0s autopkgtest [11:14:21]: starting date and time: 2026-02-10 11:14:21+0000 0s autopkgtest [11:14:21]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [11:14:21]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.df_awj30/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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-26/26~34ea-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu4-ram16-disk100-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-18.secgroup --name adt-resolute-amd64-bbmap-20260210-111421-juju-7f2275-prod-proposed-migration-environment-20-f054e960-f981-4bf2-97c2-a3d8ffc93f51 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-bbmap-20260210-111421-juju-7f2275-prod-proposed-migration-environment-20-f054e960-f981-4bf2-97c2-a3d8ffc93f51 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 84s autopkgtest [11:15:45]: testbed dpkg architecture: amd64 84s autopkgtest [11:15:45]: testbed apt version: 3.1.14 85s autopkgtest [11:15:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s autopkgtest [11:15:46]: testbed release detected to be: None 85s autopkgtest [11:15:46]: updating testbed package index (apt update) 86s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 86s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 86s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [179 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.9 kB] 86s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 86s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB] 86s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [265 kB] 86s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6492 B] 86s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 86s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [706 kB] 86s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1698 kB] 86s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [35.9 kB] 86s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 87s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 87s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 87s Fetched 5034 kB in 1s (4556 kB/s) 88s Reading package lists... 88s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 88s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 88s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 88s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 89s Reading package lists... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 90s The following package was automatically installed and is no longer required: 90s libpython3.13 90s Use 'sudo apt autoremove' to remove it. 90s The following NEW packages will be installed: 90s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 90s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 90s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 90s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 90s The following packages will be upgraded: 90s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 90s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 90s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 90s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 90s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbrotli1 libbsd0 90s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 90s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 90s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 90s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 90s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 90s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 90s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 90s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 90s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 90s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 90s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 90s 91 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 237 MB of archives. 90s After this operation, 339 MB of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 90s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 90s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 90s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 90s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 90s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 90s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 90s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 90s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 90s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 90s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 90s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 90s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 90s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 90s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 90s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 90s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 90s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 90s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 90s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 90s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 90s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 90s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 90s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 91s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 91s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 91s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 91s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 91s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 91s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 91s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 91s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 91s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 91s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 91s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 91s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 91s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 91s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 91s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 91s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 91s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 91s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 91s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 91s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 91s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 91s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 91s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 91s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 91s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 91s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 91s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 91s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 91s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 91s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 91s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 91s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 91s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 91s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 91s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 91s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.565 [13.3 kB] 91s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 91s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 92s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 92s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 92s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 92s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 92s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 92s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli1 amd64 1.2.0-3 [343 kB] 92s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 92s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 92s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 92s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 92s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 92s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 92s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 92s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 92s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 93s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 93s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 144s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 146s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 146s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 146s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 146s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 146s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 146s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 146s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 149s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 149s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 149s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 150s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 150s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 150s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 150s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 150s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 150s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 150s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.565 [13.1 kB] 150s dpkg-preconfigure: unable to re-open stdin: No such file or directory 150s Fetched 237 MB in 60s (3931 kB/s) 150s (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 ... 83957 files and directories currently installed.) 150s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 150s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 151s Setting up debianutils (5.23.2build1) ... 151s (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 ... 83957 files and directories currently installed.) 151s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 151s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 151s Setting up dash (0.5.12-12ubuntu3) ... 151s (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 ... 83957 files and directories currently installed.) 151s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 151s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 151s Setting up findutils (4.10.0-3build2) ... 151s (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 ... 83957 files and directories currently installed.) 151s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 151s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 151s Setting up sed (4.9-2build3) ... 151s (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 ... 83957 files and directories currently installed.) 151s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 151s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 151s Setting up tar (1.35+dfsg-3.1build2) ... 151s (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 ... 83957 files and directories currently installed.) 151s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 151s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 151s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 151s Selecting previously unselected package gcc-16-base:amd64. 