0s autopkgtest [13:18:57]: starting date and time: 2025-11-01 13:18:57+0000 0s autopkgtest [13:18:57]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [13:18:57]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8ktexmkt/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:openjdk-26 --apt-upgrade bbmap --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openjdk-26/26~22ea-2' -- lxd -r lxd-armhf-10.145.243.160 lxd-armhf-10.145.243.160:autopkgtest/ubuntu/resolute/armhf 20s autopkgtest [13:19:17]: testbed dpkg architecture: armhf 23s autopkgtest [13:19:20]: testbed apt version: 3.1.6ubuntu2 26s autopkgtest [13:19:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [13:19:25]: testbed release detected to be: None 36s autopkgtest [13:19:33]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 38s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [87.8 kB] 38s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [87.8 kB] 38s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [87.8 kB] 38s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [49.4 kB] 38s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 38s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [2242 kB] 39s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [138 kB] 39s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [196 kB] 39s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 39s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1563 kB] 39s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [28.5 kB] 39s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1414 kB] 39s Get:14 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [311 kB] 39s Get:15 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.2 MB] 39s Get:16 http://ftpmaster.internal/ubuntu resolute/restricted Sources [12.5 kB] 39s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1373 kB] 39s Get:18 http://ftpmaster.internal/ubuntu resolute/restricted armhf Packages [1232 B] 39s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.1 MB] 40s Get:20 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [183 kB] 43s Fetched 44.1 MB in 5s (9110 kB/s) 44s Reading package lists... 50s autopkgtest [13:19:47]: upgrading testbed (apt dist-upgrade and autopurge) 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s The following NEW packages will be installed: 52s python3.14-gdbm 52s The following packages will be upgraded: 52s apparmor apt base-files bind9-dnsutils bind9-host bind9-libs binutils 52s binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils 52s cloud-init cloud-init-base distro-info-data dpkg dpkg-dev eject fdisk 52s gcc-15-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnu-coreutils grep 52s libapparmor1 libapt-pkg7.0 libatomic1 libaudit-common libaudit1 libbinutils 52s libblkid1 libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 libdpkg-perl 52s libdrm-common libdrm2 libelf1t64 libfdisk1 libfribidi0 libgcc-s1 52s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpg-error-l10n 52s libgpg-error0 libhogweed6t64 libjson-c5 liblastlog2-2 libmount1 52s libnettle8t64 libnewt0.52 libnftables1 libnl-3-200 libnl-route-3-200 52s libp11-kit0 libpython3.13-minimal libpython3.13-stdlib librtmp1 libseccomp2 52s libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe2 52s libsmartcols1 libstdc++6 libuchardet0 libuuid1 libxml2-16 login 52s lto-disabled-list mount nano nftables publicsuffix python-apt-common 52s python3-apt python3-bcrypt python3-blinker python3-cffi-backend python3-dbus 52s python3-gdbm python3-inflect python3-jwt python3-lazr.uri python3-markupsafe 52s python3-more-itertools python3-oauthlib python3-openssl python3-pyparsing 52s python3-yaml python3-zipp python3.13 python3.13-gdbm python3.13-minimal 52s sensible-utils sudo-rs tzdata ubuntu-pro-client ubuntu-pro-client-l10n 52s usb.ids util-linux uuid-runtime whiptail 53s 105 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 28.4 MB of archives. 53s After this operation, 1137 kB of additional disk space will be used. 53s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf base-files armhf 14ubuntu4 [75.4 kB] 53s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libatomic1 armhf 15.2.0-7ubuntu1 [7818 B] 53s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-base armhf 15.2.0-7ubuntu1 [58.4 kB] 53s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-s1 armhf 15.2.0-7ubuntu1 [40.5 kB] 53s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++6 armhf 15.2.0-7ubuntu1 [731 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libapt-pkg7.0 armhf 3.1.11 [1157 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg armhf 1.22.21ubuntu4 [1245 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf grep armhf 3.12-1 [165 kB] 53s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf eject armhf 2.41.2-4ubuntu1 [65.9 kB] 53s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf fdisk armhf 2.41.2-4ubuntu1 [164 kB] 53s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libblkid1 armhf 2.41.2-4ubuntu1 [174 kB] 53s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libmount1 armhf 2.41.2-4ubuntu1 [206 kB] 53s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libsmartcols1 armhf 2.41.2-4ubuntu1 [143 kB] 53s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf mount armhf 2.41.2-4ubuntu1 [166 kB] 53s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf uuid-runtime armhf 2.41.2-4ubuntu1 [67.6 kB] 53s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libuuid1 armhf 2.41.2-4ubuntu1 [43.8 kB] 53s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libfdisk1 armhf 2.41.2-4ubuntu1 [222 kB] 53s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf bsdutils armhf 1:2.41.2-4ubuntu1 [98.2 kB] 53s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf util-linux armhf 2.41.2-4ubuntu1 [1146 kB] 53s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf bsdextrautils armhf 2.41.2-4ubuntu1 [101 kB] 53s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libselinux1 armhf 3.8.1-1build2 [81.3 kB] 53s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libseccomp2 armhf 2.6.0-2ubuntu3 [53.5 kB] 53s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf apt armhf 3.1.11 [1434 kB] 54s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf gnu-coreutils armhf 9.7-3ubuntu1 [1209 kB] 54s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit-common all 1:4.0.5-1build2 [6596 B] 54s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libcap-ng0 armhf 0.8.5-4build3 [14.0 kB] 54s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit1 armhf 1:4.0.5-1build2 [51.7 kB] 54s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf login armhf 1:4.16.0-2+really2.41.2-4ubuntu1 [109 kB] 54s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13 armhf 3.13.9-1 [753 kB] 54s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-minimal armhf 3.13.9-1 [2058 kB] 54s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-stdlib armhf 3.13.9-1 [1957 kB] 54s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-minimal armhf 3.13.9-1 [873 kB] 54s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf tzdata all 2025b-5ubuntu1 [198 kB] 54s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf liblastlog2-2 armhf 2.41.2-4ubuntu1 [34.6 kB] 54s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage-common all 3.8.1-1build1 [7916 B] 54s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libsepol2 armhf 3.9-2 [286 kB] 54s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage2 armhf 3.8.1-1build1 [89.2 kB] 54s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libgpg-error-l10n all 1.56-2 [9066 B] 54s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libgpg-error0 armhf 1.56-2 [69.2 kB] 54s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf sensible-utils all 0.0.26 [27.0 kB] 54s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf distro-info-data all 0.68 [7378 B] 54s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-girepository-2.0 armhf 1.86.0-6 [25.3 kB] 54s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-glib-2.0 armhf 2.86.1-1 [182 kB] 54s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libglib2.0-0t64 armhf 2.86.1-1 [1482 kB] 54s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libgirepository-1.0-1 armhf 1.86.0-6 [111 kB] 54s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libapparmor1 armhf 5.0.0~alpha1-0ubuntu8.1 [52.9 kB] 54s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libelf1t64 armhf 0.193-3 [50.9 kB] 54s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libfribidi0 armhf 1.0.16-3 [24.1 kB] 54s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libglib2.0-data all 2.86.1-1 [56.7 kB] 54s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libnettle8t64 armhf 3.10.2-1 [189 kB] 54s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf libhogweed6t64 armhf 3.10.2-1 [188 kB] 54s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-c5 armhf 0.18+ds-1.1 [33.3 kB] 54s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf libnewt0.52 armhf 0.52.25-1ubuntu2 [39.9 kB] 54s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libp11-kit0 armhf 0.25.9-2 [265 kB] 54s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf libxml2-16 armhf 2.14.5+dfsg-0.2build1 [527 kB] 54s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf python-apt-common all 3.0.0ubuntu2 [21.7 kB] 54s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf python3-apt armhf 3.0.0ubuntu2 [189 kB] 54s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cffi-backend armhf 2.0.0-2 [99.1 kB] 54s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf python3-dbus armhf 1.4.0-1build1 [113 kB] 54s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf python3-yaml armhf 6.0.2-2 [181 kB] 54s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf sudo-rs armhf 0.2.8-1ubuntu5.1 [548 kB] 54s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-pro-client-l10n armhf 37.1ubuntu0 [19.8 kB] 54s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-pro-client armhf 37.1ubuntu0 [260 kB] 54s Get:64 http://ftpmaster.internal/ubuntu resolute/main armhf whiptail armhf 0.52.25-1ubuntu2 [17.1 kB] 54s Get:65 http://ftpmaster.internal/ubuntu resolute/main armhf apparmor armhf 5.0.0~alpha1-0ubuntu8.1 [631 kB] 54s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-dnsutils armhf 1:9.20.11-1ubuntu3 [156 kB] 54s Get:67 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-host armhf 1:9.20.11-1ubuntu3 [46.5 kB] 54s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-libs armhf 1:9.20.11-1ubuntu3 [1202 kB] 54s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm-common all 2.4.127-1ubuntu1 [9716 B] 54s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm2 armhf 2.4.127-1ubuntu1 [37.8 kB] 54s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf nftables armhf 1.1.5-2 [73.2 kB] 54s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf libnftables1 armhf 1.1.5-2 [329 kB] 54s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf libnl-route-3-200 armhf 3.11.0-2 [173 kB] 54s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf libnl-3-200 armhf 3.11.0-2 [51.2 kB] 54s Get:75 http://ftpmaster.internal/ubuntu resolute/main armhf libuchardet0 armhf 0.0.8-2 [74.1 kB] 54s Get:76 http://ftpmaster.internal/ubuntu resolute/main armhf nano armhf 8.6-1 [279 kB] 54s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf publicsuffix all 20251016.1743-0.1 [136 kB] 54s Get:78 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-gdbm armhf 3.13.9-1 [30.9 kB] 54s Get:79 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-gdbm armhf 3.14.0-4 [31.3 kB] 54s Get:80 http://ftpmaster.internal/ubuntu resolute/main armhf python3-gdbm armhf 3.13.9-1 [8884 B] 54s Get:81 http://ftpmaster.internal/ubuntu resolute/main armhf usb.ids all 2025.09.15-1 [224 kB] 54s Get:82 http://ftpmaster.internal/ubuntu resolute/main armhf libctf0 armhf 2.45-8ubuntu1 [75.7 kB] 54s Get:83 http://ftpmaster.internal/ubuntu resolute/main armhf libctf-nobfd0 armhf 2.45-8ubuntu1 [78.9 kB] 54s Get:84 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-arm-linux-gnueabihf armhf 2.45-8ubuntu1 [1022 kB] 54s Get:85 http://ftpmaster.internal/ubuntu resolute/main armhf libbinutils armhf 2.45-8ubuntu1 [411 kB] 54s Get:86 http://ftpmaster.internal/ubuntu resolute/main armhf binutils armhf 2.45-8ubuntu1 [3234 B] 54s Get:87 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-common armhf 2.45-8ubuntu1 [221 kB] 54s Get:88 http://ftpmaster.internal/ubuntu resolute/main armhf libsframe2 armhf 2.45-8ubuntu1 [13.3 kB] 54s Get:89 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB] 55s Get:90 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B] 55s Get:91 http://ftpmaster.internal/ubuntu resolute/main armhf python3-blinker all 1.9.0-2 [10.8 kB] 55s Get:92 http://ftpmaster.internal/ubuntu resolute/main armhf python3-jwt all 2.10.1-3 [21.1 kB] 55s Get:93 http://ftpmaster.internal/ubuntu resolute/main armhf python3-oauthlib all 3.3.1-1 [93.5 kB] 55s Get:94 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg-dev all 1.22.21ubuntu4 [1088 kB] 55s Get:95 http://ftpmaster.internal/ubuntu resolute/main armhf libdpkg-perl all 1.22.21ubuntu4 [280 kB] 55s Get:96 http://ftpmaster.internal/ubuntu resolute/main armhf lto-disabled-list all 71 [12.5 kB] 55s Get:97 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.1.0-2build6 [320 kB] 55s Get:98 http://ftpmaster.internal/ubuntu resolute/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-3 [52.1 kB] 55s Get:99 http://ftpmaster.internal/ubuntu resolute/main armhf python3-more-itertools all 10.8.0-1 [63.5 kB] 55s Get:100 http://ftpmaster.internal/ubuntu resolute/main armhf python3-inflect all 7.5.0-1 [33.9 kB] 55s Get:101 http://ftpmaster.internal/ubuntu resolute/main armhf python3-lazr.uri all 1.0.6-7 [13.8 kB] 55s Get:102 http://ftpmaster.internal/ubuntu resolute/main armhf python3-markupsafe armhf 3.0.3-1 [12.1 kB] 55s Get:103 http://ftpmaster.internal/ubuntu resolute/main armhf python3-openssl all 25.1.0-1 [46.4 kB] 55s Get:104 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pyparsing all 3.1.3-1 [87.0 kB] 55s Get:105 http://ftpmaster.internal/ubuntu resolute/main armhf python3-zipp all 3.23.0-1 [10.4 kB] 55s Get:106 http://ftpmaster.internal/ubuntu resolute/main armhf python3-bcrypt armhf 4.3.0-2 [251 kB] 56s Preconfiguring packages ... 