common (1:7.7+23ubuntu3) ... 256s Setting up libdeflate0:arm64 (1.23-1) ... 256s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 256s Setting up python3-pytz (2025.1-3) ... 256s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 256s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 256s Setting up python3-freetype (2.5.1-1) ... 257s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 257s Setting up python3-platformdirs (4.3.6-1) ... 257s Setting up python3-tz (2025.1-3) ... 257s Setting up python3-fs (2.4.16-7) ... 257s Setting up unicode-data (15.1.0-1) ... 257s Setting up python3-decorator (5.1.1-5) ... 257s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 257s Setting up libblas3:arm64 (3.12.1-2) ... 257s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to 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(1.26.1-2build2) ... 279s Setting up blt (2.5.3+dfsg-8) ... 279s Setting up python3-tk:arm64 (3.13.1-1) ... 279s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 279s Setting up python3-rlpycairo (0.3.0-3) ... 279s Setting up python3-reportlab (4.3.1-1) ... 280s Setting up python3-fonttools (4.55.3-2build1) ... 281s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 281s Setting up python3-matplotlib (3.8.3-7build1) ... 282s Processing triggers for libc-bin (2.41-1ubuntu1) ... 282s Processing triggers for man-db (2.13.0-1) ... 283s Processing triggers for sgml-base (1.31) ... 284s Setting up w3c-sgml-lib (1.3-3) ... 310s Setting up python3-biopython (1.85+dfsg-2build1) ... 311s Setting up python3-pauvre (0.2.3-4) ... 312s autopkgtest [01:32:14]: test run-unit-test: [----------------------- 312s 312s #git clone https://github.com/wdecoster/nanotest.git 312s 312s pauvre -h 312s usage: pauvre [-h] [-v] 312s {browser,custommargin,marginplot,redwood,stats,synplot} ... 312s 312s options: 312s -h, --help show this help message and exit 312s -v, --version Installed pauvre version 312s 312s [sub-commands]: 312s {browser,custommargin,marginplot,redwood,stats,synplot} 312s browser an adaptable genome browser with various track types 312s custommargin plot custom marginal histograms of tab-delimited files 312s marginplot plot a marginal histogram of a fastq file 312s redwood make a redwood plot from a bam file 312s stats outputs stats from a fastq file 312s synplot make a synteny plot from a gff file, protein 312s alignment, and partition file 312s 312s pauvre marginplot -h 312s usage: pauvre marginplot [-h] [-q] [--dpi dpi] [-f FASTQ] 312s [--fileform STRING [STRING ...]] 312s [--filt_maxlen FILT_MAXLEN] 312s [--filt_maxqual FILT_MAXQUAL] 312s [--filt_minlen FILT_MINLEN] 312s [--filt_minqual FILT_MINQUAL] [--kmerdf KMERDF] [-n] 312s [--no_timestamp] [-o BASENAME] 312s [--plot_maxlen PLOT_MAXLEN] 312s [--plot_maxqual PLOT_MAXQUAL] 312s [--plot_minlen PLOT_MINLEN] 312s [--plot_minqual PLOT_MINQUAL] [--lengthbin LENGTHBIN] 312s [--qualbin QUALBIN] [-t TITLE] [-y] 312s 312s options: 312s -h, --help show this help message and exit 312s -q, --quiet Do not output warnings to stderr 312s --dpi dpi Change the dpi from the default 600 if you need it 312s higher 312s -f, --fastq FASTQ The input FASTQ file. 312s --fileform STRING [STRING ...] 312s Which output format would you like? Def.=png 312s --filt_maxlen FILT_MAXLEN 312s This sets the max read length filter reads. 312s --filt_maxqual FILT_MAXQUAL 312s This sets the max mean read quality to filter reads. 312s --filt_minlen FILT_MINLEN 312s This sets the min read length to filter reads. 312s --filt_minqual FILT_MINQUAL 312s This sets the min mean read quality to filter reads. 312s --kmerdf KMERDF Pass the filename of a data matrix if you would like 312s to plot read length versus number of kmers in that 312s read. The data matrix is a tab-separated text file 312s with columns "id length numks and kmers", where: 312s = read id = the length of the read = 312s the number of canonical kmers in the read = a 312s list representation of kmers ie ['GAT', 'GTA'] 312s -n, --no_transparent Specify this option if you don't want a transparent 312s background. Default is on. 312s --no_timestamp Turn off time stamps in the filename output. 312s -o, --output_base_name BASENAME 312s Specify a base name for the output file(s). The input 312s file base name is the default. 312s --plot_maxlen PLOT_MAXLEN 312s Sets the maximum viewing area in the length dimension. 312s --plot_maxqual PLOT_MAXQUAL 312s Sets the maximum viewing area in the quality 312s dimension. 312s --plot_minlen PLOT_MINLEN 312s Sets the minimum viewing area in the length dimension. 312s --plot_minqual PLOT_MINQUAL 312s Sets the minimum viewing area in the quality 312s dimension. 312s --lengthbin LENGTHBIN 312s This sets the bin size to use for length. 312s --qualbin QUALBIN This sets the bin size to use for quality 312s -t, --title TITLE This sets the title for the whole plot. Use --title 312s "Crustacean's DNA read quality" if you need single 312s quote or apostrophe inside title. 312s -y, --add-yaxes Add Y-axes to both marginal histograms. 313s pauvre marginplot -f nanotest/reads.fastq.gz 315s Keeping reads that satisfy: length >= 0 and meanQual >= 0 316s # Fastq stats for reads.fastq.gz, reads >= 0bp 316s numReads: 371 316s %totalNumReads: 100.00 316s numBasepairs: 8611871 316s %totalBasepairs: 100.00 316s meanLen: 23212.590296495957 316s medianLen: 9390.0 316s minLen: 212 316s maxLen: 393431 316s N50: 60395 316s L50: 36 316s 316s # Fastq stats for reads.fastq.gz, reads >= 1000bp 316s numReads: 349 316s %totalNumReads: 94.07 316s numBasepairs: 8599196 316s %totalBasepairs: 99.85 316s meanLen: 24639.530085959886 316s medianLen: 10585.0 316s minLen: 1009 316s maxLen: 393431 316s N50: 60395 316s L50: 36 316s 316s # Fastq stats for reads.fastq.gz, reads >= 5000bp 316s numReads: 246 316s %totalNumReads: 66.31 316s numBasepairs: 8296771 316s %totalBasepairs: 96.34 316s meanLen: 33726.71138211382 316s medianLen: 17146.0 316s minLen: 5082 316s maxLen: 393431 316s N50: 61111 316s L50: 33 