151s (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 ... 83957 files and directories currently installed.) 151s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 151s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 151s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 151s (Reading database ... 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158s Setting up ubuntu-kernel-accessories (1.565) ... 158s Setting up libgpm2:amd64 (1.20.7-12build1) ... 158s Setting up libgdbm6t64:amd64 (1.26-1build1) ... 158s Setting up linux-modules-6.19.0-3-generic (6.19.0-3.3) ... 160s Setting up libgdbm-compat4t64:amd64 (1.26-1build1) ... 160s Setting up bpftool (7.7.0+6.19.0-3.3) ... 160s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 160s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 160s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 160s Setting up libbrotli1:amd64 (1.2.0-3) ... 160s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 160s Setting up libsensors-config (1:3.6.2-2build1) ... 160s Setting up less (668-1build1) ... 160s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 160s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 160s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 160s amd64-microcode: microcode will be updated at next boot 160s Setting up man-db (2.13.1-1build1) ... 160s Updating database of manual pages ... 161s man-db.service is a disabled or a static unit not running, not starting it. 161s Setting up libjansson4:amd64 (2.14-2build4) ... 161s Setting up libglib2.0-data (2.87.2-2) ... 161s Setting up pollinate (4.33-4ubuntu5) ... 172s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 172s Setting up libwrap0:amd64 (7.6.q-36build2) ... 172s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 173s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 173s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 173s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 173s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 173s Setting up patch (2.8-2build1) ... 173s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 173s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 173s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 173s Setting up lsof (4.99.4+dfsg-2build2) ... 173s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 173s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 173s Setting up dracut-install (109-11ubuntu1) ... 173s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 173s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 173s Setting up pnp.ids (0.394-1build1) ... 173s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 173s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 173s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 173s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 173s Setting up mawk (1.3.4.20260129-1) ... 173s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 173s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 173s Setting up linux-image-virtual (6.19.0-3.3) ... 173s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 173s Setting up libbsd0:amd64 (0.12.2-2build2) ... 173s Setting up libdrm-common (2.4.131-1) ... 173s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 173s Setting up dbus-bin (1.16.2-2ubuntu3) ... 173s Setting up libonig5:amd64 (6.9.10-1build1) ... 173s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 173s Setting up ethtool (1:6.15-3build1) ... 173s Setting up python3-referencing (0.36.2-1ubuntu2) ... 173s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 173s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 173s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 173s Setting up tcpdump (4.99.5-2ubuntu3) ... 173s Setting up linux-image-generic (6.19.0-3.3) ... 173s Setting up wget (1.25.0-2ubuntu4) ... 173s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 173s Setting up iptables (1.8.11-2ubuntu3) ... 174s Setting up iproute2 (6.18.0-1ubuntu1) ... 174s Setting up linux-headers-generic (6.19.0-3.3) ... 174s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 174s Setting up hwdata (0.394-1build1) ... 174s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 174s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 174s No schema files found: doing nothing. 174s Setting up dbus (1.16.2-2ubuntu3) ... 174s A reboot is required to replace the running dbus-daemon. 174s Please reboot the system when convenient. 174s Setting up shared-mime-info (2.4-5build3) ... 175s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 175s Setting up pciutils (1:3.14.0-1build2) ... 175s Setting up python3-markdown-it (3.0.0-3build1) ... 175s Setting up libdrm2:amd64 (2.4.131-1) ... 175s Setting up libpython3.14:amd64 (3.14.2-1) ... 175s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 175s Setting up linux-tools-common (6.19.0-3.3) ... 175s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 175s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 175s Setting up apt (3.1.15) ... 176s Setting up linux-headers-virtual (6.19.0-3.3) ... 176s Setting up linux-generic (6.19.0-3.3) ... 176s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 176s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 176s Setting up ubuntu-standard (1.565) ... 176s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 176s Setting up linux-virtual (6.19.0-3.3) ... 176s Setting up linux-perf (6.19.0-3.3) ... 176s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 176s Processing triggers for debianutils (5.23.2build1) ... 176s Processing triggers for install-info (7.2-5) ... 176s Processing triggers for initramfs-tools (0.150ubuntu7) ... 176s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 182s Processing triggers for libc-bin (2.42-2ubuntu4) ... 182s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 182s /etc/kernel/postinst.d/initramfs-tools: 182s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 187s /etc/kernel/postinst.d/zz-update-grub: 187s Sourcing file `/etc/default/grub' 187s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 187s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 187s Generating grub configuration file ... 187s Found linux image: /boot/vmlinuz-6.19.0-3-generic 187s Found initrd image: /boot/initrd.img-6.19.0-3-generic 187s Found linux image: /boot/vmlinuz-6.18.0-9-generic 187s Found initrd image: /boot/initrd.img-6.18.0-9-generic 187s Warning: os-prober will not be executed to detect other bootable partitions. 187s Systems on them will not be added to the GRUB boot configuration. 187s Check GRUB_DISABLE_OS_PROBER documentation entry. 187s Adding boot menu entry for UEFI Firmware Settings ... 187s done 187s autopkgtest [11:17:28]: upgrading testbed (apt dist-upgrade and autopurge) 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s Calculating upgrade... 189s The following package was automatically installed and is no longer required: 189s libpython3.13 189s Use 'sudo apt autoremove' to remove it. 189s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Solving dependencies... 189s The following packages will be REMOVED: 189s libpython3.13* 189s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 189s After this operation, 7599 kB disk space will be freed. 189s (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 ... 125273 files and directories currently installed.) 189s Removing libpython3.13:amd64 (3.13.11-1) ... 189s Processing triggers for libc-bin (2.42-2ubuntu4) ... 190s autopkgtest [11:17:31]: rebooting testbed after setup commands that affected boot 219s autopkgtest [11:18:00]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 221s autopkgtest [11:18:02]: @@@@@@@@@@@@@@@@@@@@ apt-source bbmap 222s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (dsc) [2286 B] 222s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (tar) [5748 kB] 222s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bbmap 39.20+dfsg-3 (diff) [27.0 kB] 222s gpgv: Signature made Fri Nov 7 18:57:54 2025 UTC 222s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 222s gpgv: issuer "emollier@debian.org" 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./bbmap_39.20+dfsg-3.dsc: no acceptable signature found 223s autopkgtest [11:18:04]: testing package bbmap version 39.20+dfsg-3 224s autopkgtest [11:18:05]: build not needed 225s autopkgtest [11:18:06]: test run-unit-test: preparing testbed 225s Reading package lists... 226s Building dependency tree... 226s Reading state information... 226s Solving dependencies... 226s The following NEW packages will be installed: 226s bbmap bbmap-jni ca-certificates-java default-jre-headless java-common 226s libapache-pom-java libcommons-cli-java libcommons-codec-java 226s libcommons-io-java libcommons-parent-java libjpeg-turbo8 libjpeg8 226s libjs-jquery liblcms2-2 liblog4j1.2-java libmpj-java libpcsclite1 226s openjdk-21-jre-headless python-biopython-doc 226s 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 77.7 MB of archives. 226s After this operation, 256 MB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 226s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapache-pom-java all 33-2build1 [5976 B] 226s Get:3 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-parent-java all 56-1build1 [11.1 kB] 226s Get:4 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-codec-java all 1.18.0-1 [303 kB] 226s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-io-java all 2.19.0-1 [491 kB] 226s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblog4j1.2-java all 1.2.17-11build1 [445 kB] 226s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpj-java all 0.44+dfsg-4build1 [445 kB] 226s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 ca-certificates-java all 20240118build1 [11.7 kB] 226s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 java-common all 0.76build1 [6956 B] 226s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 226s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 226s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 226s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcsclite1 amd64 2.4.1-1 [24.6 kB] 226s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 openjdk-21-jre-headless amd64 21.0.10+7-1 [46.5 MB] 228s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 default-jre-headless amd64 2:1.21-76build1 [3266 B] 228s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 bbmap all 39.20+dfsg-3 [10.6 MB] 228s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 bbmap-jni amd64 39.20+dfsg-3 [28.1 kB] 228s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 228s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 229s Fetched 77.7 MB in 3s (28.0 MB/s) 229s Selecting previously unselected package libcommons-cli-java. 229s (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 ... 125269 files and directories currently installed.) 229s Preparing to unpack .../00-libcommons-cli-java_1.6.0-1_all.deb ... 229s Unpacking libcommons-cli-java (1.6.0-1) ... 229s Selecting previously unselected package libapache-pom-java. 229s Preparing to unpack .../01-libapache-pom-java_33-2build1_all.deb ... 229s Unpacking libapache-pom-java (33-2build1) ... 229s Selecting previously unselected package libcommons-parent-java. 229s Preparing to unpack .../02-libcommons-parent-java_56-1build1_all.deb ... 229s Unpacking libcommons-parent-java (56-1build1) ... 