56s Fetched 28.4 MB in 3s (10.5 MB/s) 56s (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 ... 61081 files and directories currently installed.) 56s Preparing to unpack .../base-files_14ubuntu4_armhf.deb ... 56s Unpacking base-files (14ubuntu4) over (14ubuntu3) ... 56s Setting up base-files (14ubuntu4) ... 56s Installing new version of config file /etc/issue ... 56s Installing new version of config file /etc/issue.net ... 56s Installing new version of config file /etc/lsb-release ... 57s motd-news.service is a disabled or a static unit not running, not starting it. 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libatomic1_15.2.0-7ubuntu1_armhf.deb ... 57s Unpacking libatomic1:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 57s Preparing to unpack .../gcc-15-base_15.2.0-7ubuntu1_armhf.deb ... 57s Unpacking gcc-15-base:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up gcc-15-base:armhf (15.2.0-7ubuntu1) ... 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libgcc-s1_15.2.0-7ubuntu1_armhf.deb ... 57s Unpacking libgcc-s1:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up libgcc-s1:armhf (15.2.0-7ubuntu1) ... 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libstdc++6_15.2.0-7ubuntu1_armhf.deb ... 57s Unpacking libstdc++6:armhf (15.2.0-7ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up libstdc++6:armhf (15.2.0-7ubuntu1) ... 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libapt-pkg7.0_3.1.11_armhf.deb ... 57s Unpacking libapt-pkg7.0:armhf (3.1.11) over (3.1.6ubuntu2) ... 57s Setting up libapt-pkg7.0:armhf (3.1.11) ... 57s (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 ... 61082 files and directories currently installed.) 57s Preparing to unpack .../dpkg_1.22.21ubuntu4_armhf.deb ... 57s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 58s Setting up dpkg (1.22.21ubuntu4) ... 58s (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 ... 61082 files and directories currently installed.) 58s Preparing to unpack .../archives/grep_3.12-1_armhf.deb ... 58s Unpacking grep (3.12-1) over (3.11-4build1) ... 58s Setting up grep (3.12-1) ... 58s (Reading database ... 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.../38-python3.13-gdbm_3.13.9-1_armhf.deb ... 66s Unpacking python3.13-gdbm (3.13.9-1) over (3.13.7-1) ... 66s Selecting previously unselected package python3.14-gdbm. 66s Preparing to unpack .../39-python3.14-gdbm_3.14.0-4_armhf.deb ... 66s Unpacking python3.14-gdbm (3.14.0-4) ... 66s Preparing to unpack .../40-python3-gdbm_3.13.9-1_armhf.deb ... 66s Unpacking python3-gdbm:armhf (3.13.9-1) over (3.13.5-1) ... 66s Preparing to unpack .../41-usb.ids_2025.09.15-1_all.deb ... 66s Unpacking usb.ids (2025.09.15-1) over (2025.07.26-1) ... 66s Preparing to unpack .../42-libctf0_2.45-8ubuntu1_armhf.deb ... 66s Unpacking libctf0:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../43-libctf-nobfd0_2.45-8ubuntu1_armhf.deb ... 66s Unpacking libctf-nobfd0:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../44-binutils-arm-linux-gnueabihf_2.45-8ubuntu1_armhf.deb ... 66s Unpacking binutils-arm-linux-gnueabihf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../45-libbinutils_2.45-8ubuntu1_armhf.deb ... 66s Unpacking libbinutils:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../46-binutils_2.45-8ubuntu1_armhf.deb ... 66s Unpacking binutils (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../47-binutils-common_2.45-8ubuntu1_armhf.deb ... 66s Unpacking binutils-common:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../48-libsframe2_2.45-8ubuntu1_armhf.deb ... 66s Unpacking libsframe2:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../49-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ... 67s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 67s Preparing to unpack .../50-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ... 67s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 67s Preparing to unpack .../51-python3-blinker_1.9.0-2_all.deb ... 67s Unpacking python3-blinker (1.9.0-2) over (1.9.0-1) ... 67s Preparing to unpack .../52-python3-jwt_2.10.1-3_all.deb ... 67s Unpacking python3-jwt (2.10.1-3) over (2.10.1-2) ... 67s Preparing to unpack .../53-python3-oauthlib_3.3.1-1_all.deb ... 67s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 67s Preparing to unpack .../54-dpkg-dev_1.22.21ubuntu4_all.deb ... 67s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 67s Preparing to unpack .../55-libdpkg-perl_1.22.21ubuntu4_all.deb ... 67s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 67s Preparing to unpack .../56-lto-disabled-list_71_all.deb ... 67s Unpacking lto-disabled-list (71) over (69) ... 67s Preparing to unpack .../57-libbrotli1_1.1.0-2build6_armhf.deb ... 67s Unpacking libbrotli1:armhf (1.1.0-2build6) over (1.1.0-2build5) ... 67s Preparing to unpack .../58-librtmp1_2.4+20151223.gitfa8646d.1-3_armhf.deb ... 67s Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-3) over (2.4+20151223.gitfa8646d.1-2build8) ... 68s Preparing to unpack .../59-python3-more-itertools_10.8.0-1_all.deb ... 68s Unpacking python3-more-itertools (10.8.0-1) over (10.7.0-1) ... 68s Preparing to unpack .../60-python3-inflect_7.5.0-1_all.deb ... 68s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 68s Preparing to unpack .../61-python3-lazr.uri_1.0.6-7_all.deb ... 68s Unpacking python3-lazr.uri (1.0.6-7) over (1.0.6-6) ... 68s Preparing to unpack .../62-python3-markupsafe_3.0.3-1_armhf.deb ... 68s Unpacking python3-markupsafe (3.0.3-1) over (2.1.5-1build4) ... 68s Preparing to unpack .../63-python3-openssl_25.1.0-1_all.deb ... 68s Unpacking python3-openssl (25.1.0-1) over (25.0.0-1) ... 68s Preparing to unpack .../64-python3-pyparsing_3.1.3-1_all.deb ... 68s Unpacking python3-pyparsing (3.1.3-1) over (3.1.2-1) ... 68s Preparing to unpack .../65-python3-zipp_3.23.0-1_all.deb ... 68s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 68s Preparing to unpack .../66-python3-bcrypt_4.3.0-2_armhf.deb ... 68s Unpacking python3-bcrypt (4.3.0-2) over (4.2.0-2.1build1) ... 69s Setting up python3-more-itertools (10.8.0-1) ... 69s Setting up lto-disabled-list (71) ... 69s Setting up libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) ... 69s Setting up libnewt0.52:armhf (0.52.25-1ubuntu2) ... 69s Setting up libnftables1:armhf (1.1.5-2) ... 69s Setting up nftables (1.1.5-2) ... 69s Setting up bsdextrautils (2.41.2-4ubuntu1) ... 69s Setting up python3-jwt (2.10.1-3) ... 69s Setting up distro-info-data (0.68) ... 69s Setting up libxml2-16:armhf (2.14.5+dfsg-0.2build1) ... 69s Setting up libsframe2:armhf (2.45-8ubuntu1) ... 69s Setting up python3-openssl (25.1.0-1) ... 70s Setting up python3-bcrypt (4.3.0-2) ... 70s Setting up libbrotli1:armhf (1.1.0-2build6) ... 70s Setting up binutils-common:armhf (2.45-8ubuntu1) ... 70s Setting up libctf-nobfd0:armhf (2.45-8ubuntu1) ... 70s Setting up python3-yaml (6.0.2-2) ... 70s Setting up python3-lazr.uri (1.0.6-7) ... 70s Setting up python3-zipp (3.23.0-1) ... 70s Setting up python3-markupsafe (3.0.3-1) ... 70s Setting up libelf1t64:armhf (0.193-3) ... 70s Setting up tzdata (2025b-5ubuntu1) ... 70s 70s Current default time zone: 'Etc/UTC' 70s Local time is now: Sat Nov 1 13:20:07 UTC 2025. 70s Universal Time is now: Sat Nov 1 13:20:07 UTC 2025. 70s Run 'dpkg-reconfigure tzdata' if you wish to change it. 70s 70s Setting up eject (2.41.2-4ubuntu1) ... 70s Setting up libpython3.13-minimal:armhf (3.13.9-1) ... 70s Setting up apparmor (5.0.0~alpha1-0ubuntu8.1) ... 70s Installing new version of config file /etc/apparmor.d/fusermount3 ... 71s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 72s Reloading AppArmor profiles 72s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "babeld". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "alsamixer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "bwrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "bgpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "bfdd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "eigrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "dnstracer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "hostname". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "iotop-c". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "dig". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "fabricd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "fusermount3". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "isisd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "gs". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ldpd". /sbin/apparmor_parser: Unable to replace "compressor". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "locale". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "john". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Unable to replace "lsblk". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "irssi". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "linux-boot-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "lsusb". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "mosquitto". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "nslookup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "nhrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "mbsync". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ospf6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "os-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "notify-send". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "nc.openbsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ospfd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "pathd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "pim6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "pbrd". /sbin/apparmor_parser: Unable to replace "ripd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "pimd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ripngd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "openvpn". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "qpdf". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "proftpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "staticd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ssh-keyscan". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "tinyproxy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "systemd-detect-virt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "mx-extract". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "rygel". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "cmds". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "tnftp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "wg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "/usr/sbin/chronyd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "dumpcap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "tshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Unable to replace "vrrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "who". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "znc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 72s /sbin/apparmor_parser: Unable to replace "wg-quick". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 72s 73s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 73s 73s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 73s 73s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 73s 73s Error: At least one profile failed to load 73s Setting up python3-inflect (7.5.0-1) ... 73s Setting up libnettle8t64:armhf (3.10.2-1) ... 73s Setting up libglib2.0-data (2.86.1-1) ... 73s Setting up python3-pyparsing (3.1.3-1) ... 73s Setting up python3.14-gdbm (3.14.0-4) ... 73s Setting up libfribidi0:armhf (1.0.16-3) ... 73s Setting up libp11-kit0:armhf (0.25.9-2) ... 73s Setting up libatomic1:armhf (15.2.0-7ubuntu1) ... 73s Setting up usb.ids (2025.09.15-1) ... 73s Setting up libdpkg-perl (1.22.21ubuntu4) ... 73s Setting up libfdisk1:armhf (2.41.2-4ubuntu1) ... 73s Setting up nano (8.6-1) ... 73s Installing new version of config file /etc/nanorc ... 73s Setting up whiptail (0.52.25-1ubuntu2) ... 73s Setting up python-apt-common (3.0.0ubuntu2) ... 73s Setting up libhogweed6t64:armhf (3.10.2-1) ... 73s Setting up mount (2.41.2-4ubuntu1) ... 73s Setting up sensible-utils (0.0.26) ... 73s Setting up uuid-runtime (2.41.2-4ubuntu1) ... 74s uuidd.service is a disabled or a static unit not running, not starting it. 74s Setting up libuchardet0:armhf (0.0.8-2) ... 74s Setting up libnl-3-200:armhf (3.11.0-2) ... 74s Setting up python3.13-minimal (3.13.9-1) ... 75s Setting up libbinutils:armhf (2.45-8ubuntu1) ... 75s Setting up libgpg-error-l10n (1.56-2) ... 75s Setting up libdrm-common (2.4.127-1ubuntu1) ... 75s Setting up libpython3.13-stdlib:armhf (3.13.9-1) ... 75s Setting up libjson-c5:armhf (0.18+ds-1.1) ... 75s Setting up publicsuffix (20251016.1743-0.1) ... 75s Setting up sudo-rs (0.2.8-1ubuntu5.1) ... 75s Setting up python3-cffi-backend:armhf (2.0.0-2) ... 75s Setting up python3.13-gdbm (3.13.9-1) ... 75s Setting up login (1:4.16.0-2+really2.41.2-4ubuntu1) ... 75s Setting up python3-blinker (1.9.0-2) ... 75s Setting up libctf0:armhf (2.45-8ubuntu1) ... 75s Setting up bind9-libs:armhf (1:9.20.11-1ubuntu3) ... 75s Setting up python3.13 (3.13.9-1) ... 76s Setting up python3-gdbm:armhf (3.13.9-1) ... 76s Setting up python3-apt (3.0.0ubuntu2) ... 76s Setting up fdisk (2.41.2-4ubuntu1) ... 76s Setting up libnl-route-3-200:armhf (3.11.0-2) ... 76s Setting up libglib2.0-0t64:armhf (2.86.1-1) ... 76s No schema files found: doing nothing. 76s Setting up python3-oauthlib (3.3.1-1) ... 76s Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-3) ... 76s Setting up gir1.2-glib-2.0:armhf (2.86.1-1) ... 76s Setting up libdrm2:armhf (2.4.127-1ubuntu1) ... 76s Setting up libgirepository-1.0-1:armhf (1.86.0-6) ... 76s Setting up bind9-host (1:9.20.11-1ubuntu3) ... 76s Setting up binutils-arm-linux-gnueabihf (2.45-8ubuntu1) ... 76s Setting up ubuntu-pro-client (37.1ubuntu0) ... 77s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 77s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 77s 78s Setting up ubuntu-pro-client-l10n (37.1ubuntu0) ... 78s Setting up python3-dbus (1.4.0-1build1) ... 78s Setting up binutils (2.45-8ubuntu1) ... 78s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ... 78s Encountered debconf setting for cloud-init-base/datasources. 80s Setting up dpkg-dev (1.22.21ubuntu4) ... 80s Setting up gir1.2-girepository-2.0:armhf (1.86.0-6) ... 80s Setting up bind9-dnsutils (1:9.20.11-1ubuntu3) ... 80s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ... 80s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 80s Processing triggers for systemd (257.9-0ubuntu2) ... 80s Processing triggers for man-db (2.13.1-1) ... 82s Processing triggers for plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu1) ... 82s Processing triggers for procps (2:4.0.4-8ubuntu3) ... 82s Processing triggers for install-info (7.1.1-1ubuntu1) ... 82s Processing triggers for libc-bin (2.42-0ubuntu3) ... 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Solving dependencies... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s autopkgtest [13:20:25]: rebooting testbed after setup commands that affected boot 129s autopkgtest [13:21:06]: testbed running kernel: Linux 6.8.0-86-generic #87~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 29 09:26:46 UTC 2 155s autopkgtest [13:21:32]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 171s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (dsc) [2286 B] 171s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (tar) [5748 kB] 171s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-2 (diff) [26.8 kB] 171s gpgv: Signature made Sun Apr 6 17:54:51 2025 UTC 171s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 171s gpgv: issuer "emollier@debian.org" 171s gpgv: Can't check signature: No public key 171s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-2.dsc: no acceptable signature found 171s autopkgtest [13:21:48]: testing package bbmap version 39.20+dfsg-2 173s autopkgtest [13:21:50]: build not needed 176s autopkgtest [13:21:53]: test run-unit-test: preparing testbed 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Solving dependencies... 179s The following NEW packages will be installed: 179s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 179s libapache-pom-java libcommons-cli-java libcommons-codec-java 179s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 179s libjs-jquery libjs-sphinxdoc libjs-underscore liblcms2-2 liblog4j1.2-java 179s libmpj-java libnspr4 libnss3 libpcsclite1 openjdk-21-jre-headless 179s python-biopython-doc 179s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 179s Need to get 72.6 MB of archives. 179s After this operation, 227 MB of additional disk space will be used. 179s Get:1 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-cli-java all 1.6.0-1 [59.9 kB] 179s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf libapache-pom-java all 33-2 [5874 B] 179s Get:3 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 179s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-codec-java all 1.18.0-1 [303 kB] 179s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf libcommons-io-java all 2.19.0-1 [491 kB] 179s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf liblog4j1.2-java all 1.2.17-11 [439 kB] 179s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf libmpj-java all 0.44+dfsg-4 [443 kB] 179s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf ca-certificates-java all 20240118 [11.6 kB] 179s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf java-common all 0.76 [6852 B] 179s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 180s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu2 [127 kB] 180s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 180s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libnspr4 armhf 2:4.36-1ubuntu2 [95.6 kB] 180s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libnss3 armhf 2:3.114-1 [1323 kB] 180s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libpcsclite1 armhf 2.3.3-1 [24.8 kB] 180s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf openjdk-21-jre-headless armhf 21.0.9+10-1 [39.8 MB] 188s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf default-jre-headless armhf 2:1.21-76 [3182 B] 188s Get:18 http://ftpmaster.internal/ubuntu resolute/universe armhf bbmap all 39.20+dfsg-2 [10.6 MB] 190s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf bbmap-jni armhf 39.20+dfsg-2 [20.7 kB] 190s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 190s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 190s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 190s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 194s Fetched 72.6 MB in 15s (4759 kB/s) 194s Selecting previously unselected package libcommons-cli-java. 194s (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 ... 61071 files and directories currently installed.) 194s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 194s Unpacking libcommons-cli-java (1.6.0-1) ... 194s Selecting previously unselected package libapache-pom-java. 194s Preparing to unpack .../01-libapache-pom-java_33-2_all.deb ... 194s Unpacking libapache-pom-java (33-2) ... 194s Selecting previously unselected package libcommons-parent-java. 195s Preparing to unpack .../02-libcommons-parent-java_56-1_all.deb ... 195s Unpacking libcommons-parent-java (56-1) ... 195s Selecting previously unselected package libcommons-codec-java. 195s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 195s Unpacking libcommons-codec-java (1.18.0-1) ... 195s Selecting previously unselected package libcommons-io-java. 195s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 195s Unpacking libcommons-io-java (2.19.0-1) ... 195s Selecting previously unselected package liblog4j1.2-java. 195s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11_all.deb ... 195s Unpacking liblog4j1.2-java (1.2.17-11) ... 195s Selecting previously unselected package libmpj-java. 195s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4_all.deb ... 195s Unpacking libmpj-java (0.44+dfsg-4) ... 195s Selecting previously unselected package ca-certificates-java. 195s Preparing to unpack .../07-ca-certificates-java_20240118_all.deb ... 195s Unpacking ca-certificates-java (20240118) ... 195s Selecting previously unselected package java-common. 195s Preparing to unpack .../08-java-common_0.76_all.deb ... 195s Unpacking java-common (0.76) ... 195s Selecting previously unselected package liblcms2-2:armhf. 195s Preparing to unpack .../09-liblcms2-2_2.16-2_armhf.deb ... 195s Unpacking liblcms2-2:armhf (2.16-2) ... 195s Selecting previously unselected package libjpeg-turbo8:armhf. 195s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu2_armhf.deb ... 195s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 195s Selecting previously unselected package libjpeg8:armhf. 195s Preparing to unpack .../11-libjpeg8_8c-2ubuntu11_armhf.deb ... 195s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 195s Selecting previously unselected package libnspr4:armhf. 195s Preparing to unpack .../12-libnspr4_2%3a4.36-1ubuntu2_armhf.deb ... 195s Unpacking libnspr4:armhf (2:4.36-1ubuntu2) ... 195s Selecting previously unselected package libnss3:armhf. 195s Preparing to unpack .../13-libnss3_2%3a3.114-1_armhf.deb ... 195s Unpacking libnss3:armhf (2:3.114-1) ... 195s Selecting previously unselected package libpcsclite1:armhf. 195s Preparing to unpack .../14-libpcsclite1_2.3.3-1_armhf.deb ... 195s Unpacking libpcsclite1:armhf (2.3.3-1) ... 195s Selecting previously unselected package openjdk-21-jre-headless:armhf. 195s Preparing to unpack .../15-openjdk-21-jre-headless_21.0.9+10-1_armhf.deb ... 195s Unpacking openjdk-21-jre-headless:armhf (21.0.9+10-1) ... 196s Selecting previously unselected package default-jre-headless. 196s Preparing to unpack .../16-default-jre-headless_2%3a1.21-76_armhf.deb ... 196s Unpacking default-jre-headless (2:1.21-76) ... 196s Selecting previously unselected package bbmap. 196s Preparing to unpack .../17-bbmap_39.20+dfsg-2_all.deb ... 196s Unpacking bbmap (39.20+dfsg-2) ... 196s Selecting previously unselected package bbmap-jni. 196s Preparing to unpack .../18-bbmap-jni_39.20+dfsg-2_armhf.deb ... 196s Unpacking bbmap-jni (39.20+dfsg-2) ... 196s Selecting previously unselected package libjs-jquery. 196s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 196s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 196s Selecting previously unselected package libjs-underscore. 196s Preparing to unpack .../20-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 196s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 196s Selecting previously unselected package libjs-sphinxdoc. 196s Preparing to unpack .../21-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 196s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 196s Selecting previously unselected package python-biopython-doc. 196s Preparing to unpack .../22-python-biopython-doc_1.85+dfsg-4_all.deb ... 196s Unpacking python-biopython-doc (1.85+dfsg-4) ... 197s Setting up liblcms2-2:armhf (2.16-2) ... 