316s 316s # Fastq stats for reads.fastq.gz, reads >= 10000bp 316s numReads: 178 316s %totalNumReads: 47.98 316s numBasepairs: 7817574 316s %totalBasepairs: 90.78 316s meanLen: 43918.95505617977 316s medianLen: 25216.5 316s minLen: 10192 316s maxLen: 393431 316s N50: 67193 316s L50: 30 316s 316s 316s Basepairs >= bin by mean PHRED and length 316s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 316s 0 8611871 7722755 6661156 4720156 2513562 895545 11781 0 316s 250 8611434 7722543 6660944 4719944 2513350 895333 11781 0 316s 500 8608955 7720456 6659643 4718643 2512881 894864 11781 0 316s 750 8604011 7718007 6657705 4717235 2512207 894190 11781 0 316s 1000 8599196 7714763 6654461 4713991 2509728 892515 11781 0 316s 1500 8589389 7708620 6650781 4710311 2507384 892515 11781 0 316s 2000 8554914 7676064 6618225 4682910 2492830 889226 11781 0 316s 2500 8523841 7647182 6591756 4667150 2483798 884829 11781 0 316s 3000 8491143 7627966 6575417 4653398 2480966 884829 11781 0 316s 3500 8446296 7586240 6536848 4617937 2451870 872464 11781 0 316s 4000 8394095 7534039 6484647 4572910 2432856 872464 11781 0 316s 4500 8344217 7488243 6447269 4556363 2424476 864084 11781 0 316s 5000 8296771 7440797 6409287 4528136 2405499 859337 11781 0 316s 5500 8244099 7398741 6367231 4507086 2400051 853889 6333 0 316s 6000 8187360 7347687 6316177 4456032 2377109 842317 6333 0 316s 6500 8118352 7291309 6272099 4418146 2357938 829533 0 0 316s 7000 8077764 7257349 6244869 4404380 2351024 829533 0 0 316s 7500 8034618 7214203 6209041 4383008 2336942 815451 0 0 316s 8000 7988407 7175507 6170345 4351953 2313576 807622 0 0 316s 8500 7938916 7142561 6137399 4327467 2297332 807622 0 0 316s 9000 7912979 7116624 6119996 4310064 2288474 798764 0 0 316s 9500 7857026 7060671 6091684 4300567 2278977 798764 0 0 316s 10000 7817574 7021219 6072011 4290587 2268997 798764 0 0 316s 11000 7722033 6946925 6008613 4237810 2237463 798764 0 0 316s 12000 7618324 6854352 5928031 4191306 2202157 775443 0 0 316s 13000 7417005 6678203 5790564 4116603 2177804 763380 0 0 316s 14000 7335708 6610502 5736644 4062683 2150377 735953 0 0 316s 15000 7277461 6552255 5678397 4004436 2106447 721422 0 0 316s 16000 7216282 6506170 5632312 3973573 2106447 721422 0 0 316s 17000 7099358 6389246 5532373 3890471 2056275 704705 0 0 316s 18000 7028757 6318645 5461772 3819870 1985674 687130 0 0 316s 19000 6954493 6262568 5405695 3782448 1967023 668479 0 0 316s 20000 6875713 6183788 5346904 3743003 1967023 668479 0 0 316s 21000 6752924 6081496 5264907 3681828 1905848 627955 0 0 316s 22000 6645406 6017177 5200588 3639354 1863374 606840 0 0 316s 23000 6555755 5927526 5110937 3571882 1818321 584599 0 0 316s 24000 6509051 5880822 5064233 3525178 1818321 584599 0 0 316s 25000 6410673 5782444 4989966 3475825 1793534 584599 0 0 316s 26000 6360240 5732011 4964634 3475825 1793534 584599 0 0 316s 27000 6254597 5626368 4885462 3423050 1740759 558501 0 0 316s 28000 6171485 5543256 4802350 3395216 1712925 530667 0 0 316s 29000 6029142 5400913 4688628 3281494 1684138 501880 0 0 316s 30000 5882027 5253798 4541513 3163672 1654590 501880 0 0 316s 31000 5821490 5193261 4480976 3103135 1624358 471648 0 0 316s 32000 5758286 5130057 4417772 3039931 1592823 471648 0 0 316s 33000 5726083 5097854 4385569 3007728 1592823 471648 0 0 316s 34000 5726083 5097854 4385569 3007728 1592823 471648 0 0 316s 35000 5657458 5063791 4351506 2973665 1592823 471648 0 0 316s 36000 5550544 4956877 4315610 2937769 1592823 471648 0 0 316s 37000 5440987 4847320 4278774 2900933 1555987 471648 0 0 316s 38000 5440987 4847320 4278774 2900933 1555987 471648 0 0 316s 39000 5402415 4847320 4278774 2900933 1555987 471648 0 0 316s 40000 5402415 4847320 4278774 2900933 1555987 471648 0 0 316s 45000 5193644 4721367 4194028 2860812 1555987 471648 0 0 316s 50000 4960568 4534952 4007613 2674397 1508336 423997 0 0 316s 55000 4750881 4325265 3797926 2464710 1352765 320689 0 0 316s 60000 4344431 3918815 3450507 2293175 1181230 263588 0 0 316s 65000 4101203 3736226 3267918 2171697 1120835 203193 0 0 316s 70000 3833468 3535098 3135269 2039048 1120835 203193 0 0 316s 75000 3470049 3246162 2846333 1893802 975589 203193 0 0 316s 80000 3311125 3087238 2766576 1814045 975589 203193 0 0 316s 85000 3228980 3005093 2684431 1814045 975589 203193 0 0 316s 90000 2967292 2829470 2508808 1726901 888445 203193 0 0 316s 95000 2967292 2829470 2508808 1726901 888445 203193 0 0 316s 100000 2674343 2536521 2215859 1530166 691710 105463 0 0 316s 120000 2232740 2094918 1774256 1189896 468021 0 0 0 316s 140000 1699582 1699582 1378920 930176 341725 0 0 0 316s 160000 1699582 1699582 1378920 930176 341725 0 0 0 316s 180000 1699582 1699582 1378920 930176 341725 0 0 0 316s 200000 1504562 1504562 1183900 735156 341725 0 0 0 316s 220000 1504562 1504562 1183900 735156 341725 0 0 0 316s 240000 1055818 1055818 735156 735156 341725 0 0 0 316s 260000 1055818 1055818 735156 735156 341725 0 0 0 316s 280000 1055818 1055818 735156 735156 341725 0 0 0 316s 300000 1055818 1055818 735156 735156 341725 0 0 0 316s 320000 1055818 1055818 735156 735156 341725 0 0 0 316s 340000 735156 735156 735156 735156 341725 0 0 0 316s 360000 393431 393431 393431 393431 0 0 0 0 316s 380000 393431 393431 393431 393431 0 0 0 0 316s 400000 0 0 0 0 0 0 0 0 316s 316s Number of reads >= bin by mean Phred+Len 316s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 316s 0 371 321 277 207 114 49 2 0 316s 250 369 320 276 206 113 48 2 0 316s 500 363 315 273 203 112 47 2 0 316s 750 355 311 270 201 111 46 2 0 316s 1000 349 307 266 197 108 44 2 0 316s 1500 341 302 263 194 106 44 2 0 316s 2000 322 284 245 179 98 42 2 0 316s 2500 308 271 233 172 94 40 2 0 316s 3000 296 264 227 167 93 40 2 0 316s 3500 282 251 215 156 84 36 2 0 316s 4000 268 237 201 144 79 36 2 0 316s 4500 256 226 192 140 77 34 2 0 316s 5000 246 216 184 134 73 33 2 0 316s 5500 236 208 176 130 72 32 1 0 316s 6000 226 199 167 121 68 30 1 0 316s 6500 215 190 160 115 65 28 0 0 316s 7000 209 185 156 113 64 28 0 0 316s 7500 203 179 151 110 62 26 0 0 