229s Selecting previously unselected package libcommons-codec-java. 229s Preparing to unpack .../03-libcommons-codec-java_1.18.0-1_all.deb ... 229s Unpacking libcommons-codec-java (1.18.0-1) ... 229s Selecting previously unselected package libcommons-io-java. 229s Preparing to unpack .../04-libcommons-io-java_2.19.0-1_all.deb ... 229s Unpacking libcommons-io-java (2.19.0-1) ... 229s Selecting previously unselected package liblog4j1.2-java. 229s Preparing to unpack .../05-liblog4j1.2-java_1.2.17-11build1_all.deb ... 229s Unpacking liblog4j1.2-java (1.2.17-11build1) ... 229s Selecting previously unselected package libmpj-java. 229s Preparing to unpack .../06-libmpj-java_0.44+dfsg-4build1_all.deb ... 229s Unpacking libmpj-java (0.44+dfsg-4build1) ... 229s Selecting previously unselected package ca-certificates-java. 229s Preparing to unpack .../07-ca-certificates-java_20240118build1_all.deb ... 229s Unpacking ca-certificates-java (20240118build1) ... 229s Selecting previously unselected package java-common. 229s Preparing to unpack .../08-java-common_0.76build1_all.deb ... 229s Unpacking java-common (0.76build1) ... 229s Selecting previously unselected package liblcms2-2:amd64. 229s Preparing to unpack .../09-liblcms2-2_2.17-1_amd64.deb ... 229s Unpacking liblcms2-2:amd64 (2.17-1) ... 229s Selecting previously unselected package libjpeg-turbo8:amd64. 229s Preparing to unpack .../10-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 229s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 229s Selecting previously unselected package libjpeg8:amd64. 229s Preparing to unpack .../11-libjpeg8_8c-2ubuntu12_amd64.deb ... 229s Unpacking libjpeg8:amd64 (8c-2ubuntu12) ... 229s Selecting previously unselected package libpcsclite1:amd64. 229s Preparing to unpack .../12-libpcsclite1_2.4.1-1_amd64.deb ... 229s Unpacking libpcsclite1:amd64 (2.4.1-1) ... 229s Selecting previously unselected package openjdk-21-jre-headless:amd64. 229s Preparing to unpack .../13-openjdk-21-jre-headless_21.0.10+7-1_amd64.deb ... 229s Unpacking openjdk-21-jre-headless:amd64 (21.0.10+7-1) ... 230s Selecting previously unselected package default-jre-headless. 230s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76build1_amd64.deb ... 230s Unpacking default-jre-headless (2:1.21-76build1) ... 230s Selecting previously unselected package bbmap. 230s Preparing to unpack .../15-bbmap_39.20+dfsg-3_all.deb ... 230s Unpacking bbmap (39.20+dfsg-3) ... 230s Selecting previously unselected package bbmap-jni. 230s Preparing to unpack .../16-bbmap-jni_39.20+dfsg-3_amd64.deb ... 230s Unpacking bbmap-jni (39.20+dfsg-3) ... 230s Selecting previously unselected package libjs-jquery. 230s Preparing to unpack .../17-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 230s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 230s Selecting previously unselected package python-biopython-doc. 230s Preparing to unpack .../18-python-biopython-doc_1.86+dfsg-1_all.deb ... 230s Unpacking python-biopython-doc (1.86+dfsg-1) ... 230s Setting up liblcms2-2:amd64 (2.17-1) ... 230s Setting up java-common (0.76build1) ... 230s Setting up libcommons-cli-java (1.6.0-1) ... 230s Setting up liblog4j1.2-java (1.2.17-11build1) ... 230s Setting up libapache-pom-java (33-2build1) ... 230s Setting up libpcsclite1:amd64 (2.4.1-1) ... 230s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 230s Setting up bbmap-jni (39.20+dfsg-3) ... 230s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 230s Setting up ca-certificates-java (20240118build1) ... 230s No JRE found. Skipping Java certificates setup. 230s Setting up libjpeg8:amd64 (8c-2ubuntu12) ... 230s Setting up openjdk-21-jre-headless:amd64 (21.0.10+7-1) ... 230s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 230s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 230s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 230s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 230s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 230s Setting up libcommons-parent-java (56-1build1) ... 230s Setting up python-biopython-doc (1.86+dfsg-1) ... 230s Setting up libcommons-codec-java (1.18.0-1) ... 230s Setting up libcommons-io-java (2.19.0-1) ... 230s Setting up libmpj-java (0.44+dfsg-4build1) ... 230s Processing triggers for libc-bin (2.42-2ubuntu4) ... 230s Processing triggers for man-db (2.13.1-1build1) ... 231s Processing triggers for ca-certificates-java (20240118build1) ... 231s Adding debian:ACCVRAIZ1.pem 231s Adding debian:AC_RAIZ_FNMT-RCM.pem 231s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 231s Adding debian:ANF_Secure_Server_Root_CA.pem 231s Adding debian:Actalis_Authentication_Root_CA.pem 231s Adding debian:AffirmTrust_Commercial.pem 231s Adding debian:AffirmTrust_Networking.pem 231s Adding debian:AffirmTrust_Premium.pem 231s Adding debian:AffirmTrust_Premium_ECC.pem 231s Adding debian:Amazon_Root_CA_1.pem 231s Adding debian:Amazon_Root_CA_2.pem 231s Adding debian:Amazon_Root_CA_3.pem 231s Adding debian:Amazon_Root_CA_4.pem 231s Adding debian:Atos_TrustedRoot_2011.pem 231s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 231s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 231s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 231s Adding debian:BJCA_Global_Root_CA1.pem 231s Adding debian:BJCA_Global_Root_CA2.pem 231s Adding debian:Baltimore_CyberTrust_Root.pem 231s Adding debian:Buypass_Class_2_Root_CA.pem 231s Adding debian:Buypass_Class_3_Root_CA.pem 231s Adding debian:CA_Disig_Root_R2.pem 231s Adding debian:CFCA_EV_ROOT.pem 231s Adding debian:COMODO_Certification_Authority.pem 231s Adding debian:COMODO_ECC_Certification_Authority.pem 231s Adding debian:COMODO_RSA_Certification_Authority.pem 231s Adding debian:Certainly_Root_E1.pem 231s Adding debian:Certainly_Root_R1.pem 231s Adding debian:Certigna.pem 231s Adding debian:Certigna_Root_CA.pem 231s Adding debian:Certum_EC-384_CA.pem 231s Adding debian:Certum_Trusted_Network_CA.pem 231s Adding debian:Certum_Trusted_Network_CA_2.pem 231s Adding debian:Certum_Trusted_Root_CA.pem 231s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 231s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 231s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 231s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 231s Adding debian:Comodo_AAA_Services_root.pem 231s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 231s Adding debian:D-TRUST_BR_Root_CA_2_2023.pem 231s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 231s Adding debian:D-TRUST_EV_Root_CA_2_2023.pem 231s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 231s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 231s Adding debian:DigiCert_Assured_ID_Root_CA.pem 231s Adding debian:DigiCert_Assured_ID_Root_G2.pem 231s Adding debian:DigiCert_Assured_ID_Root_G3.pem 231s Adding debian:DigiCert_Global_Root_CA.pem 231s Adding debian:DigiCert_Global_Root_G2.pem 231s Adding debian:DigiCert_Global_Root_G3.pem 231s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 231s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 231s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 231s Adding debian:DigiCert_Trusted_Root_G4.pem 231s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 231s Adding debian:Entrust_Root_Certification_Authority.pem 231s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 231s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 231s Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem 231s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 231s Adding debian:GLOBALTRUST_2020.pem 231s Adding debian:GTS_Root_R1.pem 231s Adding debian:GTS_Root_R2.pem 231s Adding debian:GTS_Root_R3.pem 231s Adding debian:GTS_Root_R4.pem 231s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 231s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 231s Adding debian:GlobalSign_Root_CA.pem 231s Adding debian:GlobalSign_Root_CA_-_R3.pem 231s Adding debian:GlobalSign_Root_CA_-_R6.pem 231s Adding debian:GlobalSign_Root_E46.pem 231s Adding debian:GlobalSign_Root_R46.pem 231s Adding debian:Go_Daddy_Class_2_CA.pem 231s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 231s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 231s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 231s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 231s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 231s Adding debian:HiPKI_Root_CA_-_G1.pem 231s Adding debian:Hongkong_Post_Root_CA_3.pem 231s Adding debian:ISRG_Root_X1.pem 231s Adding debian:ISRG_Root_X2.pem 231s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 231s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 231s Adding debian:Izenpe.com.pem 231s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 231s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 231s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 231s Adding debian:NAVER_Global_Root_Certification_Authority.pem 231s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 231s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 231s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 231s Adding debian:QuoVadis_Root_CA_1_G3.pem 231s Adding debian:QuoVadis_Root_CA_2.pem 231s Adding debian:QuoVadis_Root_CA_2_G3.pem 231s Adding debian:QuoVadis_Root_CA_3.pem 231s Adding debian:QuoVadis_Root_CA_3_G3.pem 231s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 231s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 231s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 231s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 231s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 231s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 231s Adding debian:SZAFIR_ROOT_CA2.pem 231s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 231s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 231s Adding debian:SecureSign_Root_CA12.pem 231s Adding debian:SecureSign_Root_CA14.pem 231s Adding debian:SecureSign_Root_CA15.pem 231s Adding debian:SecureTrust_CA.pem 231s Adding debian:Secure_Global_CA.pem 231s Adding debian:Security_Communication_ECC_RootCA1.pem 231s Adding debian:Security_Communication_RootCA2.pem 231s Adding debian:Starfield_Class_2_CA.pem 231s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 231s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 231s Adding debian:SwissSign_Gold_CA_-_G2.pem 231s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 231s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 231s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 231s Adding debian:TWCA_CYBER_Root_CA.pem 231s Adding debian:TWCA_Global_Root_CA.pem 231s Adding debian:TWCA_Root_Certification_Authority.pem 231s Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem 231s Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem 231s Adding debian:TeliaSonera_Root_CA_v1.pem 231s Adding debian:Telia_Root_CA_v2.pem 231s Adding debian:TrustAsia_Global_Root_CA_G3.pem 231s Adding debian:TrustAsia_Global_Root_CA_G4.pem 231s Adding debian:Trustwave_Global_Certification_Authority.pem 231s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 231s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 231s Adding debian:TunTrust_Root_CA.pem 231s Adding debian:UCA_Extended_Validation_Root.pem 231s Adding debian:UCA_Global_G2_Root.pem 231s Adding debian:USERTrust_ECC_Certification_Authority.pem 231s Adding debian:USERTrust_RSA_Certification_Authority.pem 231s Adding debian:XRamp_Global_CA_Root.pem 231s Adding debian:certSIGN_ROOT_CA.pem 231s Adding debian:certSIGN_Root_CA_G2.pem 231s Adding debian:e-Szigno_Root_CA_2017.pem 231s Adding debian:ePKI_Root_Certification_Authority.pem 231s Adding debian:emSign_ECC_Root_CA_-_C3.pem 231s Adding debian:emSign_ECC_Root_CA_-_G3.pem 231s Adding debian:emSign_Root_CA_-_C1.pem 231s Adding debian:emSign_Root_CA_-_G1.pem 231s Adding debian:vTrus_ECC_Root_CA.pem 231s Adding debian:vTrus_Root_CA.pem 231s done. 231s Setting up bbmap (39.20+dfsg-3) ... 