197s Setting up java-common (0.76) ... 197s Setting up libcommons-cli-java (1.6.0-1) ... 197s Setting up liblog4j1.2-java (1.2.17-11) ... 197s Setting up libnspr4:armhf (2:4.36-1ubuntu2) ... 197s Setting up libapache-pom-java (33-2) ... 197s Setting up libpcsclite1:armhf (2.3.3-1) ... 197s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu2) ... 197s Setting up bbmap-jni (39.20+dfsg-2) ... 197s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 197s Setting up ca-certificates-java (20240118) ... 197s No JRE found. Skipping Java certificates setup. 197s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 197s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 197s Setting up libcommons-parent-java (56-1) ... 197s Setting up libnss3:armhf (2:3.114-1) ... 197s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 197s Setting up python-biopython-doc (1.85+dfsg-4) ... 197s Setting up libcommons-codec-java (1.18.0-1) ... 197s Setting up openjdk-21-jre-headless:armhf (21.0.9+10-1) ... 197s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode 197s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 197s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 197s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 197s update-alternatives: using /usr/lib/jvm/java-21-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 197s Setting up libcommons-io-java (2.19.0-1) ... 197s Setting up libmpj-java (0.44+dfsg-4) ... 197s Processing triggers for libc-bin (2.42-0ubuntu3) ... 197s Processing triggers for man-db (2.13.1-1) ... 197s Processing triggers for ca-certificates-java (20240118) ... 198s Adding debian:ACCVRAIZ1.pem 198s Adding debian:AC_RAIZ_FNMT-RCM.pem 198s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 198s Adding debian:ANF_Secure_Server_Root_CA.pem 198s Adding debian:Actalis_Authentication_Root_CA.pem 198s Adding debian:AffirmTrust_Commercial.pem 198s Adding debian:AffirmTrust_Networking.pem 198s Adding debian:AffirmTrust_Premium.pem 198s Adding debian:AffirmTrust_Premium_ECC.pem 198s Adding debian:Amazon_Root_CA_1.pem 198s Adding debian:Amazon_Root_CA_2.pem 198s Adding debian:Amazon_Root_CA_3.pem 198s Adding debian:Amazon_Root_CA_4.pem 198s Adding debian:Atos_TrustedRoot_2011.pem 198s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 198s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 198s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 198s Adding debian:BJCA_Global_Root_CA1.pem 198s Adding debian:BJCA_Global_Root_CA2.pem 198s Adding debian:Baltimore_CyberTrust_Root.pem 198s Adding debian:Buypass_Class_2_Root_CA.pem 198s Adding debian:Buypass_Class_3_Root_CA.pem 198s Adding debian:CA_Disig_Root_R2.pem 198s Adding debian:CFCA_EV_ROOT.pem 198s Adding debian:COMODO_Certification_Authority.pem 198s Adding debian:COMODO_ECC_Certification_Authority.pem 198s Adding debian:COMODO_RSA_Certification_Authority.pem 198s Adding debian:Certainly_Root_E1.pem 198s Adding debian:Certainly_Root_R1.pem 198s Adding debian:Certigna.pem 198s Adding debian:Certigna_Root_CA.pem 198s Adding debian:Certum_EC-384_CA.pem 198s Adding debian:Certum_Trusted_Network_CA.pem 198s Adding debian:Certum_Trusted_Network_CA_2.pem 198s Adding debian:Certum_Trusted_Root_CA.pem 198s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 198s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 198s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 198s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 198s Adding debian:Comodo_AAA_Services_root.pem 198s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 198s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 198s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 198s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 198s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 198s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 198s Adding debian:DigiCert_Assured_ID_Root_CA.pem 198s Adding debian:DigiCert_Assured_ID_Root_G2.pem 198s Adding debian:DigiCert_Assured_ID_Root_G3.pem 198s Adding debian:DigiCert_Global_Root_CA.pem 198s Adding debian:DigiCert_Global_Root_G2.pem 198s Adding debian:DigiCert_Global_Root_G3.pem 198s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 198s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 198s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 198s Adding debian:DigiCert_Trusted_Root_G4.pem 198s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 198s Adding debian:Entrust_Root_Certification_Authority.pem 198s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 198s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 198s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 198s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 198s Adding debian:GLOBALTRUST_2020.pem 198s Adding debian:GTS_Root_R1.pem 198s Adding debian:GTS_Root_R2.pem 198s Adding debian:GTS_Root_R3.pem 198s Adding debian:GTS_Root_R4.pem 198s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 198s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 198s Adding debian:GlobalSign_Root_CA.pem 198s Adding debian:GlobalSign_Root_CA_-_R3.pem 198s Adding debian:GlobalSign_Root_CA_-_R6.pem 198s Adding debian:GlobalSign_Root_E46.pem 198s Adding debian:GlobalSign_Root_R46.pem 198s Adding debian:Go_Daddy_Class_2_CA.pem 198s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 198s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 198s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 198s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 198s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 198s Adding debian:HiPKI_Root_CA_-_G1.pem 198s Adding debian:Hongkong_Post_Root_CA_3.pem 198s Adding debian:ISRG_Root_X1.pem 198s Adding debian:ISRG_Root_X2.pem 198s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 198s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 198s Adding debian:Izenpe.com.pem 198s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 198s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 198s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 198s Adding debian:NAVER_Global_Root_Certification_Authority.pem 198s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 198s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 198s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 198s Adding debian:QuoVadis_Root_CA_1_G3.pem 198s Adding debian:QuoVadis_Root_CA_2.pem 198s Adding debian:QuoVadis_Root_CA_2_G3.pem 198s Adding debian:QuoVadis_Root_CA_3.pem 198s Adding debian:QuoVadis_Root_CA_3_G3.pem 198s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 198s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 198s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 198s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 198s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 198s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 198s Adding debian:SZAFIR_ROOT_CA2.pem 198s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 198s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 198s Adding debian:SecureSign_Root_CA12.pem 198s Adding debian:SecureSign_Root_CA14.pem 198s Adding debian:SecureSign_Root_CA15.pem 198s Adding debian:SecureTrust_CA.pem 198s Adding debian:Secure_Global_CA.pem 198s Adding debian:Security_Communication_ECC_RootCA1.pem 198s Adding debian:Security_Communication_RootCA2.pem 198s Adding debian:Starfield_Class_2_CA.pem 198s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 198s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 198s Adding debian:SwissSign_Gold_CA_-_G2.pem 198s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 198s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 198s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 198s Adding debian:TWCA_CYBER_Root_CA.pem 198s Adding debian:TWCA_Global_Root_CA.pem 198s Adding debian:TWCA_Root_Certification_Authority.pem 198s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 198s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 198s Adding debian:TeliaSonera_Root_CA_v1.pem 198s Adding debian:Telia_Root_CA_v2.pem 198s Adding debian:TrustAsia_Global_Root_CA_G3.pem 198s Adding debian:TrustAsia_Global_Root_CA_G4.pem 198s Adding debian:Trustwave_Global_Certification_Authority.pem 198s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 198s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 198s Adding debian:TunTrust_Root_CA.pem 198s Adding debian:UCA_Extended_Validation_Root.pem 198s Adding debian:UCA_Global_G2_Root.pem 198s Adding debian:USERTrust_ECC_Certification_Authority.pem 198s Adding debian:USERTrust_RSA_Certification_Authority.pem 198s Adding debian:XRamp_Global_CA_Root.pem 198s Adding debian:certSIGN_ROOT_CA.pem 198s Adding debian:certSIGN_Root_CA_G2.pem 198s Adding debian:e-Szigno_Root_CA_2017.pem 198s Adding debian:ePKI_Root_Certification_Authority.pem 198s Adding debian:emSign_ECC_Root_CA_-_C3.pem 198s Adding debian:emSign_ECC_Root_CA_-_G3.pem 198s Adding debian:emSign_Root_CA_-_C1.pem 198s Adding debian:emSign_Root_CA_-_G1.pem 198s Adding debian:vTrus_ECC_Root_CA.pem 198s Adding debian:vTrus_Root_CA.pem 198s done. 198s Setting up bbmap (39.20+dfsg-2) ... 198s Setting up default-jre-headless (2:1.21-76) ... 208s autopkgtest [13:22:25]: test run-unit-test: [----------------------- 210s 210s # bbmap 210s bbmap.sh --version 210s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 210s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 210s BBTools version 39.20 210s For help, please run the shellscript with no parameters, or look in /docs/. 210s bbmap.sh --help 210s 210s BBMap 210s Written by Brian Bushnell, from Dec. 2010 - present 210s Last modified September 15, 2022 210s 210s Description: Fast and accurate splice-aware read aligner. 210s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 210s 210s To index: bbmap.sh ref= 210s To map: bbmap.sh in= out= 210s To map without writing an index: 210s bbmap.sh ref= in= out= nodisk 210s 210s in=stdin will accept reads from standard in, and out=stdout will write to 210s standard out, but file extensions are still needed to specify the format of the 210s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 210s standard in; out=stdout.sam.gz will write gzipped sam. 210s 210s Indexing Parameters (required when building the index): 210s nodisk=f Set to true to build index in memory and write nothing 210s to disk except output. 210s ref= Specify the reference sequence. Only do this ONCE, 210s when building the index (unless using 'nodisk'). 210s build=1 If multiple references are indexed in the same directory, 210s each needs a unique numeric ID (unless using 'nodisk'). 210s k=13 Kmer length, range 8-15. Longer is faster but uses 210s more memory. Shorter is more sensitive. 210s If indexing and mapping are done in two steps, K should 210s be specified each time. 210s path=<.> Specify the location to write the index, if you don't 210s want it in the current working directory. 210s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 210s number (reduces RAM by 50% and sensitivity slightly). 210s Should be enabled both when building the index AND 210s when mapping. 210s rebuild=f Force a rebuild of the index (ref= should be set). 210s 210s Input Parameters: 210s build=1 Designate index to use. Corresponds to the number 210s specified when building the index. 210s in= Primary reads input; required parameter. 210s in2= For paired reads in two files. 210s interleaved=auto True forces paired/interleaved input; false forces 210s single-ended mapping. If not specified, interleaved 210s status will be autodetected from read names. 210s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 210s BBMap and 6000 for BBMapPacBio. Only works for FASTA 210s input (use 'maxlen' for FASTQ input). The default for 210s bbmap.sh is 500, and for mapPacBio.sh is 6000. 210s unpigz=f Spawn a pigz (parallel gzip) process for faster 210s decompression than using Java. 210s Requires pigz to be installed. 210s touppercase=t (tuc) Convert lowercase letters in reads to upper case 210s (otherwise they will not match the reference). 210s 210s Sampling Parameters: 210s 210s reads=-1 Set to a positive number N to only process the first N 210s reads (or pairs), then quit. -1 means use all reads. 210s samplerate=1 Set to a number from 0 to 1 to randomly select that 210s fraction of reads for mapping. 1 uses all reads. 