316s 8000 197 174 146 106 59 25 0 0 316s 8500 191 170 142 103 57 25 0 0 316s 9000 188 167 140 101 56 24 0 0 316s 9500 182 161 137 100 55 24 0 0 316s 10000 178 157 135 99 54 24 0 0 316s 11000 169 150 129 94 51 24 0 0 316s 12000 160 142 122 90 48 22 0 0 316s 13000 144 128 111 84 46 21 0 0 316s 14000 138 123 107 80 44 19 0 0 316s 15000 134 119 103 76 41 18 0 0 316s 16000 130 116 100 74 41 18 0 0 316s 17000 123 109 94 69 38 17 0 0 316s 18000 119 105 90 65 34 16 0 0 316s 19000 115 102 87 63 33 15 0 0 316s 20000 111 98 84 61 33 15 0 0 316s 21000 105 93 80 58 30 13 0 0 316s 22000 100 90 77 56 28 12 0 0 316s 23000 96 86 73 53 26 11 0 0 316s 24000 94 84 71 51 26 11 0 0 316s 25000 90 80 68 49 25 11 0 0 316s 26000 88 78 67 49 25 11 0 0 316s 27000 84 74 64 47 23 10 0 0 316s 28000 81 71 61 46 22 9 0 0 316s 29000 76 66 57 42 21 8 0 0 316s 30000 71 61 52 38 20 8 0 0 316s 31000 69 59 50 36 19 7 0 0 316s 32000 67 57 48 34 18 7 0 0 316s 33000 66 56 47 33 18 7 0 0 316s 34000 66 56 47 33 18 7 0 0 316s 35000 64 55 46 32 18 7 0 0 316s 36000 61 52 45 31 18 7 0 0 316s 37000 58 49 44 30 17 7 0 0 316s 38000 58 49 44 30 17 7 0 0 316s 39000 57 49 44 30 17 7 0 0 316s 40000 57 49 44 30 17 7 0 0 316s 45000 52 46 42 29 17 7 0 0 316s 50000 47 42 38 25 16 6 0 0 316s 55000 43 38 34 21 13 4 0 0 316s 60000 36 31 28 18 10 3 0 0 316s 65000 32 28 25 16 9 2 0 0 316s 70000 28 25 23 14 9 2 0 0 316s 75000 23 21 19 12 7 2 0 0 316s 80000 21 19 18 11 7 2 0 0 316s 85000 20 18 17 11 7 2 0 0 316s 90000 17 16 15 10 6 2 0 0 316s 95000 17 16 15 10 6 2 0 0 316s 100000 14 13 12 8 4 1 0 0 316s 120000 10 9 8 5 2 0 0 0 316s 140000 6 6 5 3 1 0 0 0 316s 160000 6 6 5 3 1 0 0 0 316s 180000 6 6 5 3 1 0 0 0 316s 200000 5 5 4 2 1 0 0 0 316s 220000 5 5 4 2 1 0 0 0 316s 240000 3 3 2 2 1 0 0 0 316s 260000 3 3 2 2 1 0 0 0 316s 280000 3 3 2 2 1 0 0 0 316s 300000 3 3 2 2 1 0 0 0 316s 320000 3 3 2 2 1 0 0 0 316s 340000 2 2 2 2 1 0 0 0 316s 360000 1 1 1 1 0 0 0 0 316s 380000 1 1 1 1 0 0 0 0 316s 400000 0 0 0 0 0 0 0 0 316s plotting in the following window: 316s 0 <= Q-score (x-axis) <= 14.0 316s 0 <= length (y-axis) <= 223383 317s 317s pauvre marginplot -f nanotest/reads.fastq.gz -t "my title" --filt_maxlen 30000 319s Keeping reads that satisfy: length >= 0 and meanQual >= 0 and length <= 30000 320s plotting in the following window: 320s 0 <= Q-score (x-axis) <= 14.0 320s 0 <= length (y-axis) <= 29294 321s # Fastq stats for reads.fastq.gz, reads >= 0bp 321s numReads: 300 321s %totalNumReads: 100.00 321s numBasepairs: 2729844 321s %totalBasepairs: 100.00 321s meanLen: 9099.48 321s medianLen: 6204.5 321s minLen: 212 321s maxLen: 29590 321s N50: 15222 321s L50: 61 321s 321s # Fastq stats for reads.fastq.gz, reads >= 1000bp 321s numReads: 278 321s %totalNumReads: 92.67 321s numBasepairs: 2717169 321s %totalBasepairs: 99.54 321s meanLen: 9773.989208633093 321s medianLen: 6910.0 321s minLen: 1009 321s maxLen: 29590 321s N50: 15222 321s L50: 61 321s 321s # Fastq stats for reads.fastq.gz, reads >= 5000bp 321s numReads: 175 321s %totalNumReads: 58.33 321s numBasepairs: 2414744 321s %totalBasepairs: 88.46 321s meanLen: 13798.537142857143 321s medianLen: 12063.0 321s minLen: 5082 321s maxLen: 29590 321s N50: 17307 321s L50: 52 321s 321s # Fastq stats for reads.fastq.gz, reads >= 10000bp 321s numReads: 107 321s %totalNumReads: 35.67 321s numBasepairs: 1935547 321s %totalBasepairs: 70.90 321s meanLen: 18089.22429906542 321s medianLen: 16881.0 321s minLen: 10192 321s maxLen: 29590 321s N50: 20295 321s L50: 39 321s 321s 321s Basepairs >= bin by mean PHRED and length 321s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 321s 0 2729844 2468957 2119643 1556484 858972 393665 11781 0 321s 250 2729407 2468745 2119431 1556272 858760 393453 11781 0 321s 500 2726928 2466658 2118130 1554971 858291 392984 11781 0 321s 750 2721984 2464209 2116192 1553563 857617 392310 11781 0 321s 1000 2717169 2460965 2112948 1550319 855138 390635 11781 0 321s 1500 2707362 2454822 2109268 1546639 852794 390635 11781 0 321s 2000 2672887 2422266 2076712 1519238 838240 387346 11781 0 321s 2500 2641814 2393384 2050243 1503478 829208 382949 11781 0 321s 3000 2609116 2374168 2033904 1489726 826376 382949 11781 0 321s 3500 2564269 2332442 1995335 1454265 797280 370584 11781 0 321s 4000 2512068 2280241 1943134 1409238 778266 370584 11781 0 321s 4500 2462190 2234445 1905756 1392691 769886 362204 11781 0 321s 5000 2414744 2186999 1867774 1364464 750909 357457 11781 0 321s 5500 2362072 2144943 1825718 1343414 745461 352009 6333 0 321s 6000 2305333 2093889 1774664 1292360 722519 340437 6333 0 321s 6500 2236325 2037511 1730586 1254474 703348 327653 0 0 321s 7000 2195737 2003551 1703356 1240708 696434 327653 0 0 321s 7500 2152591 1960405 1667528 1219336 682352 313571 0 0 321s 8000 2106380 1921709 1628832 1188281 658986 305742 0 0 321s 8500 2056889 1888763 1595886 1163795 642742 305742 0 0 321s 9000 2030952 1862826 1578483 1146392 633884 296884 0 0 321s 9500 1974999 1806873 1550171 1136895 624387 296884 0 0 321s 10000 1935547 1767421 1530498 1126915 614407 296884 0 0 321s 11000 1840006 1693127 1467100 1074138 582873 296884 0 0 321s 12000 1736297 1600554 1386518 1027634 547567 273563 0 0 321s 13000 1534978 1424405 1249051 952931 523214 261500 0 0 321s 14000 1453681 1356704 1195131 899011 495787 234073 0 0 321s 15000 1395434 1298457 1136884 840764 451857 219542 0 0 321s 16000 1334255 1252372 1090799 809901 451857 219542 0 0 321s 17000 1217331 1135448 990860 726799 401685 202825 0 0 321s 18000 1146730 1064847 920259 656198 331084 185250 0 0 321s 19000 1072466 1008770 864182 618776 312433 166599 0 0 321s 20000 993686 929990 805391 579331 312433 166599 0 0 321s 21000 870897 827698 723394 518156 251258 126075 0 0 321s 22000 763379 763379 659075 475682 208784 104960 0 0 321s 23000 673728 673728 569424 408210 163731 82719 0 0 321s 24000 627024 627024 522720 361506 163731 82719 0 0 321s 25000 528646 528646 448453 312153 138944 82719 0 0 321s 26000 478213 478213 423121 312153 138944 82719 0 0 321s 27000 372570 372570 343949 259378 