231s Setting up default-jre-headless (2:1.21-76build1) ... 232s autopkgtest [11:18:13]: test run-unit-test: [----------------------- 232s 232s # bbmap 232s bbmap.sh --version 232s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 232s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 --version 232s BBTools version 39.20 232s For help, please run the shellscript with no parameters, or look in /docs/. 232s bbmap.sh --help 232s 232s BBMap 232s Written by Brian Bushnell, from Dec. 2010 - present 232s Last modified September 15, 2022 232s 232s Description: Fast and accurate splice-aware read aligner. 232s Please read bbmap/docs/guides/BBMapGuide.txt for more information. 232s 232s To index: bbmap.sh ref= 232s To map: bbmap.sh in= out= 232s To map without writing an index: 232s bbmap.sh ref= in= out= nodisk 232s 232s in=stdin will accept reads from standard in, and out=stdout will write to 232s standard out, but file extensions are still needed to specify the format of the 232s input and output files e.g. in=stdin.fa.gz will read gzipped fasta from 232s standard in; out=stdout.sam.gz will write gzipped sam. 232s 232s Indexing Parameters (required when building the index): 232s nodisk=f Set to true to build index in memory and write nothing 232s to disk except output. 232s ref= Specify the reference sequence. Only do this ONCE, 232s when building the index (unless using 'nodisk'). 232s build=1 If multiple references are indexed in the same directory, 232s each needs a unique numeric ID (unless using 'nodisk'). 232s k=13 Kmer length, range 8-15. Longer is faster but uses 232s more memory. Shorter is more sensitive. 232s If indexing and mapping are done in two steps, K should 232s be specified each time. 232s path=<.> Specify the location to write the index, if you don't 232s want it in the current working directory. 232s usemodulo=f Throw away ~80% of kmers based on remainder modulo a 232s number (reduces RAM by 50% and sensitivity slightly). 232s Should be enabled both when building the index AND 232s when mapping. 232s rebuild=f Force a rebuild of the index (ref= should be set). 232s 232s Input Parameters: 232s build=1 Designate index to use. Corresponds to the number 232s specified when building the index. 232s in= Primary reads input; required parameter. 232s in2= For paired reads in two files. 232s interleaved=auto True forces paired/interleaved input; false forces 232s single-ended mapping. If not specified, interleaved 232s status will be autodetected from read names. 232s fastareadlen=500 Break up FASTA reads longer than this. Max is 500 for 232s BBMap and 6000 for BBMapPacBio. Only works for FASTA 232s input (use 'maxlen' for FASTQ input). The default for 232s bbmap.sh is 500, and for mapPacBio.sh is 6000. 232s unpigz=f Spawn a pigz (parallel gzip) process for faster 232s decompression than using Java. 232s Requires pigz to be installed. 232s touppercase=t (tuc) Convert lowercase letters in reads to upper case 232s (otherwise they will not match the reference). 232s 232s Sampling Parameters: 232s 232s reads=-1 Set to a positive number N to only process the first N 232s reads (or pairs), then quit. -1 means use all reads. 232s samplerate=1 Set to a number from 0 to 1 to randomly select that 232s fraction of reads for mapping. 1 uses all reads. 232s skipreads=0 Set to a number N to skip the first N reads (or pairs), 232s then map the rest. 232s 232s Mapping Parameters: 232s fast=f This flag is a macro which sets other paramters to run 232s faster, at reduced sensitivity. Bad for RNA-seq. 232s slow=f This flag is a macro which sets other paramters to run 232s slower, at greater sensitivity. 'vslow' is even slower. 232s maxindel=16000 Don't look for indels longer than this. Lower is faster. 232s Set to >=100k for RNAseq with long introns like mammals. 232s strictmaxindel=f When enabled, do not allow indels longer than 'maxindel'. 232s By default these are not sought, but may be found anyway. 232s tipsearch=100 Look this far for read-end deletions with anchors 232s shorter than K, using brute force. 232s minid=0.76 Approximate minimum alignment identity to look for. 232s Higher is faster and less sensitive. 232s minhits=1 Minimum number of seed hits required for candidate sites. 232s Higher is faster. 232s local=f Set to true to use local, rather than global, alignments. 232s This will soft-clip ugly ends of poor alignments. 232s perfectmode=f Allow only perfect mappings when set to true (very fast). 232s semiperfectmode=f Allow only perfect and semiperfect (perfect except for 232s N's in the reference) mappings. 232s threads=auto (t) Set to number of threads desired. By default, uses 232s all cores available. 232s ambiguous=best (ambig) Set behavior on ambiguously-mapped reads (with 232s multiple top-scoring mapping locations). 232s best (use the first best site) 232s toss (consider unmapped) 232s random (select one top-scoring site randomly) 232s all (retain all top-scoring sites) 232s samestrandpairs=f (ssp) Specify whether paired reads should map to the 232s same strand or opposite strands. 232s requirecorrectstrand=t (rcs) Forbid pairing of reads without correct strand 232s orientation. Set to false for long-mate-pair libraries. 232s killbadpairs=f (kbp) If a read pair is mapped with an inappropriate 232s insert size or orientation, the read with the lower 232s mapping quality is marked unmapped. 232s pairedonly=f (po) Treat unpaired reads as unmapped. Thus they will 232s be sent to 'outu' but not 'outm'. 232s rcomp=f Reverse complement both reads prior to mapping (for LMP 232s outward-facing libraries). 232s rcompmate=f Reverse complement read2 prior to mapping. 232s pairlen=32000 Set max allowed distance between paired reads. 232s (insert size)=(pairlen)+(read1 length)+(read2 length) 232s rescuedist=1200 Don't try to rescue paired reads if avg. insert size 232s greater than this. Lower is faster. 232s rescuemismatches=32 Maximum mismatches allowed in a rescued read. Lower 232s is faster. 232s averagepairdist=100 (apd) Initial average distance between paired reads. 232s Varies dynamically; does not need to be specified. 232s deterministic=f Run in deterministic mode. In this case it is good 232s to set averagepairdist. BBMap is deterministic 232s without this flag if using single-ended reads, 232s or run singlethreaded. 232s bandwidthratio=0 (bwr) If above zero, restrict alignment band to this 232s fraction of read length. Faster but less accurate. 232s bandwidth=0 (bw) Set the bandwidth directly. 232s fraction of read length. Faster but less accurate. 232s usejni=f (jni) Do alignments faster, in C code. Requires 232s compiling the C code; details are in /jni/README.txt. 232s maxsites2=800 Don't analyze (or print) more than this many alignments 232s per read. 232s ignorefrequentkmers=t (ifk) Discard low-information kmers that occur often. 232s excludefraction=0.03 (ef) Fraction of kmers to ignore. For example, 0.03 232s will ignore the most common 3% of kmers. 232s greedy=t Use a greedy algorithm to discard the least-useful 232s kmers on a per-read basis. 232s kfilter=0 If positive, potential mapping sites must have at 232s least this many consecutive exact matches. 232s 232s 232s Quality and Trimming Parameters: 232s qin=auto Set to 33 or 64 to specify input quality value ASCII 232s offset. 33 is Sanger, 64 is old Solexa. 232s qout=auto Set to 33 or 64 to specify output quality value ASCII 232s offset (only if output format is fastq). 232s qtrim=f Quality-trim ends before mapping. Options are: 232s 'f' (false), 'l' (left), 'r' (right), and 'lr' (both). 232s untrim=f Undo trimming after mapping. Untrimmed bases will be 232s soft-clipped in cigar strings. 232s trimq=6 Trim regions with average quality below this 232s (phred algorithm). 232s mintrimlength=60 (mintl) Don't trim reads to be shorter than this. 232s fakefastaquality=-1 (ffq) Set to a positive number 1-50 to generate fake 232s quality strings for fasta input reads. 232s ignorebadquality=f (ibq) Keep going, rather than crashing, if a read has 232s out-of-range quality values. 232s usequality=t Use quality scores when determining which read kmers 232s to use as seeds. 232s minaveragequality=0 (maq) Do not map reads with average quality below this. 232s maqb=0 If positive, calculate maq from this many initial bases. 232s 232s Output Parameters: 232s out= Write all reads to this file. 232s outu= Write only unmapped reads to this file. Does not 232s include unmapped paired reads with a mapped mate. 232s outm= Write only mapped reads to this file. Includes 232s unmapped paired reads with a mapped mate. 232s mappedonly=f If true, treats 'out' like 'outm'. 232s bamscript= (bs) Write a shell script to that will turn 232s the sam output into a sorted, indexed bam file. 232s ordered=f Set to true to output reads in same order as input. 232s Slower and uses more memory. 232s overwrite=f (ow) Allow process to overwrite existing files. 232s secondary=f Print secondary alignments. 232s sssr=0.95 (secondarysitescoreratio) Print only secondary alignments 232s with score of at least this fraction of primary. 232s ssao=f (secondarysiteasambiguousonly) Only print secondary 232s alignments for ambiguously-mapped reads. 232s maxsites=5 Maximum number of total alignments to print per read. 232s Only relevant when secondary=t. 232s quickmatch=f Generate cigar strings more quickly. 232s trimreaddescriptions=f (trd) Truncate read and ref names at the first whitespace, 232s assuming that the remainder is a comment or description. 232s ziplevel=2 (zl) Compression level for zip or gzip output. 232s pigz=f Spawn a pigz (parallel gzip) process for faster 232s compression than Java. Requires pigz to be installed. 232s machineout=f Set to true to output statistics in machine-friendly 232s 'key=value' format. 232s printunmappedcount=f Print the total number of unmapped reads and bases. 232s If input is paired, the number will be of pairs 232s for which both reads are unmapped. 232s showprogress=0 If positive, print a '.' every X reads. 232s showprogress2=0 If positive, print the number of seconds since the 232s last progress update (instead of a '.'). 232s renamebyinsert=f Renames reads based on their mapped insert size. 232s 232s Bloom-Filtering Parameters (bloomfilter.sh is the standalone version). 232s bloom=f Use a Bloom filter to ignore reads not sharing kmers 232s with the reference. This uses more memory, but speeds 232s mapping when most reads don't match the reference. 232s bloomhashes=2 Number of hash functions. 232s bloomminhits=3 Number of consecutive hits to be considered matched. 232s bloomk=31 Bloom filter kmer length. 232s bloomserial=t Use the serialized Bloom filter for greater loading 232s speed, if available. If not, generate and write one. 232s 232s Post-Filtering Parameters: 232s idfilter=0 Independant of minid; sets exact minimum identity 232s allowed for alignments to be printed. Range 0 to 1. 