0s autopkgtest [21:41:17]: starting date: 2024-03-07 0s autopkgtest [21:41:17]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [21:41:17]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k_u6dlf9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:wget,src:libpsl,src:openssl --apt-upgrade prokka --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=wget/1.21.4-1ubuntu2 libpsl/0.21.2-1.1 openssl/3.0.10-1ubuntu5' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-13.secgroup --name adt-noble-arm64-prokka-20240307-214117-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 217s autopkgtest [21:44:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 218s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 219s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [1813 kB] 219s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [23.8 kB] 219s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [321 kB] 219s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 219s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [443 kB] 219s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 219s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 219s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 219s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2170 kB] 219s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 219s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [21.5 kB] 219s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 226s Fetched 4945 kB in 3s (1963 kB/s) 227s Reading package lists... 236s Reading package lists... 237s Building dependency tree... 237s Reading state information... 238s Calculating upgrade... 239s The following packages will be REMOVED: 239s libefiboot1 libefivar1 libpsl5 libssl3 239s The following NEW packages will be installed: 239s libefiboot1t64 libefivar1t64 libpsl5t64 libssl3t64 239s The following packages will be upgraded: 239s dmsetup grub-common grub2-common libdevmapper1.02.1 libproc2-0 openssl 239s pci.ids procps wget 239s 9 upgraded, 4 newly installed, 4 to remove and 0 not upgraded. 239s Need to get 7315 kB of archives. 239s After this operation, 100 kB of additional disk space will be used. 239s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu1 [128 kB] 239s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 grub2-common arm64 2.12-1ubuntu4 [671 kB] 240s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 grub-common arm64 2.12-1ubuntu4 [2174 kB] 241s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libefivar1t64 arm64 38-3.1 [55.1 kB] 241s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libefiboot1t64 arm64 38-3.1 [40.5 kB] 241s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 wget arm64 1.21.4-1ubuntu2 [330 kB] 241s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 241s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.10-1ubuntu5 [982 kB] 241s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.10-1ubuntu5 [1763 kB] 242s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu1 [58.4 kB] 242s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-4ubuntu1 [708 kB] 242s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 dmsetup arm64 2:1.02.185-3ubuntu1 [74.5 kB] 242s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 pci.ids all 0.0~2024.02.02-1 [273 kB] 243s Preconfiguring packages ... 243s Fetched 7315 kB in 3s (2667 kB/s) 243s (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 ... 75860 files and directories currently installed.) 243s Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu1_arm64.deb ... 243s Unpacking libdevmapper1.02.1:arm64 (2:1.02.185-3ubuntu1) over (2:1.02.185-2ubuntu1) ... 243s Preparing to unpack .../grub2-common_2.12-1ubuntu4_arm64.deb ... 243s Unpacking grub2-common (2.12-1ubuntu4) over (2.12-1ubuntu3) ... 243s Preparing to unpack .../grub-common_2.12-1ubuntu4_arm64.deb ... 243s Unpacking grub-common (2.12-1ubuntu4) over (2.12-1ubuntu3) ... 244s dpkg: libefivar1:arm64: dependency problems, but removing anyway as you requested: 244s mokutil depends on libefivar1 (>= 37). 244s libefiboot1:arm64 depends on libefivar1 (>= 38). 244s efibootmgr depends on libefivar1 (>= 38). 244s 244s (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 ... 75860 files and directories currently installed.) 244s Removing libefivar1:arm64 (38-3) ... 244s Selecting previously unselected package libefivar1t64:arm64. 244s (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 ... 75855 files and directories currently installed.) 244s Preparing to unpack .../libefivar1t64_38-3.1_arm64.deb ... 244s Unpacking libefivar1t64:arm64 (38-3.1) ... 244s dpkg: libefiboot1:arm64: dependency problems, but removing anyway as you requested: 244s efibootmgr depends on libefiboot1 (>= 38). 