86169 56621 0 0 321s 28000 289458 289458 260837 231544 58335 28787 0 0 321s 29000 147115 147115 147115 117822 29548 0 0 0 321s 30000 0 0 0 0 0 0 0 0 321s 321s Number of reads >= bin by mean Phred+Len 321s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 321s 0 300 260 225 169 94 41 2 0 321s 250 298 259 224 168 93 40 2 0 321s 500 292 254 221 165 92 39 2 0 321s 750 284 250 218 163 91 38 2 0 321s 1000 278 246 214 159 88 36 2 0 321s 1500 270 241 211 156 86 36 2 0 321s 2000 251 223 193 141 78 34 2 0 321s 2500 237 210 181 134 74 32 2 0 321s 3000 225 203 175 129 73 32 2 0 321s 3500 211 190 163 118 64 28 2 0 321s 4000 197 176 149 106 59 28 2 0 321s 4500 185 165 140 102 57 26 2 0 321s 5000 175 155 132 96 53 25 2 0 321s 5500 165 147 124 92 52 24 1 0 321s 6000 155 138 115 83 48 22 1 0 321s 6500 144 129 108 77 45 20 0 0 321s 7000 138 124 104 75 44 20 0 0 321s 7500 132 118 99 72 42 18 0 0 321s 8000 126 113 94 68 39 17 0 0 321s 8500 120 109 90 65 37 17 0 0 321s 9000 117 106 88 63 36 16 0 0 321s 9500 111 100 85 62 35 16 0 0 321s 10000 107 96 83 61 34 16 0 0 321s 11000 98 89 77 56 31 16 0 0 321s 12000 89 81 70 52 28 14 0 0 321s 13000 73 67 59 46 26 13 0 0 321s 14000 67 62 55 42 24 11 0 0 321s 15000 63 58 51 38 21 10 0 0 321s 16000 59 55 48 36 21 10 0 0 321s 17000 52 48 42 31 18 9 0 0 321s 18000 48 44 38 27 14 8 0 0 321s 19000 44 41 35 25 13 7 0 0 321s 20000 40 37 32 23 13 7 0 0 321s 21000 34 32 28 20 10 5 0 0 321s 22000 29 29 25 18 8 4 0 0 321s 23000 25 25 21 15 6 3 0 0 321s 24000 23 23 19 13 6 3 0 0 321s 25000 19 19 16 11 5 3 0 0 321s 26000 17 17 15 11 5 3 0 0 321s 27000 13 13 12 9 3 2 0 0 321s 28000 10 10 9 8 2 1 0 0 321s 29000 5 5 5 4 1 0 0 0 321s 30000 0 0 0 0 0 0 0 0 321s 321s pauvre marginplot -f nanotest/reads.fastq.gz -y --filt_minqual 7 --fileform svg 323s Keeping reads that satisfy: length >= 0 and meanQual >= 7.0 323s # Fastq stats for reads.fastq.gz, reads >= 0bp 323s numReads: 371 323s %totalNumReads: 100.00 323s numBasepairs: 8611871 323s %totalBasepairs: 100.00 323s meanLen: 23212.590296495957 323s medianLen: 9390.0 323s minLen: 212 323s maxLen: 393431 323s N50: 60395 323s L50: 36 323s 323s # Fastq stats for reads.fastq.gz, reads >= 1000bp 323s numReads: 349 323s %totalNumReads: 94.07 323s numBasepairs: 8599196 323s %totalBasepairs: 99.85 323s meanLen: 24639.530085959886 323s medianLen: 10585.0 323s minLen: 1009 323s maxLen: 393431 323s N50: 60395 323s L50: 36 323s 323s # Fastq stats for reads.fastq.gz, reads >= 5000bp 323s numReads: 246 323s %totalNumReads: 66.31 323s numBasepairs: 8296771 323s %totalBasepairs: 96.34 323s meanLen: 33726.71138211382 323s medianLen: 17146.0 323s minLen: 5082 323s maxLen: 393431 323s N50: 61111 323s L50: 33 323s 323s # Fastq stats for reads.fastq.gz, reads >= 10000bp 323s numReads: 178 323s %totalNumReads: 47.98 323s numBasepairs: 7817574 323s %totalBasepairs: 90.78 323s meanLen: 43918.95505617977 323s medianLen: 25216.5 323s minLen: 10192 323s maxLen: 393431 323s N50: 67193 323s L50: 30 323s 323s 323s Basepairs >= bin by mean PHRED and length 323s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 323s 0 8611871 7722755 6661156 4720156 2513562 895545 11781 0 323s 250 8611434 7722543 6660944 4719944 2513350 895333 11781 0 323s 500 8608955 7720456 6659643 4718643 2512881 894864 11781 0 323s 750 8604011 7718007 6657705 4717235 2512207 894190 11781 0 323s 1000 8599196 7714763 6654461 4713991 2509728 892515 11781 0 323s 1500 8589389 7708620 6650781 4710311 2507384 892515 11781 0 323s 2000 8554914 7676064 6618225 4682910 2492830 889226 11781 0 323s 2500 8523841 7647182 6591756 4667150 2483798 884829 11781 0 323s 3000 8491143 7627966 6575417 4653398 2480966 884829 11781 0 323s 3500 8446296 7586240 6536848 4617937 2451870 872464 11781 0 323s 4000 8394095 7534039 6484647 4572910 2432856 872464 11781 0 323s 4500 8344217 7488243 6447269 4556363 2424476 864084 11781 0 323s 5000 8296771 7440797 6409287 4528136 2405499 859337 11781 0 323s 5500 8244099 7398741 6367231 4507086 2400051 853889 6333 0 323s 6000 8187360 7347687 6316177 4456032 2377109 842317 6333 0 323s 6500 8118352 7291309 6272099 4418146 2357938 829533 0 0 323s 7000 8077764 7257349 6244869 4404380 2351024 829533 0 0 323s 7500 8034618 7214203 6209041 4383008 2336942 815451 0 0 323s 8000 7988407 7175507 6170345 4351953 2313576 807622 0 0 323s 8500 7938916 7142561 6137399 4327467 2297332 807622 0 0 323s 9000 7912979 7116624 6119996 4310064 2288474 798764 0 0 323s 9500 7857026 7060671 6091684 4300567 2278977 798764 0 0 323s 10000 7817574 7021219 6072011 4290587 2268997 798764 0 0 323s 11000 7722033 6946925 6008613 4237810 2237463 798764 0 0 323s 12000 7618324 6854352 5928031 4191306 2202157 775443 0 0 323s 13000 7417005 6678203 5790564 4116603 2177804 763380 0 0 323s 14000 7335708 6610502 5736644 4062683 2150377 735953 0 0 323s 15000 7277461 6552255 5678397 4004436 2106447 721422 0 0 323s 16000 7216282 6506170 5632312 3973573 2106447 721422 0 0 323s 17000 7099358 6389246 5532373 3890471 2056275 704705 0 0 323s 18000 7028757 6318645 5461772 3819870 1985674 687130 0 0 323s 19000 6954493 6262568 5405695 3782448 1967023 668479 0 0 323s 20000 6875713 6183788 5346904 3743003 1967023 668479 0 0 323s 21000 6752924 6081496 5264907 3681828 1905848 627955 0 0 323s 22000 6645406 6017177 5200588 3639354 1863374 606840 0 0 323s 23000 6555755 5927526 5110937 3571882 1818321 584599 0 0 323s 24000 6509051 5880822 5064233 3525178 1818321 584599 0 0 323s 25000 6410673 5782444 4989966 3475825 1793534 584599 0 0 323s 26000 6360240 5732011 4964634 3475825 1793534 584599 0 0 323s 27000 6254597 5626368 4885462 3423050 1740759 558501 0 0 323s 28000 6171485 5543256 4802350 3395216 1712925 530667 0 0 323s 29000 6029142 5400913 4688628 3281494 1684138 501880 0 0 323s 30000 5882027 5253798 4541513 3163672 1654590 501880 0 0 323s 31000 5821490 5193261 4480976 3103135 1624358 471648 0 0 323s 32000 5758286 5130057 4417772 3039931 1592823 471648 0 0 323s 33000 5726083 5097854 4385569 3007728 1592823 471648 0 0 323s 34000 5726083 5097854 4385569 