232s subfilter=-1 Ban alignments with more than this many substitutions. 232s insfilter=-1 Ban alignments with more than this many insertions. 232s delfilter=-1 Ban alignments with more than this many deletions. 232s indelfilter=-1 Ban alignments with more than this many indels. 232s editfilter=-1 Ban alignments with more than this many edits. 232s inslenfilter=-1 Ban alignments with an insertion longer than this. 232s dellenfilter=-1 Ban alignments with a deletion longer than this. 232s nfilter=-1 Ban alignments with more than this many ns. This 232s includes nocall, noref, and off scaffold ends. 232s 232s Sam flags and settings: 232s noheader=f Disable generation of header lines. 232s sam=1.4 Set to 1.4 to write Sam version 1.4 cigar strings, 232s with = and X, or 1.3 to use M. 232s saa=t (secondaryalignmentasterisks) Use asterisks instead of 232s bases for sam secondary alignments. 232s cigar=t Set to 'f' to skip generation of cigar strings (faster). 232s keepnames=f Keep original names of paired reads, rather than 232s ensuring both reads have the same name. 232s intronlen=999999999 Set to a lower number like 10 to change 'D' to 'N' in 232s cigar strings for deletions of at least that length. 232s rgid= Set readgroup ID. All other readgroup fields 232s can be set similarly, with the flag rgXX= 232s If you set a readgroup flag to the word 'filename', 232s e.g. rgid=filename, the input file name will be used. 232s mdtag=f Write MD tags. 232s nhtag=f Write NH tags. 232s xmtag=f Write XM tags (may only work correctly with ambig=all). 232s amtag=f Write AM tags. 232s nmtag=f Write NM tags. 232s xstag=f Set to 'xs=fs', 'xs=ss', or 'xs=us' to write XS tags 232s for RNAseq using firststrand, secondstrand, or 232s unstranded libraries. Needed by Cufflinks. 232s JGI mainly uses 'firststrand'. 232s stoptag=f Write a tag indicating read stop location, prefixed by YS:i: 232s lengthtag=f Write a tag indicating (query,ref) alignment lengths, 232s prefixed by YL:Z: 232s idtag=f Write a tag indicating percent identity, prefixed by YI:f: 232s inserttag=f Write a tag indicating insert size, prefixed by X8:Z: 232s scoretag=f Write a tag indicating BBMap's raw score, prefixed by YR:i: 232s timetag=f Write a tag indicating this read's mapping time, prefixed by X0:i: 232s boundstag=f Write a tag indicating whether either read in the pair 232s goes off the end of the reference, prefixed by XB:Z: 232s notags=f Turn off all optional tags. 232s 232s Histogram and statistics output parameters: 232s scafstats= Statistics on how many reads mapped to which scaffold. 232s refstats= Statistics on how many reads mapped to which reference 232s file; only for BBSplit. 232s sortscafs=t Sort scaffolds or references by read count. 232s bhist= Base composition histogram by position. 232s qhist= Quality histogram by position. 232s aqhist= Histogram of average read quality. 232s bqhist= Quality histogram designed for box plots. 232s lhist= Read length histogram. 232s ihist= Write histogram of insert sizes (for paired reads). 232s ehist= Errors-per-read histogram. 232s qahist= Quality accuracy histogram of error rates versus 232s quality score. 232s indelhist= Indel length histogram. 232s mhist= Histogram of match, sub, del, and ins rates by 232s read location. 232s gchist= Read GC content histogram. 232s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 232s gcpairs=t Use average GC of paired reads. 232s idhist= Histogram of read count versus percent identity. 232s idbins=100 Number idhist bins. Set to 'auto' to use read length. 232s statsfile=stderr Mapping statistics are printed here. 232s 232s Coverage output parameters (these may reduce speed and use more RAM): 232s covstats= Per-scaffold coverage info. 232s rpkm= Per-scaffold RPKM/FPKM counts. 232s covhist= Histogram of # occurrences of each depth level. 232s basecov= Coverage per base location. 232s bincov= Print binned coverage per location (one line per X bases). 232s covbinsize=1000 Set the binsize for binned coverage output. 232s nzo=t Only print scaffolds with nonzero coverage. 232s twocolumn=f Change to true to print only ID and Avg_fold instead of 232s all 6 columns to the 'out=' file. 232s 32bit=f Set to true if you need per-base coverage over 64k. 232s strandedcov=f Track coverage for plus and minus strand independently. 232s startcov=f Only track start positions of reads. 232s secondarycov=t Include coverage of secondary alignments. 232s physcov=f Calculate physical coverage for paired reads. 232s This includes the unsequenced bases. 232s delcoverage=t (delcov) Count bases covered by deletions as covered. 232s True is faster than false. 232s covk=0 If positive, calculate kmer coverage statistics. 232s 232s Java Parameters: 232s -Xmx This will set Java's memory usage, 232s overriding autodetection. 232s -Xmx20g will specify 20 gigs of RAM, and -Xmx800m 232s will specify 800 megs. The max is typically 85% of 232s physical memory. The human genome requires around 24g, 232s or 12g with the 'usemodulo' flag. The index uses 232s roughly 6 bytes per reference base. 232s -eoom This flag will cause the process to exit if an 232s out-of-memory exception occurs. Requires Java 8u92+. 232s -da Disable assertions. 232s 232s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter 232s any problems, or post at: http://seqanswers.com/forums/showthread.php?t=41057 232s 232s bbmap.sh ref=example.fasta 233s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 233s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta 233s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta] 233s Version 39.20 233s 233s No output file. 233s Writing reference. 233s 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] 233s 233s Set genScaffoldInfo=true 233s Writing chunk 1 233s Set genome to 1 233s 233s Loaded Reference: 0.003 seconds. 233s Loading index for chunk 1-1, build 1 233s No index available; generating from reference genome: /tmp/autopkgtest.m81D1v/autopkgtest_tmp/ref/index/1/chr1_index_k13_c16_b1.block 233s Indexing threads started for block 0-1 233s Indexing threads finished for block 0-1 233s Generated Index: 0.593 seconds. 233s No reads to process; quitting. 233s 233s Total time: 0.682 seconds. 233s test -d ref 233s bbmap.sh in=misc_dna_as_sanger.fastq out=out.sam 233s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 233s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 in=misc_dna_as_sanger.fastq out=out.sam 233s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=misc_dna_as_sanger.fastq, out=out.sam] 233s Version 39.20 233s 233s Retaining first best site only for ambiguous mappings. 233s Set genome to 1 233s 233s Loaded Reference: 0.014 seconds. 233s Loading index for chunk 1-1, build 1 234s Generated Index: 0.270 seconds. 236s Analyzed Index: 1.831 seconds. 236s Started output stream: 0.016 seconds. 236s Cleared Memory: 0.114 seconds. 236s Processing reads in single-ended mode. 236s Started read stream. 236s Started 4 mapping threads. 236s Detecting finished threads: 0, 1, 2, 3 236s 236s ------------------ Results ------------------ 236s 236s Genome: 1 236s Key Length: 13 236s Max Indel: 16000 236s Minimum Score Ratio: 0.56 236s Mapping Mode: normal 236s Reads Used: 4 (153 bases) 236s 236s Mapping: 0.072 seconds. 236s Reads/sec: 55.79 236s kBases/sec: 2.13 236s 236s 236s Read 1 data: pct reads num reads pct bases num bases 236s 236s mapped: 0.0000% 0 0.0000% 0 236s unambiguous: 0.0000% 0 0.0000% 0 236s ambiguous: 0.0000% 0 0.0000% 0 236s low-Q discards: 25.0000% 1 19.6078% 30 236s 236s perfect best site: 0.0000% 0 0.0000% 0 236s semiperfect site: 0.0000% 0 0.0000% 0 236s 236s Match Rate: NA NA NaN% 0 236s Error Rate: NaN% 0 NaN% 0 236s Sub Rate: NaN% 0 NaN% 0 236s Del Rate: NaN% 0 NaN% 0 236s Ins Rate: NaN% 0 NaN% 0 236s N Rate: NaN% 0 NaN% 0 236s 236s Total time: 2.378 seconds. 236s test -r out.sam 236s bbmap.sh ref=example.fasta in=example.fastq out=out2.sam nodisk 236s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 236s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar align2.BBMap build=1 overwrite=true fastareadlen=500 ref=example.fasta in=example.fastq out=out2.sam nodisk 236s Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=example.fasta, in=example.fastq, out=out2.sam, nodisk] 236s Version 39.20 236s 236s Retaining first best site only for ambiguous mappings. 236s 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] 236s 236s Set genScaffoldInfo=true 236s Set genome to 1 236s 236s Loaded Reference: 0.001 seconds. 236s Loading index for chunk 1-1, build 1 236s Indexing threads started for block 0-1 236s Indexing threads finished for block 0-1 236s Generated Index: 0.158 seconds. 238s Analyzed Index: 1.860 seconds. 238s Started output stream: 0.014 seconds. 238s Cleared Memory: 0.114 seconds. 238s Processing reads in single-ended mode. 238s Started read stream. 238s Started 4 mapping threads. 238s Detecting finished threads: 0, 1, 2, 3 238s 238s ------------------ Results ------------------ 238s 238s Genome: 1 238s Key Length: 13 238s Max Indel: 16000 238s Minimum Score Ratio: 0.56 238s Mapping Mode: normal 238s Reads Used: 3 (75 bases) 238s 238s Mapping: 0.079 seconds. 238s Reads/sec: 38.03 238s kBases/sec: 0.95 238s 238s 238s Read 1 data: pct reads num reads pct bases num bases 238s 238s mapped: 100.0000% 3 100.0000% 75 238s unambiguous: 100.0000% 3 100.0000% 75 238s ambiguous: 0.0000% 0 0.0000% 0 238s low-Q discards: 0.0000% 0 0.0000% 0 238s 238s perfect best site: 100.0000% 3 100.0000% 75 238s semiperfect site: 100.0000% 3 100.0000% 75 238s 238s Match Rate: NA NA 100.0000% 75 238s Error Rate: 0.0000% 0 0.0000% 0 238s Sub Rate: 0.0000% 0 0.0000% 0 238s Del Rate: 0.0000% 0 0.0000% 0 238s Ins Rate: 0.0000% 0 0.0000% 0 238s N Rate: 0.0000% 0 0.0000% 0 238s 238s Total time: 2.311 seconds. 238s test -r out2.sam 238s 238s # bbduk 238s bbduk.sh --version 238s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 238s java -ea -Xmx3078m -Xms3078m -cp /usr/share/java/bbmap.jar jgi.BBDuk --version 239s BBTools version 39.20 239s For help, please run the shellscript with no parameters, or look in /docs/. 239s 239s Written by Brian Bushnell 239s Last modified November 18, 2024 239s 239s Description: Compares reads to the kmers in a reference dataset, optionally 239s allowing an edit distance. Splits the reads into two outputs - those that 239s match the reference, and those that don't. Can also trim (remove) the matching 239s parts of the reads rather than binning the reads. 239s Please read bbmap/docs/guides/BBDukGuide.txt for more information. 239s 239s Usage: bbduk.sh in= out= ref= 239s 239s Input may be stdin or a fasta or fastq file, compressed or uncompressed. 239s If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 239s fasta input, set in=stdin.fa.gz 239s 239s Input parameters: 239s in= Main input. in=stdin.fq will pipe from stdin. 239s in2= Input for 2nd read of pairs in a different file. 239s ref= Comma-delimited list of reference files. 239s In addition to filenames, you may also use the keywords: 239s adapters, artifacts, phix, lambda, pjet, mtst, kapa 239s literal= Comma-delimited list of literal reference sequences. 