210s skipreads=0 Set to a number N to skip the first N reads (or pairs), 210s then map the rest. 210s 210s Mapping Parameters: 210s fast=f This flag is a macro which sets other paramters to run 210s faster, at reduced sensitivity. Bad for RNA-seq. 210s slow=f This flag is a macro which sets other paramters to run 210s slower, at greater sensitivity. 'vslow' is even slower. 210s maxindel=16000 Don't look for indels longer than this. Lower is faster. 210s Set to >=100k for RNAseq with long introns like mammals. 210s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 210s By default these are not sought, but may be found anyway. 210s tipsearch=100 Look this far for read-end deletions with anchors 210s shorter than K, using brute force. 210s minid=0.76 Approximate minimum alignment identity to look for. 210s Higher is faster and less sensitive. 210s minhits=1 Minimum number of seed hits required for candidate sites. 210s Higher is faster. 210s local=f Set to true to use local, rather than global, alignments. 210s This will soft-clip ugly ends of poor alignments. 210s perfectmode=f Allow only perfect mappings when set to true (very fast). 210s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 210s N's in the reference) mappings. 210s threads=auto (t) Set to number of threads desired. By default, uses 210s all cores available. 210s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 210s multiple top-scoring mapping locations). 210s best (use the first best site) 210s toss (consider unmapped) 210s random (select one top-scoring site randomly) 210s all (retain all top-scoring sites) 210s samestrandpairs=f (ssp) Specify whether paired reads should map to the 210s same strand or opposite strands. 210s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 210s orientation. Set to false for long-mate-pair libraries. 210s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 210s insert size or orientation, the read with the lower 210s mapping quality is marked unmapped. 210s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 210s be sent to 'outu' but not 'outm'. 210s rcomp=f Reverse complement both reads prior to mapping (for LMP 210s outward-facing libraries). 210s rcompmate=f Reverse complement read2 prior to mapping. 210s pairlen=32000 Set max allowed distance between paired reads. 210s (insert size)=(pairlen)+(read1 length)+(read2 length) 210s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 210s greater than this. Lower is faster. 210s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 210s is faster. 210s averagepairdist=100 (apd) Initial average distance between paired reads. 210s Varies dynamically; does not need to be specified. 210s deterministic=f Run in deterministic mode. In this case it is good 210s to set averagepairdist. BBMap is deterministic 210s without this flag if using single-ended reads, 210s or run singlethreaded. 210s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 210s fraction of read length. Faster but less accurate. 210s bandwidth=0 (bw) Set the bandwidth directly. 210s fraction of read length. Faster but less accurate. 210s usejni=f (jni) Do alignments faster, in C code. Requires 210s compiling the C code; details are in /jni/README.txt. 210s maxsites2=800 Don't analyze (or print) more than this many alignments 210s per read. 210s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 210s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 210s will ignore the most common 3% of kmers. 210s greedy=t Use a greedy algorithm to discard the least-useful 210s kmers on a per-read basis. 210s kfilter=0 If positive, potential mapping sites must have at 210s least this many consecutive exact matches. 210s 210s 210s Quality and Trimming Parameters: 210s qin=auto Set to 33 or 64 to specify input quality value ASCII 210s offset. 33 is Sanger, 64 is old Solexa. 210s qout=auto Set to 33 or 64 to specify output quality value ASCII 210s offset (only if output format is fastq). 210s qtrim=f Quality-trim ends before mapping. Options are: 210s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 210s untrim=f Undo trimming after mapping. Untrimmed bases will be 210s soft-clipped in cigar strings. 210s trimq=6 Trim regions with average quality below this 210s (phred algorithm). 210s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 210s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 210s quality strings for fasta input reads. 210s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 210s out-of-range quality values. 210s usequality=t Use quality scores when determining which read kmers 210s to use as seeds. 210s minaveragequality=0 (maq) Do not map reads with average quality below this. 210s maqb=0 If positive, calculate maq from this many initial bases. 210s 210s Output Parameters: 210s out= Write all reads to this file. 210s outu= Write only unmapped reads to this file. Does not 210s include unmapped paired reads with a mapped mate. 210s outm= Write only mapped reads to this file. Includes 210s unmapped paired reads with a mapped mate. 210s mappedonly=f If true, treats 'out' like 'outm'. 210s bamscript= (bs) bbmap.sh ref=example.fasta 210s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 210s Write a shell script to that will turn 210s the sam output into a sorted, indexed bam file. 210s ordered=f Set to true to output reads in same order as input. 210s Slower and uses more memory. 210s overwrite=f (ow) Allow process to overwrite existing files. 210s secondary=f Print secondary alignments. 210s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 210s with score of at least this fraction of primary. 210s ssao=f (secondarysiteasambiguousonly) Only print secondary 210s alignments for ambiguously-mapped reads. 210s maxsites=5 Maximum number of total alignments to print per read. 210s Only relevant when secondary=t. 210s quickmatch=f Generate cigar strings more quickly. 210s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 210s assuming that the remainder is a comment or description. 210s ziplevel=2 (zl) Compression level for zip or gzip output. 210s pigz=f Spawn a pigz (parallel gzip) process for faster 210s compression than Java. Requires pigz to be installed. 210s machineout=f Set to true to output statistics in machine-friendly 210s 'key=value' format. 210s printunmappedcount=f Print the total number of unmapped reads and bases. 210s If input is paired, the number will be of pairs 210s for which both reads are unmapped. 210s showprogress=0 If positive, print a '.' every X reads. 210s showprogress2=0 If positive, print the number of seconds since the 210s last progress update (instead of a '.'). 210s renamebyinsert=f Renames reads based on their mapped insert size. 210s 210s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 210s bloom=f Use a Bloom filter to ignore reads not sharing kmers 210s with the reference. This uses more memory, but speeds 210s mapping when most reads don't match the reference. 210s bloomhashes=2 Number of hash functions. 210s bloomminhits=3 Number of consecutive hits to be considered matched. 210s bloomk=31 Bloom filter kmer length. 210s bloomserial=t Use the serialized Bloom filter for greater loading 210s speed, if available. If not, generate and write one. 210s 210s Post-Filtering Parameters: 210s idfilter=0 Independant of minid; sets exact minimum identity 210s allowed for alignments to be printed. Range 0 to 1. 210s subfilter=-1 Ban alignments with more than this many substitutions. 210s insfilter=-1 Ban alignments with more than this many insertions. 210s delfilter=-1 Ban alignments with more than this many deletions. 210s indelfilter=-1 Ban alignments with more than this many indels. 210s editfilter=-1 Ban alignments with more than this many edits. 210s inslenfilter=-1 Ban alignments with an insertion longer than this. 210s dellenfilter=-1 Ban alignments with a deletion longer than this. 210s nfilter=-1 Ban alignments with more than this many ns. This 210s includes nocall, noref, and off scaffold ends. 210s 210s Sam flags and settings: 210s noheader=f Disable generation of header lines. 210s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 210s with = and X, or 1.3 to use M. 210s saa=t (secondaryalignmentasterisks) Use asterisks instead of 210s bases for sam secondary alignments. 210s cigar=t Set to 'f' to skip generation of cigar strings (faster). 210s keepnames=f Keep original names of paired reads, rather than 210s ensuring both reads have the same name. 210s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 210s cigar strings for deletions of at least that length. 210s rgid= Set readgroup ID. All other readgroup fields 210s can be set similarly, with the flag rgXX= 210s If you set a readgroup flag to the word 'filename', 210s e.g. rgid=filename, the input file name will be used. 210s mdtag=f Write MD tags. 210s nhtag=f Write NH tags. 210s xmtag=f Write XM tags (may only work correctly with ambig=all). 210s amtag=f Write AM tags. 210s nmtag=f Write NM tags. 210s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 210s for RNAseq using firststrand, secondstrand, or 210s unstranded libraries. Needed by Cufflinks. 210s JGI mainly uses 'firststrand'. 210s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 210s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 210s prefixed by YL:Z: 210s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 210s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 210s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 210s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 210s boundstag=f Write a tag indicating whether either read in the pair 210s goes off the end of the reference, prefixed by XB:Z: 210s notags=f Turn off all optional tags. 210s 210s Histogram and statistics output parameters: 210s scafstats= Statistics on how many reads mapped to which scaffold. 210s refstats= Statistics on how many reads mapped to which reference 210s file; only for BBSplit. 210s sortscafs=t Sort scaffolds or references by read count. 210s bhist= Base composition histogram by position. 210s qhist= Quality histogram by position. 210s aqhist= Histogram of average read quality. 210s bqhist= Quality histogram designed for box plots. 210s lhist= Read length histogram. 210s ihist= Write histogram of insert sizes (for paired reads). 210s ehist= Errors-per-read histogram. 210s qahist= Quality accuracy histogram of error rates versus 210s quality score. 210s indelhist= Indel length histogram. 210s mhist= Histogram of match, sub, del, and ins rates by 210s read location. 210s gchist= Read GC content histogram. 210s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 210s gcpairs=t Use average GC of paired reads. 210s idhist= Histogram of read count versus percent identity. 210s idbins=100 Number idhist bins. Set to 'auto' to use read length. 210s statsfile=stderr Mapping statistics are printed here. 210s 210s Coverage output parameters (these may reduce speed and use more RAM): 210s covstats= Per-scaffold coverage info. 210s rpkm= Per-scaffold RPKM/FPKM counts. 210s covhist= Histogram of # occurrences of each depth level. 210s basecov= Coverage per base location. 210s bincov= Print binned coverage per location (one line per X bases). 210s covbinsize=1000 Set the binsize for binned coverage output. 210s nzo=t Only print scaffolds with nonzero coverage. 210s twocolumn=f Change to true to print only ID and Avg_fold instead of 210s all 6 columns to the 'out=' file. 210s 32bit=f Set to true if you need per-base coverage over 64k. 210s strandedcov=f Track coverage for plus and minus strand independently. 210s startcov=f Only track start positions of reads. 210s secondarycov=t Include coverage of secondary alignments. 210s physcov=f Calculate physical coverage for paired reads. 210s This includes the unsequenced bases. 210s delcoverage=t (delcov) Count bases covered by deletions as covered. 210s True is faster than false. 210s covk=0 If positive, calculate kmer coverage statistics. 210s 210s Java Parameters: 210s -Xmx This will set Java's memory usage, 210s overriding autodetection. 210s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 210s will specify 800 megs. The max is typically 85% of 210s physical memory. The human genome requires around 24g, 210s or 12g with the 'usemodulo' flag. The index uses 210s roughly 6 bytes per reference base. 210s -eoom This flag will cause the process to exit if an 210s out-of-memory exception occurs. Requires Java 8u92+. 210s -da Disable assertions. 