3007728 1592823 471648 0 0 323s 35000 5657458 5063791 4351506 2973665 1592823 471648 0 0 323s 36000 5550544 4956877 4315610 2937769 1592823 471648 0 0 323s 37000 5440987 4847320 4278774 2900933 1555987 471648 0 0 323s 38000 5440987 4847320 4278774 2900933 1555987 471648 0 0 323s 39000 5402415 4847320 4278774 2900933 1555987 471648 0 0 323s 40000 5402415 4847320 4278774 2900933 1555987 471648 0 0 323s 45000 5193644 4721367 4194028 2860812 1555987 471648 0 0 323s 50000 4960568 4534952 4007613 2674397 1508336 423997 0 0 323s 55000 4750881 4325265 3797926 2464710 1352765 320689 0 0 323s 60000 4344431 3918815 3450507 2293175 1181230 263588 0 0 323s 65000 4101203 3736226 3267918 2171697 1120835 203193 0 0 323s 70000 3833468 3535098 3135269 2039048 1120835 203193 0 0 323s 75000 3470049 3246162 2846333 1893802 975589 203193 0 0 323s 80000 3311125 3087238 2766576 1814045 975589 203193 0 0 323s 85000 3228980 3005093 2684431 1814045 975589 203193 0 0 323s 90000 2967292 2829470 2508808 1726901 888445 203193 0 0 323s 95000 2967292 2829470 2508808 1726901 888445 203193 0 0 323s 100000 2674343 2536521 2215859 1530166 691710 105463 0 0 323s 120000 2232740 2094918 1774256 1189896 468021 0 0 0 323s 140000 1699582 1699582 1378920 930176 341725 0 0 0 323s 160000 1699582 1699582 1378920 930176 341725 0 0 0 323s 180000 1699582 1699582 1378920 930176 341725 0 0 0 323s 200000 1504562 1504562 1183900 735156 341725 0 0 0 323s 220000 1504562 1504562 1183900 735156 341725 0 0 0 323s 240000 1055818 1055818 735156 735156 341725 0 0 0 323s 260000 1055818 1055818 735156 735156 341725 0 0 0 323s 280000 1055818 1055818 735156 735156 341725 0 0 0 323s 300000 1055818 1055818 735156 735156 341725 0 0 0 323s 320000 1055818 1055818 735156 735156 341725 0 0 0 323s 340000 735156 735156 735156 735156 341725 0 0 0 323s 360000 393431 393431 393431 393431 0 0 0 0 323s 380000 393431 393431 393431 393431 0 0 0 0 323s 400000 0 0 0 0 0 0 0 0 323s 323s Number of reads >= bin by mean Phred+Len 323s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 323s 0 371 321 277 207 114 49 2 0 323s 250 369 320 276 206 113 48 2 0 323s 500 363 315 273 203 112 47 2 0 323s 750 355 311 270 201 111 46 2 0 323s 1000 349 307 266 197 108 44 2 0 323s 1500 341 302 263 194 106 44 2 0 323s 2000 322 284 245 179 98 42 2 0 323s 2500 308 271 233 172 94 40 2 0 323s 3000 296 264 227 167 93 40 2 0 323s 3500 282 251 215 156 84 36 2 0 323s 4000 268 237 201 144 79 36 2 0 323s 4500 256 226 192 140 77 34 2 0 323s 5000 246 216 184 134 73 33 2 0 323s 5500 236 208 176 130 72 32 1 0 323s 6000 226 199 167 121 68 30 1 0 323s 6500 215 190 160 115 65 28 0 0 323s 7000 209 185 156 113 64 28 0 0 323s 7500 203 179 151 110 62 26 0 0 323s 8000 197 174 146 106 59 25 0 0 323s 8500 191 170 142 103 57 25 0 0 323s 9000 188 167 140 101 56 24 0 0 323s 9500 182 161 137 100 55 24 0 0 323s 10000 178 157 135 99 54 24 0 0 323s 11000 169 150 129 94 51 24 0 0 323s 12000 160 142 122 90 48 22 0 0 323s 13000 144 128 111 84 46 21 0 0 323s 14000 138 123 107 80 44 19 0 0 323s 15000 134 119 103 76 41 18 0 0 323s 16000 130 116 100 74 41 18 0 0 323s 17000 123 109 94 69 38 17 0 0 323s 18000 119 105 90 65 34 16 0 0 323s 19000 115 102 87 63 33 15 0 0 323s 20000 111 98 84 61 33 15 0 0 323s 21000 105 93 80 58 30 13 0 0 323s 22000 100 90 77 56 28 12 0 0 323s 23000 96 86 73 53 26 11 0 0 323s 24000 94 84 71 51 26 11 0 0 323s 25000 90 80 68 49 25 11 0 0 323s 26000 88 78 67 49 25 11 0 0 323s 27000 84 74 64 47 23 10 0 0 323s 28000 81 71 61 46 22 9 0 0 323s 29000 76 66 57 42 21 8 0 0 323s 30000 71 61 52 38 20 8 0 0 323s 31000 69 59 50 36 19 7 0 0 323s 32000 67 57 48 34 18 7 0 0 323s 33000 66 56 47 33 18 7 0 0 323s 34000 66 56 47 33 18 7 0 0 323s 35000 64 55 46 32 18 7 0 0 323s 36000 61 52 45 31 18 7 0 0 323s 37000 58 49 44 30 17 7 0 0 323s 38000 58 49 44 30 17 7 0 0 323s 39000 57 49 44 30 17 7 0 0 323s 40000 57 49 44 30 17 7 0 0 323s 45000 52 46 42 29 17 7 0 0 323s 50000 47 42 38 25 16 6 0 0 323s 55000 43 38 34 21 13 4 0 0 323s 60000 36 31 28 18 10 3 0 0 323s 65000 32 28 25 16 9 2 0 0 323s 70000 28 25 23 14 9 2 0 0 323s 75000 23 21 19 12 7 2 0 0 323s 80000 21 19 18 11 7 2 0 0 323s 85000 20 18 17 11 7 2 0 0 323s 90000 17 16 15 10 6 2 0 0 323s 95000 17 16 15 10 6 2 0 0 323s 100000 14 13 12 8 4 1 0 0 323s 120000 10 9 8 5 2 0 0 0 323s 140000 6 6 5 3 1 0 0 0 323s 160000 6 6 5 3 1 0 0 0 323s 180000 6 6 5 3 1 0 0 0 323s 200000 5 5 4 2 1 0 0 0 323s 220000 5 5 4 2 1 0 0 0 323s 240000 3 3 2 2 1 0 0 0 323s 260000 3 3 2 2 1 0 0 0 323s 280000 3 3 2 2 1 0 0 0 323s 300000 3 3 2 2 1 0 0 0 323s 320000 3 3 2 2 1 0 0 0 323s 340000 2 2 2 2 1 0 0 0 323s 360000 1 1 1 1 0 0 0 0 323s 380000 1 1 1 1 0 0 0 0 323s 400000 0 0 0 0 0 0 0 0 324s plotting in the following window: 324s 0 <= Q-score (x-axis) <= 14.0 324s 0 <= length (y-axis) <= 223383 325s 325s 325s pauvre stats -h 325s usage: pauvre stats [-h] [-q] [-f FASTQ] [-H] [--filt_maxlen FILT_MAXLEN] 325s [--filt_maxqual FILT_MAXQUAL] [--filt_minlen FILT_MINLEN] 325s [--filt_minqual FILT_MINQUAL] 325s 325s options: 325s -h, --help show this help message and exit 325s -q, --quiet Do not output warnings to stderr 325s -f, --fastq FASTQ The input FASTQ file. 325s -H, --histogram Make a histogram of the read lengths and saves it to a 325s new file 325s --filt_maxlen FILT_MAXLEN 325s This sets the max read length filter reads. 325s --filt_maxqual FILT_MAXQUAL 325s This sets the max mean read quality to filter reads. 325s --filt_minlen FILT_MINLEN 325s This sets the min read length to filter reads. 325s --filt_minqual FILT_MINQUAL 325s This sets the min mean read quality to filter reads. 