239s Polymers are also allowed with the 'poly' prefix; 239s for example, 'literal=ATGGT,polyGC' will add both ATGGT 239s and GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC - 32+ of them, 239s enough replicates to ensure that all kmers are present. 239s touppercase=f (tuc) Change all bases upper-case. 239s interleaved=auto (int) t/f overrides interleaved autodetection. 239s Must be set mainually when streaming fastq input. 239s qin=auto Input quality offset: 33 (Sanger), 64, or auto. 239s reads=-1 If positive, quit after processing X reads or pairs. 239s copyundefined=f (cu) Process non-AGCT IUPAC reference bases by making all 239s possible unambiguous copies. Intended for short motifs 239s or adapter barcodes, as time/memory use is exponential. 239s samplerate=1 Set lower to only process a fraction of input reads. 239s samref= Optional reference fasta for processing sam files. 239s 239s Output parameters: 239s out= (outnonmatch) Write reads here that do not contain 239s kmers matching the database. 'out=stdout.fq' will pipe 239s to standard out. 239s out2= (outnonmatch2) Use this to write 2nd read of pairs to a 239s different file. 239s outm= (outmatch) Write reads here that fail filters. In default 239s kfilter mode, this means any read with a matching kmer. 239s In any mode, it also includes reads that fail filters such 239s as minlength, mingc, maxgc, entropy, etc. In other words, 239s it includes all reads that do not go to 'out'. 239s outm2= (outmatch2) Use this to write 2nd read of pairs to a 239s different file. 239s outs= (outsingle) Use this to write singleton reads whose mate 239s was trimmed shorter than minlen. 239s stats= Write statistics about which contamininants were detected. 239s refstats= Write statistics on a per-reference-file basis. 239s rpkm= Write RPKM for each reference sequence (for RNA-seq). 239s dump= Dump kmer tables to a file, in fasta format. 239s duk= Write statistics in duk's format. *DEPRECATED* 239s nzo=t Only write statistics about ref sequences with nonzero hits. 239s overwrite=t (ow) Grant permission to overwrite files. 239s showspeed=t (ss) 'f' suppresses display of processing speed. 239s ziplevel=2 (zl) Compression level; 1 (min) through 9 (max). 239s fastawrap=70 Length of lines in fasta output. 239s qout=auto Output quality offset: 33 (Sanger), 64, or auto. 239s statscolumns=3 (cols) Number of columns for stats output, 3 or 5. 239s 5 includes base counts. 239s rename=f Rename reads to indicate which sequences they matched. 239s refnames=f Use names of reference files rather than scaffold IDs. 239s trd=f Truncate read and ref names at the first whitespace. 239s ordered=f Set to true to output reads in same order as input. 239s maxbasesout=-1 If positive, quit after writing approximately this many 239s bases to out (outu/outnonmatch). 239s maxbasesoutm=-1 If positive, quit after writing approximately this many 239s bases to outm (outmatch). 239s json=f Print to screen in json format. 239s 239s Histogram output parameters: 239s bhist= Base composition histogram by position. 239s qhist= Quality histogram by position. 239s qchist= Count of bases with each quality value. 239s aqhist= Histogram of average read quality. 239s bqhist= Quality histogram designed for box plots. 239s lhist= Read length histogram. 239s phist= Polymer length histogram. 239s gchist= Read GC content histogram. 239s enthist= Read entropy histogram. 239s ihist= Insert size histogram, for paired reads in mapped sam. 239s gcbins=100 Number gchist bins. Set to 'auto' to use read length. 239s maxhistlen=6000 Set an upper bound for histogram lengths; higher uses 239s more memory. The default is 6000 for some histograms 239s and 80000 for others. 239s 239s Histograms for mapped sam/bam files only: 239s histbefore=t Calculate histograms from reads before processing. 239s ehist= Errors-per-read histogram. 239s qahist= Quality accuracy histogram of error rates versus quality 239s score. 239s indelhist= Indel length histogram. 239s mhist= Histogram of match, sub, del, and ins rates by position. 239s idhist= Histogram of read count versus percent identity. 239s idbins=100 Number idhist bins. Set to 'auto' to use read length. 239s varfile= Ignore substitution errors listed in this file when 239s calculating error rates. Can be generated with 239s CallVariants. 239s vcf= Ignore substitution errors listed in this VCF file 239s when calculating error rates. 239s ignorevcfindels=t Also ignore indels listed in the VCF. 239s 239s Processing parameters: 239s k=27 Kmer length used for finding contaminants. Contaminants 239s shorter than k will not be found. k must be at least 1. 239s rcomp=t Look for reverse-complements of kmers in addition to 239s forward kmers. 239s maskmiddle=t (mm) Treat the middle base of a kmer as a wildcard, to 239s increase sensitivity in the presence of errors. This may 239s also be set to a number, e.g. mm=3, to mask that many bp. 239s The default mm=t corresponds to mm=1 for odd-length kmers 239s and mm=2 for even-length kmers (as of v39.04), while 239s mm=f is always equivalent to mm=0. 239s minkmerhits=1 (mkh) Reads need at least this many matching kmers 239s to be considered as matching the reference. 239s minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total 239s kmers to hit a ref, in order to be considered a match. 239s If this and minkmerhits are set, the greater is used. 239s mincovfraction=0.0 (mcf) A reads needs at least this fraction of its total 239s bases to be covered by ref kmers to be considered a match. 239s If specified, mcf overrides mkh and mkf. 239s hammingdistance=0 (hdist) Maximum Hamming distance for ref kmers (subs only). 239s Memory use is proportional to (3*K)^hdist. 239s qhdist=0 Hamming distance for query kmers; impacts speed, not memory. 239s editdistance=0 (edist) Maximum edit distance from ref kmers (subs 239s and indels). Memory use is proportional to (8*K)^edist. 239s hammingdistance2=0 (hdist2) Sets hdist for short kmers, when using mink. 239s qhdist2=0 Sets qhdist for short kmers, when using mink. 239s editdistance2=0 (edist2) Sets edist for short kmers, when using mink. 239s forbidn=f (fn) Forbids matching of read kmers bbduk.sh --help 239s bbduk.sh in1=misc_dna_as_illumina.fastq in2=misc_rna_as_illumina.fastq \ 239s qtrim=rl trimq=15 minlen=75 out=out.fastq.gz 239s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 239s java -ea -Xmx3078m -Xms3078m -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 239s 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] 239s Version 39.20 239s 239s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 239s Changed from ASCII-33 to ASCII-64 on input quality X (Q55) for base A at lines 1 and 3, position 24 while prescanning. 239s Allocating kmer table: 0.011 seconds. 239s Initial: 239s Memory: max=3227m, total=3227m, free=3196m, used=31m 239s 239s Input is being processed as paired 239s Changed from ASCII-33 to ASCII-64 on input 7: 55 -> 24 239s Started output streams: 0.013 seconds. 239s Processing time: 0.003 seconds. 239s 239s Input: 8 reads 306 bases. 239s QTrimmed: 0 reads (0.00%) 0 bases (0.00%) 239s Total Removed: 8 reads (100.00%) 306 bases (100.00%) 239s Result: 0 reads (0.00%) 0 bases (0.00%) 239s 239s Time: 0.016 seconds. 239s Reads Processed: 8 0.50k reads/sec 239s Bases Processed: 306 0.02m bases/sec 239s test -r out.fastq.gz 239s 239s # bbnorm 239s bbnorm.sh --version 239s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 239s java -ea -Xmx4000m -Xms4000m -cp /usr/share/java/bbmap.jar jgi.KmerNormalize bits=32 --version 239s containing N. 239s By default, these will match a reference 'A' if 239s hdist>0 or edist>0, to increase sensitivity. 239s removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 239s match (or either is trimmed shorter than minlen). 239s Set to false to require both. 239s trimfailures=f Instead of discarding failed reads, trim them to 1bp. 239s This makes the statistics a bit odd. 239s findbestmatch=f (fbm) If multiple matches, associate read with sequence 239s sharing most kmers. Reduces speed. 239s skipr1=f Don't do kmer-based operations on read 1. 239s skipr2=f Don't do kmer-based operations on read 2. 239s ecco=f For overlapping paired reads only. Performs error- 239s correction with BBMerge prior to kmer operations. 239s recalibrate=f (recal) Recalibrate quality scores. Requires calibration 239s matrices generated by CalcTrueQuality. 239s sam= If recalibration is desired, and matrices have not already 239s been generated, BBDuk will create them from the sam file. 239s amino=f Run in amino acid mode. Some features have not been 239s tested, but kmer-matching works fine. Maximum k is 12. 239s 239s Speed and Memory parameters: 239s threads=auto (t) Set number of threads to use; default is number of 239s logical processors. 239s prealloc=f Preallocate memory in table. Allows faster table loading 239s and more efficient memory usage, for a large reference. 239s monitor=f Kill this process if it crashes. monitor=600,0.01 would 239s kill after 600 seconds under 1% usage. 239s minrskip=1 (mns) Force minimal skip interval when indexing reference 239s kmers. 1 means use all, 2 means use every other kmer, etc. 239s maxrskip=1 (mxs) Restrict maximal skip interval when indexing 239s reference kmers. Normally all are used for scaffolds<100kb, 239s but with longer scaffolds, up to maxrskip-1 are skipped. 239s rskip= Set both minrskip and maxrskip to the same value. 239s If not set, rskip will vary based on sequence length. 239s qskip=1 Skip query kmers to increase speed. 1 means use all. 239s speed=0 Ignore this fraction of kmer space (0-15 out of 16) in both 239s reads and reference. Increases speed and reduces memory. 239s Note: Do not use more than one of 'speed', 'qskip', and 'rskip'. 239s 239s Trimming/Filtering/Masking parameters: 239s Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter. 239s All kmer processing modes are mutually exclusive. 239s Reads only get sent to 'outm' purely based on kmer matches in kfilter mode. 239s 239s ktrim=f Trim reads to remove bases matching reference kmers, plus 239s all bases to the left or right. 239s Values: 239s f (don't trim), 239s r (trim to the right), 239s l (trim to the left) 239s ktrimtips=0 Set this to a positive number to perform ktrim on both 239s ends, examining only the outermost X bases. 239s kmask= Replace bases matching ref kmers with another symbol. 239s Allows any non-whitespace character, and processes short 239s kmers on both ends if mink is set. 'kmask=lc' will 239s convert masked bases to lowercase. 239s maskfullycovered=f (mfc) Only mask bases that are fully covered by kmers. 239s ksplit=f For single-ended reads only. Reads will be split into 239s pairs around the kmer. If the kmer is at the end of the 239s read, it will be trimmed instead. Singletons will go to 239s out, and pairs will go to outm. Do not use ksplit with 239s other operations such as quality-trimming or filtering. 239s mink=0 Look for shorter kmers at read tips down to this length, 239s when k-trimming or masking. 0 means disabled. Enabling 239s this will disable maskmiddle. 239s qtrim=f Trim read ends to remove bases with quality below trimq. 239s Performed AFTER looking for kmers. Values: 239s rl (trim both ends), 239s f (neither end), 239s r (right end only), 239s l (left end only), 239s w (sliding window). 