210s 210s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 210s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 210s 210s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 211s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 211s Version 39.20 211s 211s No output file. 211s Writing reference. 211s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false] 211s 211s Set genScaffoldInfo=true 211s Writing chunk 1 211s Set genome to 1 211s 211s Loaded Reference: 0.006 seconds. 211s Loading index for chunk 1-1, build 1 211s No index available; generating from reference genome: /tmp/autopkgtest.zO3rNJ/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 211s Indexing threads started for block 0-1 211s Indexing threads finished for block 0-1 212s Generated Index: 1.646 seconds. 212s No reads to process; quitting. 212s 212s Total time: 1.862 seconds. 212s test -d ref 212s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 212s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 212s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 213s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 213s Version 39.20 213s 213s Retaining first best site only for ambiguous mappings. 213s Set genome to 1 213s 213s Loaded Reference: 0.032 seconds. 213s Loading index for chunk 1-1, build 1 213s Generated Index: 0.679 seconds. 217s Analyzed Index: 3.700 seconds. 217s Started output stream: 0.029 seconds. 217s Cleared Memory: 0.110 seconds. 217s Processing reads in single-ended mode. 217s Started read stream. 217s Started 8 mapping threads. 217s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 217s 217s ------------------ Results ------------------ 217s 217s Genome: 1 217s Key Length: 13 217s Max Indel: 16000 217s Minimum Score Ratio: 0.56 217s Mapping Mode: normal 217s Reads Used: 4 (153 bases) 217s 217s Mapping: 0.143 seconds. 217s Reads/sec: 27.96 217s kBases/sec: 1.07 217s 217s 217s Read 1 data: pct reads num reads pct bases num bases 217s 217s mapped: 0.0000% 0 0.0000% 0 217s unambiguous: 0.0000% 0 0.0000% 0 217s ambiguous: 0.0000% 0 0.0000% 0 217s low-Q discards: 25.0000% 1 19.6078% 30 217s 217s perfect best site: 0.0000% 0 0.0000% 0 217s semiperfect site: 0.0000% 0 0.0000% 0 217s 217s Match Rate: NA NA NaN% 0 217s Error Rate: NaN% 0 NaN% 0 217s Sub Rate: NaN% 0 NaN% 0 217s Del Rate: NaN% 0 NaN% 0 217s Ins Rate: NaN% 0 NaN% 0 217s N Rate: NaN% 0 NaN% 0 217s 217s Total time: 4.834 seconds. 217s test -r out.sam 217s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 217s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 217s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 218s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 218s Version 39.20 218s 218s Retaining first best site only for ambiguous mappings. 218s Executing dna.FastaToChromArrays2 [example.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true] 218s 218s Set genScaffoldInfo=true 218s Set genome to 1 218s 218s Loaded Reference: 0.002 seconds. 218s Loading index for chunk 1-1, build 1 218s Indexing threads started for block 0-1 218s Indexing threads finished for block 0-1 218s Generated Index: 0.240 seconds. 222s Analyzed Index: 3.592 seconds. 222s Started output stream: 0.032 seconds. 222s Cleared Memory: 0.131 seconds. 222s Processing reads in single-ended mode. 222s Started read stream. 222s Started 8 mapping threads. 222s Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7 222s 222s ------------------ Results ------------------ 222s 222s Genome: 1 222s Key Length: 13 222s Max Indel: 16000 222s Minimum Score Ratio: 0.56 222s Mapping Mode: normal 222s Reads Used: 3 (75 bases) 222s 222s Mapping: 0.177 seconds. 222s Reads/sec: 16.97 222s kBases/sec: 0.42 222s 222s 222s Read 1 data: pct reads num reads pct bases num bases 222s 222s mapped: 100.0000% 3 100.0000% 75 222s unambiguous: 100.0000% 3 100.0000% 75 222s ambiguous: 0.0000% 0 0.0000% 0 222s low-Q discards: 0.0000% 0 0.0000% 0 222s 222s perfect best site: 100.0000% 3 100.0000% 75 222s semiperfect site: 100.0000% 3 100.0000% 75 222s 222s Match Rate: NA NA 100.0000% 75 222s Error Rate: 0.0000% 0 0.0000% 0 222s Sub Rate: 0.0000% 0 0.0000% 0 222s Del Rate: 0.0000% 0 0.0000% 0 222s Ins Rate: 0.0000% 0 0.0000% 0 222s N Rate: 0.0000% 0 0.0000% 0 222s 222s Total time: 4.366 seconds. 222s test -r out2.sam 222s 222s # bbduk 222s bbduk.sh --version 222s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 222s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 222s BBTools version 39.20 222s For help, please run the shellscript with no parameters, or look in /docs/. 222s bbduk.sh --help 222s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 222s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 222s 222s Written by Brian Bushnell 222s Last modified November 18, 2024 222s 222s Description: Compares reads to the kmers in a reference dataset, optionally 222s allowing an edit distance. Splits the reads into two outputs - those that 222s match the reference, and those that don't. Can also trim (remove) the matching 222s parts of the reads rather than binning the reads. 222s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 222s 222s Usage: bbduk.sh in= out= ref= 222s 222s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 222s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 222s fasta input, set in=stdin.fa.gz 222s 222s Input parameters: 222s in= Main input. in=stdin.fq will pipe from stdin. 222s in2= Input for 2nd read of pairs in a different file. 222s ref= Comma-delimited list of reference files. 222s In addition to filenames, you may also use the keywords: 222s adapters, artifacts, phix, lambda, pjet, mtst, kapa 222s literal= Comma-delimited list of literal reference sequences. 222s Polymers are also allowed with the 'poly' prefix; 222s for example, 'literal=ATGGT,polyGC' will add both ATGGT 222s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 222s enough replicates to ensure that all kmers are present. 222s touppercase=f (tuc) Change all bases upper-case. 222s interleaved=auto (int) t/f overrides interleaved autodetection. 222s Must be set mainually when streaming fastq input. 222s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 222s reads=-1 If positive, quit after processing X reads or pairs. 222s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 222s possible unambiguous copies. Intended for short motifs 222s or adapter barcodes, as time/memory use is exponential. 222s samplerate=1 Set lower to only process a fraction of input reads. 222s samref= Optional reference fasta for processing sam files. 222s 222s Output parameters: 222s out= (outnonmatch) Write reads here that do not contain 222s kmers matching the database. 'out=stdout.fq' will pipe 222s to standard out. 222s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 222s different file. 222s outm= (outmatch) Write reads here that fail filters. In default 222s kfilter mode, this means any read with a matching kmer. 222s In any mode, it also includes reads that fail filters such 222s as minlength, mingc, maxgc, entropy, etc. In other words, 222s it includes all reads that do not go to 'out'. 222s outm2= (outmatch2) Use this to write 2nd read of pairs to a 222s different file. 222s outs= (outsingle) Use this to write singleton reads whose mate 222s was trimmed shorter than minlen. 222s stats= Write statistics about which contamininants were detected. 222s refstats= Write statistics on a per-reference-file basis. 222s rpkm= Write RPKM for each reference sequence (for RNA-seq). 222s dump= Dump kmer tables to a file, in fasta format. 222s duk= Write statistics in duk's format. *DEPRECATED* 222s nzo=t Only write statistics about ref sequences with nonzero hits. 222s overwrite=t (ow) Grant permission to overwrite files. 222s showspeed=t (ss) 'f' suppresses display of processing speed. 222s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 222s fastawrap=70 Length of lines in fasta output. 222s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 222s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 222s 5 includes base counts. 222s rename=f Rename reads to indicate which sequences they matched. 222s refnames=f Use names of reference files rather than scaffold IDs. 222s trd=f Truncate read and ref names at the first whitespace. 222s ordered=f Set to true to output reads in same order as input. 222s maxbasesout=-1 If positive, quit after writing approximately this many 222s bases to out (outu/outnonmatch). 222s maxbasesoutm=-1 If positive, quit after writing approximately this many 222s bases to outm (outmatch). 222s json=f Print to screen in json format. 222s 222s Histogram output parameters: 222s bhist= Base composition histogram by position. 222s qhist= Quality histogram by position. 222s qchist= Count of bases with each quality value. 222s aqhist= Histogram of average read quality. 222s bqhist= Quality histogram designed for box plots. 222s lhist= Read length histogram. 222s phist= Polymer length histogram. 222s gchist= Read GC content histogram. 222s enthist= Read entropy histogram. 222s ihist= Insert size histogram, for paired reads in mapped sam. 222s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 222s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 222s more memory. The default is 6000 for some histograms 222s and 80000 for others. 222s 222s Histograms for mapped sam/bam files only: 222s histbefore=t Calculate histograms from reads before processing. 222s ehist= Errors-per-read histogram. 222s qahist= Quality accuracy histogram of error rates versus quality 222s score. 222s indelhist= Indel length histogram. 222s mhist= Histogram of match, sub, del, and ins rates by position. 222s idhist= Histogram of read count versus percent identity. 222s idbins=100 Number idhist bins. Set to 'auto' to use read length. 222s varfile= Ignore substitution errors listed in this file when 222s calculating error rates. Can be generated with 222s CallVariants. 222s vcf= Ignore substitution errors listed in this VCF file 222s when calculating error rates. 222s ignorevcfindels=t Also ignore indels listed in the VCF. 222s 222s Processing parameters: 222s k=27 Kmer length used for finding contaminants. Contaminants 222s shorter than k will not be found. k must be at least 1. 222s rcomp=t Look for reverse-complements of kmers in addition to 222s forward kmers. 222s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 222s increase sensitivity in the presence of errors. This may 222s also be set to a number, e.g. mm=3, to mask that many bp. 222s The default mm=t corresponds to mm=1 for odd-length kmers 222s and mm=2 for even-length kmers (as of v39.04), while 222s mm=f is always equivalent to mm=0. 222s minkmerhits=1 (mkh) Reads need at least this many matching kmers 222s to be considered as matching the reference. 222s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 222s kmers to hit a ref, in order to be considered a match. 222s If this and minkmerhits are set, the greater is used. 222s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 222s bases to be covered by ref kmers to be considered a match. 222s If specified, mcf overrides mkh and mkf. 222s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 222s Memory use is proportional to (3*K)^hdist. 222s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 222s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 222s and indels). Memory use is proportional to (8*K)^edist. 222s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 222s qhdist2=0 Sets qhdist for short kmers, when using mink. 222s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 222s forbidn=f (fn) Forbids matching of read kmers containing N. 222s By default, these will match a reference 'A' if 222s hdist>0 or edist>0, to increase sensitivity. 222s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 222s match (or either is trimmed shorter than minlen). 222s Set to false to require both. 222s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 222s This makes the statistics a bit odd. 222s findbestmatch=f (fbm) If multiple matches, associate read with sequence 222s sharing most kmers. Reduces speed. 222s skipr1=f Don't do kmer-based operations on read 1. 222s skipr2=f Don't do kmer-based operations on read 2. 222s ecco=f For overlapping paired reads only. Performs error- 222s correction with BBMerge prior to kmer operations. 222s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 222s matrices generated by CalcTrueQuality. 222s sam= If recalibration is desired, and matrices have not already 222s been generated, BBDuk will create them from the sam file. 222s amino=f Run in amino acid mode. Some features have not been 222s tested, but kmer-matching works fine. Maximum k is 12. 