325s pauvre stats -f nanotest/reads.fastq.gz 328s # Fastq stats for reads.fastq.gz, reads >= 0bp 328s numReads: 371 328s %totalNumReads: 100.00 328s numBasepairs: 8611871 328s %totalBasepairs: 100.00 328s meanLen: 23212.590296495957 328s medianLen: 9390.0 328s minLen: 212 328s maxLen: 393431 328s N50: 60395 328s L50: 36 328s 328s # Fastq stats for reads.fastq.gz, reads >= 1000bp 328s numReads: 349 328s %totalNumReads: 94.07 328s numBasepairs: 8599196 328s %totalBasepairs: 99.85 328s meanLen: 24639.530085959886 328s medianLen: 10585.0 328s minLen: 1009 328s maxLen: 393431 328s N50: 60395 328s L50: 36 328s 328s # Fastq stats for reads.fastq.gz, reads >= 5000bp 328s numReads: 246 328s %totalNumReads: 66.31 328s numBasepairs: 8296771 328s %totalBasepairs: 96.34 328s meanLen: 33726.71138211382 328s medianLen: 17146.0 328s minLen: 5082 328s maxLen: 393431 328s N50: 61111 328s L50: 33 328s 328s # Fastq stats for reads.fastq.gz, reads >= 10000bp 328s numReads: 178 328s %totalNumReads: 47.98 328s numBasepairs: 7817574 328s %totalBasepairs: 90.78 328s meanLen: 43918.95505617977 328s medianLen: 25216.5 328s minLen: 10192 328s maxLen: 393431 328s N50: 67193 328s L50: 30 328s 328s 328s Basepairs >= bin by mean PHRED and length 328s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 328s 0 8611871 7722755 6661156 4720156 2513562 895545 11781 0 328s 250 8611434 7722543 6660944 4719944 2513350 895333 11781 0 328s 500 8608955 7720456 6659643 4718643 2512881 894864 11781 0 328s 750 8604011 7718007 6657705 4717235 2512207 894190 11781 0 328s 1000 8599196 7714763 6654461 4713991 2509728 892515 11781 0 328s 1500 8589389 7708620 6650781 4710311 2507384 892515 11781 0 328s 2000 8554914 7676064 6618225 4682910 2492830 889226 11781 0 328s 2500 8523841 7647182 6591756 4667150 2483798 884829 11781 0 328s 3000 8491143 7627966 6575417 4653398 2480966 884829 11781 0 328s 3500 8446296 7586240 6536848 4617937 2451870 872464 11781 0 328s 4000 8394095 7534039 6484647 4572910 2432856 872464 11781 0 328s 4500 8344217 7488243 6447269 4556363 2424476 864084 11781 0 328s 5000 8296771 7440797 6409287 4528136 2405499 859337 11781 0 328s 5500 8244099 7398741 6367231 4507086 2400051 853889 6333 0 328s 6000 8187360 7347687 6316177 4456032 2377109 842317 6333 0 328s 6500 8118352 7291309 6272099 4418146 2357938 829533 0 0 328s 7000 8077764 7257349 6244869 4404380 2351024 829533 0 0 328s 7500 8034618 7214203 6209041 4383008 2336942 815451 0 0 328s 8000 7988407 7175507 6170345 4351953 2313576 807622 0 0 328s 8500 7938916 7142561 6137399 4327467 2297332 807622 0 0 328s 9000 7912979 7116624 6119996 4310064 2288474 798764 0 0 328s 9500 7857026 7060671 6091684 4300567 2278977 798764 0 0 328s 10000 7817574 7021219 6072011 4290587 2268997 798764 0 0 328s 11000 7722033 6946925 6008613 4237810 2237463 798764 0 0 328s 12000 7618324 6854352 5928031 4191306 2202157 775443 0 0 328s 13000 7417005 6678203 5790564 4116603 2177804 763380 0 0 328s 14000 7335708 6610502 5736644 4062683 2150377 735953 0 0 328s 15000 7277461 6552255 5678397 4004436 2106447 721422 0 0 328s 16000 7216282 6506170 5632312 3973573 2106447 721422 0 0 328s 17000 7099358 6389246 5532373 3890471 2056275 704705 0 0 328s 18000 7028757 6318645 5461772 3819870 1985674 687130 0 0 328s 19000 6954493 6262568 5405695 3782448 1967023 668479 0 0 328s 20000 6875713 6183788 5346904 3743003 1967023 668479 0 0 328s 21000 6752924 6081496 5264907 3681828 1905848 627955 0 0 328s 22000 6645406 6017177 5200588 3639354 1863374 606840 0 0 328s 23000 6555755 5927526 5110937 3571882 1818321 584599 0 0 328s 24000 6509051 5880822 5064233 3525178 1818321 584599 0 0 328s 25000 6410673 5782444 4989966 3475825 1793534 584599 0 0 328s 26000 6360240 5732011 4964634 3475825 1793534 584599 0 0 328s 27000 6254597 5626368 4885462 3423050 1740759 558501 0 0 328s 28000 6171485 5543256 4802350 3395216 1712925 530667 0 0 328s 29000 6029142 5400913 4688628 3281494 1684138 501880 0 0 328s 30000 5882027 5253798 4541513 3163672 1654590 501880 0 0 328s 31000 5821490 5193261 4480976 3103135 1624358 471648 0 0 328s 32000 5758286 5130057 4417772 3039931 1592823 471648 0 0 328s 33000 5726083 5097854 4385569 3007728 1592823 471648 0 0 328s 34000 5726083 5097854 4385569 3007728 1592823 471648 0 0 328s 35000 5657458 5063791 4351506 2973665 1592823 471648 0 0 328s 36000 5550544 4956877 4315610 2937769 1592823 471648 0 0 328s 37000 5440987 4847320 4278774 2900933 1555987 471648 0 0 328s 38000 5440987 4847320 4278774 2900933 1555987 471648 0 0 328s 39000 5402415 4847320 4278774 2900933 1555987 471648 0 0 328s 40000 5402415 4847320 4278774 2900933 1555987 471648 0 0 328s 45000 5193644 4721367 4194028 2860812 1555987 471648 0 0 328s 50000 4960568 4534952 4007613 2674397 1508336 423997 0 0 328s 55000 4750881 4325265 3797926 2464710 1352765 320689 0 0 328s 60000 4344431 3918815 3450507 2293175 1181230 263588 0 0 328s 65000 4101203 3736226 3267918 2171697 1120835 203193 0 0 328s 70000 3833468 3535098 3135269 2039048 1120835 203193 0 0 328s 75000 3470049 3246162 2846333 1893802 975589 203193 0 0 328s 80000 3311125 3087238 2766576 1814045 975589 203193 0 0 328s 85000 3228980 3005093 2684431 1814045 975589 203193 0 0 328s 90000 2967292 2829470 2508808 1726901 888445 203193 0 0 328s 95000 2967292 2829470 2508808 1726901 888445 203193 0 0 328s 100000 2674343 2536521 2215859 1530166 691710 105463 0 0 328s 120000 2232740 2094918 1774256 1189896 468021 0 0 0 328s 140000 1699582 1699582 1378920 930176 341725 0 0 0 328s 160000 1699582 1699582 1378920 930176 341725 0 0 0 328s 180000 1699582 1699582 1378920 930176 341725 0 0 0 328s 200000 1504562 1504562 1183900 735156 341725 0 0 0 328s 220000 1504562 1504562 1183900 735156 341725 0 0 0 328s 240000 1055818 1055818 735156 735156 341725 0 0 0 328s 260000 1055818 1055818 735156 735156 341725 0 0 0 328s 280000 1055818 1055818 735156 735156 341725 0 0 0 328s 300000 1055818 1055818 735156 735156 341725 0 0 0 328s 320000 1055818 1055818 735156 735156 341725 0 0 0 328s 340000 735156 735156 735156 735156 341725 0 0 0 328s 360000 393431 393431 393431 393431 0 0 0 0 328s 380000 393431 393431 393431 393431 0 0 0 0 328s 400000 0 0 0 0 0 0 0 0 328s 328s Number of reads >= bin by mean Phred+Len 328s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 328s 0 371 321 277 207 114 49 2 0 328s 250 369 320 276 206 113 48 2 0 328s 500 363 315 273 203 112 47 2 0 328s 750 355 311 270 201 111 46 2 0 328s 1000 349 307 266 197 108 44 2 0 328s 