239s trimq=6 Regions with average quality BELOW this will be trimmed, 239s if qtrim is set to something other than f. Can be a 239s floating-point number like 7.3. 239s quantize Bin quality scores to reduce file size. quantize=2 will 239s eliminate all odd quality scores, while quantize=0,10,37 239s will only allow qualty scores of 0, 10, or 37. 239s trimclip=f Trim soft-clipped bases from sam files. 239s minlength=10 (ml) Reads shorter than this after trimming will be 239s discarded. Pairs will be discarded if both are shorter. 239s mlf=0 (minlengthfraction) Reads shorter than this fraction of 239s original length after trimming will be discarded. 239s maxlength= Reads longer than this after trimming will be discarded. 239s minavgquality=0 (maq) Reads with average quality (after trimming) below 239s this will be discarded. 239s maqb=0 If positive, calculate maq from this many initial bases. 239s minbasequality=0 (mbq) Reads with any base below this quality (after 239s trimming) will be discarded. 239s maxns=-1 If non-negative, reads with more Ns than this 239s (after trimming) will be discarded. 239s mcb=0 (minconsecutivebases) Discard reads without at least 239s this many consecutive called bases. 239s ottm=f (outputtrimmedtomatch) Output reads trimmed to shorter 239s than minlength to outm rather than discarding. 239s tp=0 (trimpad) Trim this much extra around matching kmers. 239s tbo=f (trimbyoverlap) Trim adapters based on where paired 239s reads overlap. 239s strictoverlap=t Adjust sensitivity for trimbyoverlap mode. 239s minoverlap=14 Require this many bases of overlap for detection. 239s mininsert=40 Require insert size of at least this for overlap. 239s Should be reduced to 16 for small RNA sequencing. 239s tpe=f (trimpairsevenly) When kmer right-trimming, trim both 239s reads to the minimum length of either. 239s forcetrimleft=0 (ftl) If positive, trim bases to the left of this position 239s (exclusive, 0-based). 239s forcetrimright=0 (ftr) If positive, trim bases to the right of this position 239s (exclusive, 0-based). 239s forcetrimright2=0 (ftr2) If positive, trim this many bases on the right end. 239s forcetrimmod=0 (ftm) If positive, right-trim length to be equal to zero, 239s modulo this number. 239s restrictleft=0 If positive, only look for kmer matches in the 239s leftmost X bases. 239s restrictright=0 If positive, only look for kmer matches in the 239s rightmost X bases. 239s NOTE: restrictleft and restrictright are mutually exclusive. If trimming 239s both ends is desired, use ktrimtips. 239s mingc=0 Discard reads with GC content below this. 239s maxgc=1 Discard reads with GC content above this. 239s gcpairs=t Use average GC of paired reads. 239s Also affects gchist. 239s tossjunk=f Discard reads with invalid characters as bases. 239s swift=f Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2. 239s 239s Header-parsing parameters - these require Illumina headers: 239s chastityfilter=f (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'. 239s barcodefilter=f Remove reads with unexpected barcodes if barcodes is set, 239s or barcodes containing 'N' otherwise. A barcode must be 239s the last part of the read header. Values: 239s t: Remove reads with bad barcodes. 239s f: Ignore barcodes. 239s crash: Crash upon encountering bad barcodes. 239s barcodes= Comma-delimited list of barcodes or files of barcodes. 239s xmin=-1 If positive, discard reads with a lesser X coordinate. 239s ymin=-1 If positive, discard reads with a lesser Y coordinate. 239s xmax=-1 If positive, discard reads with a greater X coordinate. 239s ymax=-1 If positive, discard reads with a greater Y coordinate. 239s 239s Polymer trimming: 239s trimpolya=0 If greater than 0, trim poly-A or poly-T tails of 239s at least this length on either end of reads. 239s trimpolygleft=0 If greater than 0, trim poly-G prefixes of at least this 239s length on the left end of reads. Does not trim poly-C. 239s trimpolygright=0 If greater than 0, trim poly-G tails of at least this 239s length on the right end of reads. Does not trim poly-C. 239s trimpolyg=0 This sets both left and right at once. 239s filterpolyg=0 If greater than 0, remove reads with a poly-G prefix of 239s at least this length (on the left). 239s Note: there are also equivalent poly-C flags. 239s 239s Polymer tracking: 239s pratio=base,base 'pratio=G,C' will print the ratio of G to C polymers. 239s plen=20 Length of homopolymers to count. 239s 239s Entropy/Complexity parameters: 239s entropy=-1 Set between 0 and 1 to filter reads with entropy below 239s that value. Higher is more stringent. 239s entropywindow=50 Calculate entropy using a sliding window of this length. 239s entropyk=5 Calculate entropy using kmers of this length. 239s minbasefrequency=0 Discard reads with a minimum base frequency below this. 239s entropytrim=f Values: 239s f: (false) Do not entropy-trim. 239s r: (right) Trim low entropy on the right end only. 239s l: (left) Trim low entropy on the left end only. 239s rl: (both) Trim low entropy on both ends. 239s entropymask=f Values: 239s f: (filter) Discard low-entropy sequences. 239s t: (true) Mask low-entropy parts of sequences with N. 239s lc: Change low-entropy parts of sequences to lowercase. 239s entropymark=f Mark each base with its entropy value. This is on a scale 239s of 0-41 and is reported as quality scores, so the output 239s should be fastq or fasta+qual. 239s NOTE: If set, entropytrim overrides entropymask. 239s 239s Cardinality estimation: 239s cardinality=f (loglog) Count unique kmers using the LogLog algorithm. 239s cardinalityout=f (loglogout) Count unique kmers in output reads. 239s loglogk=31 Use this kmer length for counting. 239s loglogbuckets=2048 Use this many buckets for counting. 239s khist= Kmer frequency histogram; plots number of kmers versus 239s kmer depth. This is approximate. 239s khistout= Kmer frequency histogram for output reads. 239s 239s Side Channel: 239s sideout= Output for aligned reads. 239s sideref=phix Reference for side-channel alignment; must be a single 239s sequence and virtually repeat-free at selected k. 239s sidek1=17 Kmer length for seeding alignment to reference. 239s sidek2=13 Kmer length for seeding alignment of unaligned reads 239s with an aligned mate. 239s sideminid1=0.66 Minimum identity to accept individual alignments. 239s sideminid2=0.58 Minimum identity for aligning reads with aligned mates. 239s sidemm1=1 Middle mask length for sidek1. 239s sidemm2=1 Middle mask length for sidek2. 239s Note: The side channel is a special additional output that allows alignment 239s to a secondary reference while also doing trimming. Alignment does not affect 239s whether reads go to the normal outputs (out, outm). The main purpose is to 239s simplify pipelines that need trimmed, aligned phiX reads for recalibration. 239s 239s 239s Java Parameters: 239s 239s -Xmx This will set Java's memory usage, overriding autodetection. 239s -Xmx20g will 239s specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 239s The max is typically 85% of physical memory. 239s -eoom This flag will cause the process to exit if an 239s out-of-memory exception occurs. Requires Java 8u92+. 239s -da Disable assertions. 239s 239s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 239s 239s BBTools version 39.20 239s For help, please run the shellscript with no parameters, or look in /docs/. 239s bbnorm.sh --help 239s bbnorm.sh in=sanger_full_range_original_sanger.fastq qin=33 \ 239s out=out3.fastq outt=outt.fastq hist=hist.plt 239s 239s Written by Brian Bushnell 239s Last modified October 19, 2017 239s 239s Description: Normalizes read depth based on kmer counts. 239s Can also error-correct, bin reads by kmer depth, and generate a kmer depth histogram. 239s However, Tadpole has superior error-correction to BBNorm. 239s Please read bbmap/docs/guides/BBNormGuide.txt for more information. 239s 239s Usage: bbnorm.sh in= out= outt= hist= 239s 239s Input parameters: 239s in=null Primary input. Use in2 for paired reads in a second file 239s in2=null Second input file for paired reads in two files 239s extra=null Additional files to use for input (generating hash table) but not for output 239s fastareadlen=2^31 Break up FASTA reads longer than this. Can be useful when processing scaffolded genomes 239s tablereads=-1 Use at most this many reads when building the hashtable (-1 means all) 239s kmersample=1 Process every nth kmer, and skip the rest 239s readsample=1 Process every nth read, and skip the rest 239s 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. 239s qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. 239s 239s Output parameters: 239s out= File for normalized or corrected reads. Use out2 for paired reads in a second file 239s outt= (outtoss) File for reads that were excluded from primary output 239s reads=-1 Only process this number of reads, then quit (-1 means all) 239s sampleoutput=t Use sampling on output as well as input (not used if sample rates are 1) 239s keepall=f Set to true to keep all reads (e.g. if you just want error correction). 239s 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. 239s Default is false, to prevent confusion about how there can be 0-count kmers. 239s The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter. 239s tmpdir= This will specify a directory for temp files (only needed for multipass runs). If null, they will be written to the output directory. 239s usetempdir=t Allows enabling/disabling of temporary directory; if disabled, temp files will be written to the output directory. 239s qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input). 239s rename=f Rename reads based on their kmer depth. 239s 239s Hashing parameters: 239s k=31 Kmer length (values under 32 are most efficient, but arbitrarily high values are supported) 239s 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. 239s Large values decrease accuracy for a fixed amount of memory, so use the lowest number you can that will still capture highest-depth kmers. 239s hashes=3 Number of times each kmer is hashed and stored. Higher is slower. 239s Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory. 239s 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. 239s prehashes=2 Number of hashes for prefilter. 239s prefilterbits=2 (pbits) Bits per cell in prefilter. 239s prefiltersize=0.35 Fraction of memory to allocate to prefilter. 239s buildpasses=1 More passes can sometimes increase accuracy by iteratively removing low-depth kmers 239s minq=6 Ignore kmers containing bases with quality below this 239s minprob=0.5 Ignore kmers with overall probability of correctness below this 239s 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. 239s 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. 239s 239s Normalization parameters: 239s fixspikes=f (fs) Do a slower, high-precision bloom filter lookup of kmers that appear to have an abnormally high depth due to collisions. 239s target=100 (tgt) Target normalization depth. NOTE: All depth parameters control kmer depth, not read depth. 239s For kmer depth Dk, read depth Dr, read length R, and kmer size K: Dr=Dk*(R/(R-K+1)) 239s maxdepth=-1 (max) Reads will not be downsampled when below this depth, even if they are above the target depth. 239s mindepth=5 (min) Kmers with depth below this number will not be included when calculating the depth of a read. 239s minkmers=15 (mgkpr) Reads must have at least this many kmers over min depth to be retained. Aka 'mingoodkmersperread'. 