222s 222s Speed and Memory parameters: 222s threads=auto (t) Set number of threads to use; default is number of 222s logical processors. 222s prealloc=f Preallocate memory in table. Allows faster table loading 222s and more efficient memory usage, for a large reference. 222s monitor=f Kill this process if it crashes. monitor=600,0.01 would 222s kill after 600 seconds under 1% usage. 222s minrskip=1 (mns) Force minimal skip interval when indexing reference 222s kmers. 1 means use all, 2 means use every other kmer, etc. 222s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 222s reference kmers. Normally all are used for scaffolds<100kb, 222s but with longer scaffolds, up to maxrskip-1 are skipped. 222s rskip= Set both minrskip and maxrskip to the same value. 222s If not set, rskip will vary based on sequence length. 222s qskip=1 Skip query kmers to increase speed. 1 means use all. 222s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 222s reads and reference. Increases speed and reduces memory. 222s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 222s 222s Trimming/Filtering/Masking parameters: 222s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 222s All kmer processing modes are mutually exclusive. 222s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 222s 222s ktrim=f Trim reads to remove bases matching reference kmers, plus 222s all bases to the left or right. 222s Values: 222s f (don't trim), 222s r (trim to the right), 222s l (trim to the left) 222s ktrimtips=0 Set this to a positive number to perform ktrim on both 222s ends, examining only the outermost X bases. 222s kmask= Replace bases matching ref kmers with another symbol. 222s Allows any non-whitespace character, and processes short 222s kmers on both ends if mink is set. 'kmask=lc' will 222s convert masked bases to lowercase. 222s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 222s ksplit=f For single-ended reads only. Reads will be split into 222s pairs around the kmer. If the kmer is at the end of the 222s read, it will be trimmed instead. Singletons will go to 222s out, and pairs will go to outm. Do not use ksplit with 222s other operations such as quality-trimming or filtering. 222s mink=0 Look for shorter kmers at read tips down to this length, 222s when k-trimming or masking. 0 means disabled. Enabling 222s this will disable maskmiddle. 222s qtrim=f Trim read ends to remove bases with quality below trimq. 222s Performed AFTER looking for kmers. Values: 222s rl (trim both ends), 222s f (neither end), 222s r (right end only), 222s l (left end only), 222s w (sliding window). 222s trimq=6 Regions with average quality BELOW this will be trimmed, 222s if qtrim is set to something other than f. Can be a 222s floating-point number like 7.3. 222s quantize Bin quality scores to reduce file size. quantize=2 will 222s eliminate all odd quality scores, while quantize=0,10,37 222s will only allow qualty scores of 0, 10, or 37. 222s trimclip=f Trim soft-clipped bases from sam files. 222s minlength=10 (ml) Reads shorter than this after trimming will be 222s discarded. Pairs will be discarded if both are shorter. 222s mlf=0 (minlengthfraction) Reads shorter than this fraction of 222s original length after trimming will be discarded. 222s maxlength= Reads longer than this after trimming will be discarded. 222s minavgquality=0 (maq) Reads with average quality (after trimming) below 222s this will be discarded. 222s maqb=0 If positive, calculate maq from this many initial bases. 222s minbasequality=0 (mbq) Reads with any base below this quality (after 222s trimming) will be discarded. 222s maxns=-1 If non-negative, reads with more Ns than this 222s (after trimming) will be discarded. 222s mcb=0 (minconsecutivebases) Discard reads without at least 222s this many consecutive called bases. 222s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 222s than minlength to outm rather than discarding. 222s tp=0 (trimpad) Trim this much extra around matching kmers. 222s tbo=f (trimbyoverlap) Trim adapters based on where paired 222s reads overlap. 222s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 222s minoverlap=14 Require this many bases of overlap for detection. 222s mininsert=40 Require insert size of at least this for overlap. 222s Should be reduced to 16 for small RNA sequencing. 222s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 222s reads to the minimum length of either. 222s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 222s (exclusive, 0-based). 222s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 222s (exclusive, 0-based). 222s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 222s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 222s modulo this number. 222s restrictleft=0 If positive, only look for kmer matches in the 222s leftmost X bases. 222s restrictright=0 If positive, only look for kmer matches in the 222s rightmost X bases. 222s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 222s both ends is desired, use ktrimtips. 222s mingc=0 Discard reads with GC content below this. 222s maxgc=1 Discard reads with GC content above this. 222s gcpairs=t Use average GC of paired reads. 222s Also affects gchist. 222s tossjunk=f Discard reads with invalid characters as bases. 222s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 222s 222s Header-parsing parameters - these require Illumina headers: 222s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 222s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 222s or barcodes containing 'N' otherwise. A barcode must be 222s the last part of the read header. Values: 222s t: Remove reads with bad barcodes. 222s f: Ignore barcodes. 222s crash: Crash upon encountering bad barcodes. 222s barcodes= Comma-delimited list of barcodes or files of barcodes. 222s xmin=-1 If positive, discard reads with a lesser X coordinate. 222s ymin=-1 If positive, discard reads with a lesser Y coordinate. 222s xmax=-1 If positive, discard reads with a greater X coordinate. 222s ymax=-1 If positive, discard reads with a greater Y coordinate. 222s 222s Polymer trimming: 222s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 222s at least this length on either end of reads. 222s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 222s length on the left end of reads. Does not trim poly-C. 222s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 222s length on the right end of reads. Does not trim poly-C. 222s trimpolyg=0 This sets both left and right at once. 222s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 222s at least this length (on the left). 222s Note: there are also equivalent poly-C flags. 222s 222s Polymer tracking: 222s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 222s plen=20 Length of homopolymers to count. 222s 222s Entropy/Complexity parameters: 222s entropy=-1 Set between 0 and 1 to filter reads with entropy below 222s that value. Higher is more stringent. 222s entropywindow=50 Calculate entropy using a sliding window of this length. 222s entropyk=5 Calculate entropy using kmers of this length. 222s minbasefrequency=0 Discard reads with a minimum base frequency below this. 222s entropytrim=f Values: 222s f: (false) Do not entropy-trim. 222s r: (right) Trim low entropy on the right end only. 222s l: (left) Trim low entropy on the left end only. 222s rl: (both) Trim low entropy on both ends. 222s entropymask=f Values: 222s f: (filter) Discard low-entropy sequences. 222s t: (true) Mask low-entropy parts of sequences with N. 222s lc: Change low-entropy parts of sequences to lowercase. 222s entropymark=f Mark each base with its entropy value. This is on a scale 222s of 0-41 and is reported as quality scores, so the output 222s should be fastq or fasta+qual. 222s NOTE: If set, entropytrim overrides entropymask. 222s 222s Cardinality estimation: 222s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 222s cardinalityout=f (loglogout) Count unique kmers in output reads. 222s loglogk=31 Use this kmer length for counting. 222s loglogbuckets=2048 Use this many buckets for counting. 222s khist= Kmer frequency histogram; plots number of kmers versus 222s kmer depth. This is approximate. 222s khistout= Kmer frequency histogram for output reads. 222s 222s Side Channel: 222s sideout= Output for aligned reads. 222s sideref=phix Reference for side-channel alignment; must be a single 222s sequence and virtually repeat-free at selected k. 222s sidek1=17 Kmer length for seeding alignment to reference. 222s sidek2=13 Kmer length for seeding alignment of unaligned reads 222s with an aligned mate. 222s sideminid1=0.66 Minimum identity to accept individual alignments. 222s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 222s sidemm1=1 Middle mask length for sidek1. 222s sidemm2=1 Middle mask length for sidek2. 222s Note: The side channel is a special additional output that allows alignment 222s to a secondary reference while also doing trimming. Alignment does not affect 222s whether reads go to the normal outputs (out, outm). The main purpose is to 222s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 222s 222s 222s Java Parameters: 222s 222s -Xmx This will set Java's memory usage, overriding autodetection. 222s -Xmx20g will 222s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 222s The max is typically 85% of physical memory. 222s -eoom This flag will cause the process to exit if an 222s out-of-memory exception occurs. Requires Java 8u92+. 222s -da Disable assertions. 222s 222s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 222s 222s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 222s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 223s Executing jgi.BBDuk [in1=misc_dna_as_illumina.fastq, in2=misc_rna_as_illumina.fastq, qtrim=rl, trimq=15, minlen=75, out=out.fastq.gz] 223s Version 39.20 223s 223s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 223s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 223s Allocating kmer table: 0.030 seconds. 223s Initial: 223s Memory: max=2097m, total=2097m, free=2077m, used=20m 223s 223s Input is being processed as paired 223s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 223s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 223s Started output streams: 0.024 seconds. 223s Processing time: 0.006 seconds. 223s 223s Input: 8 reads 306 bases. 223s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 223s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 223s Result: 0 reads (0.00%) 0 bases (0.00%) 223s 223s Time: 0.031 seconds. 223s Reads Processed: 8 0.25k reads/sec 223s Bases Processed: 306 0.01m bases/sec 223s test -r out.fastq.gz 223s 223s # bbnorm 223s bbnorm.sh --version 223s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 223s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 223s BBTools version 39.20 223s For help, please run the shellscript with no parameters, or look in /docs/. 223s bbnorm.sh --help 223s 223s Written by Brian Bushnell 223s Last modified October 19, 2017 223s 223s Description: Normalizes read depth based on kmer counts. 223s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 223s However, Tadpole has superior error-correction to BBNorm. 223s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 223s 223s Usage: bbnorm.sh in= out= outt= hist= 223s 223s Input parameters: 223s in=null Primary input. Use in2 for paired reads in a second file 223s in2=null Second input file for paired reads in two files 223s extra=null Additional files to use for input (generating hash table) but not for output 223s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 223s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 223s kmersample=1 Process every nth kmer, and skip the rest 223s readsample=1 Process every nth read, and skip the rest 223s interleaved=auto May be set to true or false to force the input read file to ovverride autodetection of the input file as paired interleaved. 223s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 223s 223s Output parameters: 223s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 223s outt= (outtoss) File for reads that were excluded from primary output 223s reads=-1 Only process this number of reads, then quit (-1 means all) 223s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 223s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 223s zerobin=f Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms. 223s Default is false, to prevent confusion about how there can be 0-count kmers. 