1500 341 302 263 194 106 44 2 0 328s 2000 322 284 245 179 98 42 2 0 328s 2500 308 271 233 172 94 40 2 0 328s 3000 296 264 227 167 93 40 2 0 328s 3500 282 251 215 156 84 36 2 0 328s 4000 268 237 201 144 79 36 2 0 328s 4500 256 226 192 140 77 34 2 0 328s 5000 246 216 184 134 73 33 2 0 328s 5500 236 208 176 130 72 32 1 0 328s 6000 226 199 167 121 68 30 1 0 328s 6500 215 190 160 115 65 28 0 0 328s 7000 209 185 156 113 64 28 0 0 328s 7500 203 179 151 110 62 26 0 0 328s 8000 197 174 146 106 59 25 0 0 328s 8500 191 170 142 103 57 25 0 0 328s 9000 188 167 140 101 56 24 0 0 328s 9500 182 161 137 100 55 24 0 0 328s 10000 178 157 135 99 54 24 0 0 328s 11000 169 150 129 94 51 24 0 0 328s 12000 160 142 122 90 48 22 0 0 328s 13000 144 128 111 84 46 21 0 0 328s 14000 138 123 107 80 44 19 0 0 328s 15000 134 119 103 76 41 18 0 0 328s 16000 130 116 100 74 41 18 0 0 328s 17000 123 109 94 69 38 17 0 0 328s 18000 119 105 90 65 34 16 0 0 328s 19000 115 102 87 63 33 15 0 0 328s 20000 111 98 84 61 33 15 0 0 328s 21000 105 93 80 58 30 13 0 0 328s 22000 100 90 77 56 28 12 0 0 328s 23000 96 86 73 53 26 11 0 0 328s 24000 94 84 71 51 26 11 0 0 328s 25000 90 80 68 49 25 11 0 0 328s 26000 88 78 67 49 25 11 0 0 328s 27000 84 74 64 47 23 10 0 0 328s 28000 81 71 61 46 22 9 0 0 328s 29000 76 66 57 42 21 8 0 0 328s 30000 71 61 52 38 20 8 0 0 328s 31000 69 59 50 36 19 7 0 0 328s 32000 67 57 48 34 18 7 0 0 328s 33000 66 56 47 33 18 7 0 0 328s 34000 66 56 47 33 18 7 0 0 328s 35000 64 55 46 32 18 7 0 0 328s 36000 61 52 45 31 18 7 0 0 328s 37000 58 49 44 30 17 7 0 0 328s 38000 58 49 44 30 17 7 0 0 328s 39000 57 49 44 30 17 7 0 0 328s 40000 57 49 44 30 17 7 0 0 328s 45000 52 46 42 29 17 7 0 0 328s 50000 47 42 38 25 16 6 0 0 328s 55000 43 38 34 21 13 4 0 0 328s 60000 36 31 28 18 10 3 0 0 328s 65000 32 28 25 16 9 2 0 0 328s 70000 28 25 23 14 9 2 0 0 328s 75000 23 21 19 12 7 2 0 0 328s 80000 21 19 18 11 7 2 0 0 328s 85000 20 18 17 11 7 2 0 0 328s 90000 17 16 15 10 6 2 0 0 328s 95000 17 16 15 10 6 2 0 0 328s 100000 14 13 12 8 4 1 0 0 328s 120000 10 9 8 5 2 0 0 0 328s 140000 6 6 5 3 1 0 0 0 328s 160000 6 6 5 3 1 0 0 0 328s 180000 6 6 5 3 1 0 0 0 328s 200000 5 5 4 2 1 0 0 0 328s 220000 5 5 4 2 1 0 0 0 328s 240000 3 3 2 2 1 0 0 0 328s 260000 3 3 2 2 1 0 0 0 328s 280000 3 3 2 2 1 0 0 0 328s 300000 3 3 2 2 1 0 0 0 328s 320000 3 3 2 2 1 0 0 0 328s 340000 2 2 2 2 1 0 0 0 328s 360000 1 1 1 1 0 0 0 0 328s 380000 1 1 1 1 0 0 0 0 328s 400000 0 0 0 0 0 0 0 0 328s 328s pauvre stats -f nanotest/reads.fastq.gz -H --filt_maxqual 12 330s # Fastq stats for reads.fastq.gz, reads >= 0bp 330s numReads: 371 330s %totalNumReads: 100.00 330s numBasepairs: 8611871 330s %totalBasepairs: 100.00 330s meanLen: 23212.590296495957 330s medianLen: 9390.0 330s minLen: 212 330s maxLen: 393431 330s N50: 60395 330s L50: 36 330s 330s # Fastq stats for reads.fastq.gz, reads >= 1000bp 330s numReads: 349 330s %totalNumReads: 94.07 330s numBasepairs: 8599196 330s %totalBasepairs: 99.85 330s meanLen: 24639.530085959886 330s medianLen: 10585.0 330s minLen: 1009 330s maxLen: 393431 330s N50: 60395 330s L50: 36 330s 330s # Fastq stats for reads.fastq.gz, reads >= 5000bp 330s numReads: 246 330s %totalNumReads: 66.31 330s numBasepairs: 8296771 330s %totalBasepairs: 96.34 330s meanLen: 33726.71138211382 330s medianLen: 17146.0 330s minLen: 5082 330s maxLen: 393431 330s N50: 61111 330s L50: 33 330s 330s # Fastq stats for reads.fastq.gz, reads >= 10000bp 330s numReads: 178 330s %totalNumReads: 47.98 330s numBasepairs: 7817574 330s %totalBasepairs: 90.78 330s meanLen: 43918.95505617977 330s medianLen: 25216.5 330s minLen: 10192 330s maxLen: 393431 330s N50: 67193 330s L50: 30 330s 330s 330s Basepairs >= bin by mean PHRED and length 330s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 330s 0 8611871 7722755 6661156 4720156 2513562 895545 11781 0 330s 250 8611434 7722543 6660944 4719944 2513350 895333 11781 0 330s 500 8608955 7720456 6659643 4718643 2512881 894864 11781 0 330s 750 8604011 7718007 6657705 4717235 2512207 894190 11781 0 330s 1000 8599196 7714763 6654461 4713991 2509728 892515 11781 0 330s 1500 8589389 7708620 6650781 4710311 2507384 892515 11781 0 330s 2000 8554914 7676064 6618225 4682910 2492830 889226 11781 0 330s 2500 8523841 7647182 6591756 4667150 2483798 884829 11781 0 330s 3000 8491143 7627966 6575417 4653398 2480966 884829 11781 0 330s 3500 8446296 7586240 6536848 4617937 2451870 872464 11781 0 330s 4000 8394095 7534039 6484647 4572910 2432856 872464 11781 0 330s 4500 8344217 7488243 6447269 4556363 2424476 864084 11781 0 330s 5000 8296771 7440797 6409287 4528136 2405499 859337 11781 0 330s 5500 8244099 7398741 6367231 4507086 2400051 853889 6333 0 330s 6000 8187360 7347687 6316177 4456032 2377109 842317 6333 0 330s 6500 8118352 7291309 6272099 4418146 2357938 829533 0 0 330s 7000 8077764 7257349 6244869 4404380 2351024 829533 0 0 330s 7500 8034618 7214203 6209041 4383008 2336942 815451 0 0 330s 8000 7988407 7175507 6170345 4351953 2313576 807622 0 0 330s 8500 7938916 7142561 6137399 4327467 2297332 807622 0 0 330s 9000 7912979 7116624 6119996 4310064 2288474 798764 0 0 330s 9500 7857026 7060671 6091684 4300567 2278977 798764 0 0 330s 10000 7817574 7021219 6072011 4290587 2268997 798764 0 0 330s 11000 7722033 6946925 6008613 4237810 2237463 798764 0 0 330s 12000 7618324 6854352 5928031 4191306 2202157 775443 0 0 330s 13000 7417005 6678203 5790564 4116603 2177804 763380 0 0 330s 14000 7335708 6610502 5736644 4062683 2150377 735953 0 0 330s 15000 7277461 6552255 5678397 4004436 2106447 721422 0 0 330s 16000 7216282 6506170 5632312 3973573 2106447 721422 0 0 330s 17000 7099358 6389246 5532373 3890471 2056275 704705 0 0 330s 18000 7028757 6318645 5461772 3819870 1985674 687130 0 0 330s 19000 6954493 6262568 5405695 3782448 1967023 668479 0 0 330s 20000 6875713 6183788 5346904 3743003 1967023 668479 0 0 330s 21000 6752924 6081496 5264907 3681828 1905848 627955 0 0 330s 22000 6645406 6017177 5200588 3639354 1863374 606840 0 0 330s 23000 6555755 5927526 5110937 3571882 