239s 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. 239s uselowerdepth=t (uld) For pairs, use the depth of the lower read as the depth proxy. 239s deterministic=t (dr) Generate random numbers deterministically to ensure identical output between multiple runs. May decrease speed with a huge number of threads. 239s passes=2 (p) 1 pass is the basic mode. 2 passes (default) allows greater accuracy, error detection, better contol of output depth. 239s 239s Error detection parameters: 239s hdp=90.0 (highdepthpercentile) Position in sorted kmer depth array used as proxy of a read's high kmer depth. 239s ldp=25.0 (lowdepthpercentile) Position in sorted kmer depth array used as proxy of a read's low kmer depth. 239s tossbadreads=f (tbr) Throw away reads detected as containing errors. 239s requirebothbad=f (rbb) Only toss bad pairs if both reads are bad. 239s 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. 239s highthresh=12 (ht) Threshold for high kmer. A high kmer at this or above are considered non-error. 239s lowthresh=3 (lt) Threshold for low kmer. Kmers at this and below are always considered errors. 239s 239s Error correction parameters: 239s ecc=f Set to true to correct errors. NOTE: Tadpole is now preferred for ecc as it does a better job. 239s ecclimit=3 Correct up to this many errors per read. If more are detected, the read will remain unchanged. 239s errorcorrectratio=140 (ecr) Adjacent kmers with a depth ratio of at least this much between will be classified as an error. 239s echighthresh=22 (echt) Threshold for high kmer. A kmer at this or above may be considered non-error. 239s eclowthresh=2 (eclt) Threshold for low kmer. Kmers at this and below are considered errors. 239s eccmaxqual=127 Do not correct bases with quality above this value. 239s aec=f (aggressiveErrorCorrection) Sets more aggressive values of ecr=100, ecclimit=7, echt=16, eclt=3. 239s cec=f (conservativeErrorCorrection) Sets more conservative values of ecr=180, ecclimit=2, echt=30, eclt=1, sl=4, pl=4. 239s meo=f (markErrorsOnly) Marks errors by reducing quality value of suspected errors; does not correct anything. 239s mue=t (markUncorrectableErrors) Marks errors only on uncorrectable reads; requires 'ecc=t'. 239s overlap=f (ecco) Error correct by read overlap. 239s 239s Depth binning parameters: 239s lowbindepth=10 (lbd) Cutoff for low depth bin. 239s highbindepth=80 (hbd) Cutoff for high depth bin. 239s outlow= Pairs in which both reads have a median below lbd go into this file. 239s outhigh= Pairs in which both reads have a median above hbd go into this file. 239s outmid= All other pairs go into this file. 239s 239s Histogram parameters: 239s hist= Specify a file to write the input kmer depth histogram. 239s histout= Specify a file to write the output kmer depth histogram. 239s histcol=3 (histogramcolumns) Number of histogram columns, 2 or 3. 239s pzc=f (printzerocoverage) Print lines in the histogram with zero coverage. 239s histlen=1048576 Max kmer depth displayed in histogram. Also affects statistics displayed, but does not affect normalization. 239s 239s Peak calling parameters: 239s peaks= Write the peaks to this file. Default is stdout. 239s minHeight=2 (h) Ignore peaks shorter than this. 239s minVolume=5 (v) Ignore peaks with less area than this. 239s minWidth=3 (w) Ignore peaks narrower than this. 239s minPeak=2 (minp) Ignore peaks with an X-value below this. 239s maxPeak=BIG (maxp) Ignore peaks with an X-value above this. 239s maxPeakCount=8 (maxpc) Print up to this many peaks (prioritizing height). 239s 239s Java Parameters: 239s -Xmx This will set Java's memory usage, overriding autodetection. 239s -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 239s The max is typically 85% of physical memory. 239s -eoom This flag will cause the process to exit if an 239s out-of-memory exception occurs. Requires Java 8u92+. 239s -da Disable assertions. 239s 239s Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 239s 239s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 239s java -ea -Xmx4000m -Xms4000m -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 239s Executing jgi.KmerNormalize [bits=32, in=sanger_full_range_original_sanger.fastq, qin=33, out=out3.fastq, outt=outt.fastq, hist=hist.plt] 239s 239s 239s *********** Pass 1 ********** 239s 239s 239s Settings: 239s threads: 4 239s k: 31 239s deterministic: true 239s toss error reads: false 239s passes: 1 239s bits per cell: 16 239s cells: 1495.36M 239s hashes: 3 239s base min quality: 5 239s kmer min prob: 0.5 239s 239s target depth: 400 239s min depth: 3 239s max depth: 500 239s min good kmers: 15 239s depth percentile: 64.8 239s ignore dupe kmers: true 239s fix spikes: false 239s histogram length: 65536 239s print zero cov: false 239s 240s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 240s 240s Estimated unique kmers: 4 240s 240s Table creation time: 0.951 seconds. 240s Started output threads. 240s Started output threads. 240s Table read time: 0.005 seconds. 41.67 kb/sec 240s Total reads in: 2 0.000% Kept 240s Total bases in: 188 0.000% Kept 240s Error reads in: 2 100.000% 240s Error type 1: 2 100.000% 240s Error type 2: 0 0.000% 240s Error type 3: 0 0.000% 240s 240s Wrote histogram to hist.plt 240s Total kmers counted: 128 240s Total unique kmer count: 128 240s Includes forward kmers only. 240s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 240s The most accurate value is the greater of the two. 240s 240s Percent unique: 100.00% 240s Depth average: 1.00 (unique kmers) 240s Depth median: 1 (unique kmers) 240s Depth standard deviation: 0.00 (unique kmers) 240s Corrected depth average: 0.00 240s 240s Depth average: 1.00 (all kmers) 240s Depth median: 1 (all kmers) 240s Depth standard deviation: 0.00 (all kmers) 240s 240s Approx. read depth median: 1.47 240s 240s *********** Pass 2 ********** 240s 240s 240s Settings: 240s threads: 4 240s k: 31 240s deterministic: true 240s toss error reads: false 240s passes: 1 240s bits per cell: 16 240s cells: 1495.36M 240s hashes: 3 240s base min quality: 5 240s kmer min prob: 0.5 240s 240s target depth: 100 240s min depth: 5 240s max depth: 100 240s min good kmers: 15 240s depth percentile: 54.0 240s ignore dupe kmers: true 240s fix spikes: false 240s histogram length: 65536 240s 240s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 240s 240s Estimated unique kmers: 0 240s 240s Table creation time: 0.457 seconds. 240s Started output threads. 240s Started output threads. 240s Table read time: 0.001 seconds. 0.00 kb/sec 240s Total reads in: 0 NaN% Kept 240s Total bases in: 0 NaN% Kept 240s Error reads in: 0 NaN% 240s Error type 1: 0 NaN% 240s Error type 2: 0 NaN% 240s Error type 3: 0 NaN% 240s Total kmers counted: 0 240s Total unique kmer count: 0 240s Includes forward kmers only. 240s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 240s The most accurate value is the greater of the two. 240s 240s Percent unique: NaN% 240s Depth average: NaN (unique kmers) 240s Depth median: 0 (unique kmers) 240s Depth standard deviation: NaN (unique kmers) 240s Corrected depth average: NaN 240s 240s Depth average: NaN (all kmers) 240s Depth median: 0 (all kmers) 240s Depth standard deviation: 0.00 (all kmers) 240s 240s Approx. read depth median: NaN 240s 240s Removing temp files. 240s 240s Total time: 1.466 seconds. 0.13 kb/sec 240s test -r out3.fastq 240s test -r outt.fastq 240s test -r hist.plt 240s bbnorm.sh in=illumina_full_range_original_illumina.fastq qin=64 \ 240s out=out4.fastq outt=outt2.fastq hist=hist2.plt 240s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 240s java -ea -Xmx4000m -Xms4000m -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 240s Executing jgi.KmerNormalize [bits=32, in=illumina_full_range_original_illumina.fastq, qin=64, out=out4.fastq, outt=outt2.fastq, hist=hist2.plt] 240s 240s 240s *********** Pass 1 ********** 240s 240s 240s Settings: 240s threads: 4 240s k: 31 240s deterministic: true 240s toss error reads: false 240s passes: 1 240s bits per cell: 16 240s cells: 1495.36M 240s hashes: 3 240s base min quality: 5 240s kmer min prob: 0.5 240s 240s target depth: 400 240s min depth: 3 240s max depth: 500 240s min good kmers: 15 240s depth percentile: 64.8 240s ignore dupe kmers: true 240s fix spikes: false 240s histogram length: 65536 240s print zero cov: false 240s 241s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 241s 241s Estimated unique kmers: 4 241s 241s Table creation time: 0.904 seconds. 241s Started output threads. 241s Started output threads. 241s Table read time: 0.004 seconds. 31.06 kb/sec 241s Total reads in: 2 0.000% Kept 241s Total bases in: 126 0.000% Kept 241s Error reads in: 2 100.000% 241s Error type 1: 2 100.000% 241s Error type 2: 0 0.000% 241s Error type 3: 0 0.000% 241s 241s Wrote histogram to hist2.plt 241s Total kmers counted: 66 241s Total unique kmer count: 66 241s Includes forward kmers only. 241s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 241s The most accurate value is the greater of the two. 241s 241s Percent unique: 100.00% 241s Depth average: 1.00 (unique kmers) 241s Depth median: 1 (unique kmers) 241s Depth standard deviation: 0.00 (unique kmers) 241s Corrected depth average: 0.00 241s 241s Depth average: 1.00 (all kmers) 241s Depth median: 1 (all kmers) 241s Depth standard deviation: 0.00 (all kmers) 241s 241s Approx. read depth median: 1.91 241s 241s *********** Pass 2 ********** 241s 241s 241s Settings: 241s threads: 4 241s k: 31 241s deterministic: true 241s toss error reads: false 241s passes: 1 241s bits per cell: 16 241s cells: 1495.36M 241s hashes: 3 241s base min quality: 5 241s kmer min prob: 0.5 241s 241s target depth: 100 241s min depth: 5 241s max depth: 100 241s min good kmers: 15 241s depth percentile: 54.0 241s ignore dupe kmers: true 241s fix spikes: false 241s histogram length: 65536 241s 242s Made hash table: hashes = 3 mem = 2.78 GB cells = 1494.95M used = 0.000% 242s 242s Estimated unique kmers: 0 242s 242s Table creation time: 0.464 seconds. 242s Started output threads. 242s Started output threads. 242s Table read time: 0.001 seconds. 0.00 kb/sec 242s Total reads in: 0 NaN% Kept 242s Total bases in: 0 NaN% Kept 242s Error reads in: 0 NaN% 242s Error type 1: 0 NaN% 242s Error type 2: 0 NaN% 242s Error type 3: 0 NaN% 242s Total kmers counted: 0 242s Total unique kmer count: 0 242s Includes forward kmers only. 242s The unique kmer estimate can be more accurate than the unique count, if the tables are very full. 242s The most accurate value is the greater of the two. 242s 242s Percent unique: NaN% 242s Depth average: NaN (unique kmers) 242s Depth median: 0 (unique kmers) 242s Depth standard deviation: NaN (unique kmers) 242s Corrected depth average: NaN 242s 242s Depth average: NaN (all kmers) 242s Depth median: 0 (all kmers) 242s Depth standard deviation: 0.00 (all kmers) 242s 242s Approx. read depth median: NaN 242s 242s Removing temp files. 242s 242s Total time: 1.435 seconds. 0.09 kb/sec 242s test -r out4.fastq 242s test -r outt2.fastq 242s test -r hist2.plt 242s autopkgtest [11:18:23]: test run-unit-test: -----------------------] 243s run-unit-test PASS 243s autopkgtest [11:18:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 243s autopkgtest [11:18:24]: @@@@@@@@@@@@@@@@@@@@ summary 243s run-unit-test PASS