223s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 223s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 223s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 223s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 223s rename=f Rename reads based on their kmer depth. 223s 223s Hashing parameters: 223s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 223s bits=32 Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32. Maximum kmer depth recorded is 2^cbits. Automatically reduced to 16 in 2-pass. 223s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 223s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 223s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 223s prefilter=f True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable. The prefilter is more memory-efficient because it uses 2-bit cells. 223s prehashes=2 Number of hashes for prefilter. 223s prefilterbits=2 (pbits) Bits per cell in prefilter. 223s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 223s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 223s minq=6 Ignore kmers containing bases with quality below this 223s minprob=0.5 Ignore kmers with overall probability of correctness below this 223s threads=auto (t) Spawn exactly X hashing threads (default is number of logical processors). Total active threads may exceed X due to I/O threads. 223s rdk=t (removeduplicatekmers) When true, a kmer's count will only be incremented once per read pair, even if that kmer occurs more than once. 223s 223s Normalization parameters: 223s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 223s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 223s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 223s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 223s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 223s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 223s percentile=54.0 (dp) Read depth is by default inferred from the 54th percentile of kmer depth, but this may be changed to any number 1-100. 223s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 223s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 223s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 223s 223s Error detection parameters: 223s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 223s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 223s tossbadreads=f (tbr) Throw away reads detected as containing errors. 223s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 223s errordetectratio=125 (edr) Reads with a ratio of at least this much between their high and low depth kmers will be classified as error reads. 223s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 223s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 223s 223s Error correction parameters: 223s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 223s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 223s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 223s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 223s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 223s eccmaxqual=127 Do not correct bases with quality above this value. 223s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 223s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 223s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 223s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 223s overlap=f (ecco) Error correct by read overlap. 223s 223s Depth binning parameters: 223s lowbindepth=10 (lbd) Cutoff for low depth bin. 223s highbindepth=80 (hbd) Cutoff for high depth bin. 223s outlow= Pairs in which both reads have a median below lbd go into this file. 223s outhigh= Pairs in which both reads have a median above hbd go into this file. 223s outmid= All other pairs go into this file. 223s 223s Histogram parameters: 223s hist= Specify a file to write the input kmer depth histogram. 223s histout= Specify a file to write the output kmer depth histogram. 223s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 223s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 223s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 223s 223s Peak calling parameters: 223s peaks= Write the peaks to this file. Default is stdout. 223s minHeight=2 (h) Ignore peaks shorter than this. 223s minVolume=5 (v) Ignore peaks with less area than this. 223s minWidth=3 (w) Ignore peaks narrower than this. 223s minPeak=2 (minp) Ignore peaks with an X-value below this. 223s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 223s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 223s 223s Java Parameters: 223s -Xmx This will set Java's memory usage, overriding autodetection. 223s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 223s The max is typically 85% of physical memory. 223s -eoom This flag will cause the process to exit if an 223s out-of-memory exception occurs. Requires Java 8u92+. 223s -da Disable assertions. 223s 223s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 223s 223s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 223s out=out3.fastq outt=outt.fastq hist=hist.plt 223s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 223s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=sanger_full_range_original_sanger.fastq qin=33 out=out3.fastq outt=outt.fastq hist=hist.plt 223s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 223s 223s 223s *********** Pass 1 ********** 223s 223s 223s Settings: 223s threads: 8 223s k: 31 223s deterministic: true 223s toss error reads: false 223s passes: 1 223s bits per cell: 16 223s cells: 729.90M 223s hashes: 3 223s base min quality: 5 223s kmer min prob: 0.5 223s 223s target depth: 400 223s min depth: 3 223s max depth: 500 223s min good kmers: 15 223s depth percentile: 64.8 223s ignore dupe kmers: true 223s fix spikes: false 223s histogram length: 65536 223s print zero cov: false 223s 224s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 224s 224s Estimated unique kmers: 4 224s 224s Table creation time: 0.748 seconds. 224s Started output threads. 224s Started output threads. 224s Table read time: 0.016 seconds. 11.41 kb/sec 224s Total reads in: 2 0.000% Kept 224s Total bases in: 188 0.000% Kept 224s Error reads in: 2 100.000% 224s Error type 1: 2 100.000% 224s Error type 2: 0 0.000% 224s Error type 3: 0 0.000% 224s 224s Wrote histogram to hist.plt 224s Total kmers counted: 128 224s Total unique kmer count: 128 224s Includes forward kmers only. 224s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 224s The most accurate value is the greater of the two. 224s 224s Percent unique: 100.00% 224s Depth average: 1.00 (unique kmers) 224s Depth median: 1 (unique kmers) 224s Depth standard deviation: 0.00 (unique kmers) 224s Corrected depth average: 0.00 224s 224s Depth average: 1.00 (all kmers) 224s Depth median: 1 (all kmers) 224s Depth standard deviation: 0.00 (all kmers) 224s 224s Approx. read depth median: 1.47 224s 224s *********** Pass 2 ********** 224s 224s 224s Settings: 224s threads: 8 224s k: 31 224s deterministic: true 224s toss error reads: false 224s passes: 1 224s bits per cell: 16 224s cells: 729.90M 224s hashes: 3 224s base min quality: 5 224s kmer min prob: 0.5 224s 224s target depth: 100 224s min depth: 5 224s max depth: 100 224s min good kmers: 15 224s depth percentile: 54.0 224s ignore dupe kmers: true 224s fix spikes: false 224s histogram length: 65536 224s 225s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 225s 225s Estimated unique kmers: 0 225s 225s Table creation time: 0.358 seconds. 225s Started output threads. 225s Started output threads. 225s Table read time: 0.003 seconds. 0.00 kb/sec 225s Total reads in: 0 NaN% Kept 225s Total bases in: 0 NaN% Kept 225s Error reads in: 0 NaN% 225s Error type 1: 0 NaN% 225s Error type 2: 0 NaN% 225s Error type 3: 0 NaN% 225s Total kmers counted: 0 225s Total unique kmer count: 0 225s Includes forward kmers only. 225s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 225s The most accurate value is the greater of the two. 225s 225s Percent unique: NaN% 225s Depth average: NaN (unique kmers) 225s Depth median: 0 (unique kmers) 225s Depth standard deviation: NaN (unique kmers) 225s Corrected depth average: NaN 225s 225s Depth average: NaN (all kmers) 225s Depth median: 0 (all kmers) 225s Depth standard deviation: 0.00 (all kmers) 225s 225s Approx. read depth median: NaN 225s 225s Removing temp files. 225s 225s Total time: 1.236 seconds. 0.15 kb/sec 225s test -r out3.fastq 225s test -r outt.fastq 225s test -r hist.plt 225s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 225s out=out4.fastq outt=outt2.fastq hist=hist2.plt 225s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 225s java -ea -Xmx2000m -Xms2000m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 in=illumina_full_range_original_illumina.fastq qin=64 out=out4.fastq outt=outt2.fastq hist=hist2.plt 225s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 225s 225s 225s *********** Pass 1 ********** 225s 225s 225s Settings: 225s threads: 8 225s k: 31 225s deterministic: true 225s toss error reads: false 225s passes: 1 225s bits per cell: 16 225s cells: 729.90M 225s hashes: 3 225s base min quality: 5 225s kmer min prob: 0.5 225s 225s target depth: 400 225s min depth: 3 225s max depth: 500 225s min good kmers: 15 225s depth percentile: 64.8 225s ignore dupe kmers: true 225s fix spikes: false 225s histogram length: 65536 225s print zero cov: false 225s 226s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 226s 226s Estimated unique kmers: 4 226s 226s Table creation time: 0.578 seconds. 226s Started output threads. 226s Started output threads. 226s Table read time: 0.011 seconds. 11.54 kb/sec 226s Total reads in: 2 0.000% Kept 226s Total bases in: 126 0.000% Kept 226s Error reads in: 2 100.000% 226s Error type 1: 2 100.000% 226s Error type 2: 0 0.000% 226s Error type 3: 0 0.000% 226s 226s Wrote histogram to hist2.plt 226s Total kmers counted: 66 226s Total unique kmer count: 66 226s Includes forward kmers only. 226s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 226s The most accurate value is the greater of the two. 226s 226s Percent unique: 100.00% 226s Depth average: 1.00 (unique kmers) 226s Depth median: 1 (unique kmers) 226s Depth standard deviation: 0.00 (unique kmers) 226s Corrected depth average: 0.00 226s 226s Depth average: 1.00 (all kmers) 226s Depth median: 1 (all kmers) 226s Depth standard deviation: 0.00 (all kmers) 226s 226s Approx. read depth median: 1.91 226s 226s *********** Pass 2 ********** 226s 226s 226s Settings: 226s threads: 8 226s k: 31 226s deterministic: true 226s toss error reads: false 226s passes: 1 226s bits per cell: 16 226s cells: 729.90M 226s hashes: 3 226s base min quality: 5 226s kmer min prob: 0.5 226s 226s target depth: 100 226s min depth: 5 226s max depth: 100 226s min good kmers: 15 226s depth percentile: 54.0 226s ignore dupe kmers: true 226s fix spikes: false 226s histogram length: 65536 226s 226s Made hash table: hashes = 3 mem = 1.36 GB cells = 729.70M used = 0.000% 226s 226s Estimated unique kmers: 0 226s 226s Table creation time: 0.359 seconds. 226s Started output threads. 226s Started output threads. 226s Table read time: 0.003 seconds. 0.00 kb/sec 226s Total reads in: 0 NaN% Kept 226s Total bases in: 0 NaN% Kept 226s Error reads in: 0 NaN% 226s Error type 1: 0 NaN% 226s Error type 2: 0 NaN% 226s Error type 3: 0 NaN% 226s Total kmers counted: 0 226s Total unique kmer count: 0 226s Includes forward kmers only. 226s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 226s The most accurate value is the greater of the two. 226s 226s Percent unique: NaN% 226s Depth average: NaN (unique kmers) 226s Depth median: 0 (unique kmers) 226s Depth standard deviation: NaN (unique kmers) 226s Corrected depth average: NaN 226s 226s Depth average: NaN (all kmers) 226s Depth median: 0 (all kmers) 226s Depth standard deviation: 0.00 (all kmers) 226s 226s Approx. read depth median: NaN 226s 226s Removing temp files. 226s 226s Total time: 1.442 seconds. 0.09 kb/sec 228s test -r out4.fastq 228s test -r outt2.fastq 228s test -r hist2.plt 229s autopkgtest [13:22:46]: test run-unit-test: -----------------------] 232s autopkgtest [13:22:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 232s run-unit-test PASS 236s autopkgtest [13:22:53]: @@@@@@@@@@@@@@@@@@@@ summary 236s run-unit-test PASS