1818321 584599 0 0 330s 24000 6509051 5880822 5064233 3525178 1818321 584599 0 0 330s 25000 6410673 5782444 4989966 3475825 1793534 584599 0 0 330s 26000 6360240 5732011 4964634 3475825 1793534 584599 0 0 330s 27000 6254597 5626368 4885462 3423050 1740759 558501 0 0 330s 28000 6171485 5543256 4802350 3395216 1712925 530667 0 0 330s 29000 6029142 5400913 4688628 3281494 1684138 501880 0 0 330s 30000 5882027 5253798 4541513 3163672 1654590 501880 0 0 330s 31000 5821490 5193261 4480976 3103135 1624358 471648 0 0 330s 32000 5758286 5130057 4417772 3039931 1592823 471648 0 0 330s 33000 5726083 5097854 4385569 3007728 1592823 471648 0 0 330s 34000 5726083 5097854 4385569 3007728 1592823 471648 0 0 330s 35000 5657458 5063791 4351506 2973665 1592823 471648 0 0 330s 36000 5550544 4956877 4315610 2937769 1592823 471648 0 0 330s 37000 5440987 4847320 4278774 2900933 1555987 471648 0 0 330s 38000 5440987 4847320 4278774 2900933 1555987 471648 0 0 330s 39000 5402415 4847320 4278774 2900933 1555987 471648 0 0 330s 40000 5402415 4847320 4278774 2900933 1555987 471648 0 0 330s 45000 5193644 4721367 4194028 2860812 1555987 471648 0 0 330s 50000 4960568 4534952 4007613 2674397 1508336 423997 0 0 330s 55000 4750881 4325265 3797926 2464710 1352765 320689 0 0 330s 60000 4344431 3918815 3450507 2293175 1181230 263588 0 0 330s 65000 4101203 3736226 3267918 2171697 1120835 203193 0 0 330s 70000 3833468 3535098 3135269 2039048 1120835 203193 0 0 330s 75000 3470049 3246162 2846333 1893802 975589 203193 0 0 330s 80000 3311125 3087238 2766576 1814045 975589 203193 0 0 330s 85000 3228980 3005093 2684431 1814045 975589 203193 0 0 330s 90000 2967292 2829470 2508808 1726901 888445 203193 0 0 330s 95000 2967292 2829470 2508808 1726901 888445 203193 0 0 330s 100000 2674343 2536521 2215859 1530166 691710 105463 0 0 330s 120000 2232740 2094918 1774256 1189896 468021 0 0 0 330s 140000 1699582 1699582 1378920 930176 341725 0 0 0 330s 160000 1699582 1699582 1378920 930176 341725 0 0 0 330s 180000 1699582 1699582 1378920 930176 341725 0 0 0 330s 200000 1504562 1504562 1183900 735156 341725 0 0 0 330s 220000 1504562 1504562 1183900 735156 341725 0 0 0 330s 240000 1055818 1055818 735156 735156 341725 0 0 0 330s 260000 1055818 1055818 735156 735156 341725 0 0 0 330s 280000 1055818 1055818 735156 735156 341725 0 0 0 330s 300000 1055818 1055818 735156 735156 341725 0 0 0 330s 320000 1055818 1055818 735156 735156 341725 0 0 0 330s 340000 735156 735156 735156 735156 341725 0 0 0 330s 360000 393431 393431 393431 393431 0 0 0 0 330s 380000 393431 393431 393431 393431 0 0 0 0 330s 400000 0 0 0 0 0 0 0 0 330s 330s Number of reads >= bin by mean Phred+Len 330s minLen Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 330s 0 371 321 277 207 114 49 2 0 330s 250 369 320 276 206 113 48 2 0 330s 500 363 315 273 203 112 47 2 0 330s 750 355 311 270 201 111 46 2 0 330s 1000 349 307 266 197 108 44 2 0 330s 1500 341 302 263 194 106 44 2 0 330s 2000 322 284 245 179 98 42 2 0 330s 2500 308 271 233 172 94 40 2 0 330s 3000 296 264 227 167 93 40 2 0 330s 3500 282 251 215 156 84 36 2 0 330s 4000 268 237 201 144 79 36 2 0 330s 4500 256 226 192 140 77 34 2 0 330s 5000 246 216 184 134 73 33 2 0 330s 5500 236 208 176 130 72 32 1 0 330s 6000 226 199 167 121 68 30 1 0 330s 6500 215 190 160 115 65 28 0 0 330s 7000 209 185 156 113 64 28 0 0 330s 7500 203 179 151 110 62 26 0 0 330s 8000 197 174 146 106 59 25 0 0 330s 8500 191 170 142 103 57 25 0 0 330s 9000 188 167 140 101 56 24 0 0 330s 9500 182 161 137 100 55 24 0 0 330s 10000 178 157 135 99 54 24 0 0 330s 11000 169 150 129 94 51 24 0 0 330s 12000 160 142 122 90 48 22 0 0 330s 13000 144 128 111 84 46 21 0 0 330s 14000 138 123 107 80 44 19 0 0 330s 15000 134 119 103 76 41 18 0 0 330s 16000 130 116 100 74 41 18 0 0 330s 17000 123 109 94 69 38 17 0 0 330s 18000 119 105 90 65 34 16 0 0 330s 19000 115 102 87 63 33 15 0 0 330s 20000 111 98 84 61 33 15 0 0 330s 21000 105 93 80 58 30 13 0 0 330s 22000 100 90 77 56 28 12 0 0 330s 23000 96 86 73 53 26 11 0 0 330s 24000 94 84 71 51 26 11 0 0 330s 25000 90 80 68 49 25 11 0 0 330s 26000 88 78 67 49 25 11 0 0 330s 27000 84 74 64 47 23 10 0 0 330s 28000 81 71 61 46 22 9 0 0 330s 29000 76 66 57 42 21 8 0 0 330s 30000 71 61 52 38 20 8 0 0 330s 31000 69 59 50 36 19 7 0 0 330s 32000 67 57 48 34 18 7 0 0 330s 33000 66 56 47 33 18 7 0 0 330s 34000 66 56 47 33 18 7 0 0 330s 35000 64 55 46 32 18 7 0 0 330s 36000 61 52 45 31 18 7 0 0 330s 37000 58 49 44 30 17 7 0 0 330s 38000 58 49 44 30 17 7 0 0 330s 39000 57 49 44 30 17 7 0 0 330s 40000 57 49 44 30 17 7 0 0 330s 45000 52 46 42 29 17 7 0 0 330s 50000 47 42 38 25 16 6 0 0 330s 55000 43 38 34 21 13 4 0 0 330s 60000 36 31 28 18 10 3 0 0 330s 65000 32 28 25 16 9 2 0 0 330s 70000 28 25 23 14 9 2 0 0 330s 75000 23 21 19 12 7 2 0 0 330s 80000 21 19 18 11 7 2 0 0 330s 85000 20 18 17 11 7 2 0 0 330s 90000 17 16 15 10 6 2 0 0 330s 95000 17 16 15 10 6 2 0 0 330s 100000 14 13 12 8 4 1 0 0 330s 120000 10 9 8 5 2 0 0 0 330s 140000 6 6 5 3 1 0 0 0 330s 160000 6 6 5 3 1 0 0 0 330s 180000 6 6 5 3 1 0 0 0 330s 200000 5 5 4 2 1 0 0 0 330s 220000 5 5 4 2 1 0 0 0 330s 240000 3 3 2 2 1 0 0 0 330s 260000 3 3 2 2 1 0 0 0 330s 280000 3 3 2 2 1 0 0 0 330s 300000 3 3 2 2 1 0 0 0 330s 320000 3 3 2 2 1 0 0 0 330s 340000 2 2 2 2 1 0 0 0 330s 360000 1 1 1 1 0 0 0 0 330s 380000 1 1 1 1 0 0 0 0 330s 400000 0 0 0 0 0 0 0 0 330s 331s autopkgtest [01:32:33]: test run-unit-test: -----------------------] 331s autopkgtest [01:32:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 331s run-unit-test PASS 332s autopkgtest [01:32:34]: @@@@@@@@@@@@@@@@@@@@ summary 332s run-unit-test PASS 350s nova [W] Using flock in prodstack6-arm64 350s flock: timeout while waiting to get lock 350s Creating nova instance adt-plucky-arm64-python-pauvre-20250316-012702-juju-7f2275-prod-proposed-migration-environment-2-55463627-2c5d-41c4-8acf-65f1f2f4f730 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 350s nova [W] Timed out waiting for 05ec5948-1f45-4aa0-9095-a626d7625cab to get deleted.