244s 244s (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 ... 75861 files and directories currently installed.) 244s Removing libefiboot1:arm64 (38-3) ... 244s Selecting previously unselected package libefiboot1t64:arm64. 244s (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 ... 75856 files and directories currently installed.) 244s Preparing to unpack .../libefiboot1t64_38-3.1_arm64.deb ... 244s Unpacking libefiboot1t64:arm64 (38-3.1) ... 244s Preparing to unpack .../wget_1.21.4-1ubuntu2_arm64.deb ... 244s Unpacking wget (1.21.4-1ubuntu2) over (1.21.4-1ubuntu1) ... 244s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 244s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 244s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 244s 245s (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 ... 75862 files and directories currently installed.) 245s Removing libpsl5:arm64 (0.21.2-1build1) ... 245s Selecting previously unselected package libpsl5t64:arm64. 245s (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 ... 75857 files and directories currently installed.) 245s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 245s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 245s Preparing to unpack .../openssl_3.0.10-1ubuntu5_arm64.deb ... 245s Unpacking openssl (3.0.10-1ubuntu5) over (3.0.10-1ubuntu4) ... 245s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 245s u-boot-tools depends on libssl3 (>= 3.0.0). 245s tnftp depends on libssl3 (>= 3.0.0). 245s tcpdump depends on libssl3 (>= 3.0.0). 245s systemd-resolved depends on libssl3 (>= 3.0.0). 245s systemd depends on libssl3 (>= 3.0.0). 245s sudo depends on libssl3 (>= 3.0.0). 245s sbsigntool depends on libssl3 (>= 3.0.0). 245s rsync depends on libssl3 (>= 3.0.0). 245s python3-cryptography depends on libssl3 (>= 3.0.0). 245s openssh-server depends on libssl3 (>= 3.0.10). 245s openssh-client depends on libssl3 (>= 3.0.10). 245s mtd-utils depends on libssl3 (>= 3.0.0). 245s mokutil depends on libssl3 (>= 3.0.0). 245s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 245s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 245s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 245s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 245s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 245s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 245s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 245s libnvme1 depends on libssl3 (>= 3.0.0). 245s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 245s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 245s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 245s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 245s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 245s kmod depends on libssl3 (>= 3.0.0). 245s dhcpcd-base depends on libssl3 (>= 3.0.0). 245s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 245s 245s (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 ... 75863 files and directories currently installed.) 245s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 245s Selecting previously unselected package libssl3t64:arm64. 245s (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 ... 75852 files and directories currently installed.) 245s Preparing to unpack .../libssl3t64_3.0.10-1ubuntu5_arm64.deb ... 245s Unpacking libssl3t64:arm64 (3.0.10-1ubuntu5) ... 245s Preparing to unpack .../libproc2-0_2%3a4.0.4-4ubuntu1_arm64.deb ... 245s Unpacking libproc2-0:arm64 (2:4.0.4-4ubuntu1) over (2:4.0.4-2ubuntu1) ... 246s Preparing to unpack .../procps_2%3a4.0.4-4ubuntu1_arm64.deb ... 246s Unpacking procps (2:4.0.4-4ubuntu1) over (2:4.0.4-2ubuntu1) ... 246s Preparing to unpack .../dmsetup_2%3a1.02.185-3ubuntu1_arm64.deb ... 246s Unpacking dmsetup (2:1.02.185-3ubuntu1) over (2:1.02.185-2ubuntu1) ... 246s Preparing to unpack .../pci.ids_0.0~2024.02.02-1_all.deb ... 246s Unpacking pci.ids (0.0~2024.02.02-1) over (0.0~2023.11.11-1) ... 246s Setting up pci.ids (0.0~2024.02.02-1) ... 246s Setting up libssl3t64:arm64 (3.0.10-1ubuntu5) ... 246s Setting up libefivar1t64:arm64 (38-3.1) ... 246s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 246s Setting up libproc2-0:arm64 (2:4.0.4-4ubuntu1) ... 246s Setting up libdevmapper1.02.1:arm64 (2:1.02.185-3ubuntu1) ... 246s Setting up dmsetup (2:1.02.185-3ubuntu1) ... 246s Setting up procps (2:4.0.4-4ubuntu1) ... 247s Setting up libefiboot1t64:arm64 (38-3.1) ... 247s Setting up openssl (3.0.10-1ubuntu5) ... 247s Setting up wget (1.21.4-1ubuntu2) ... 247s Setting up grub-common (2.12-1ubuntu4) ... 247s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 250s Setting up grub2-common (2.12-1ubuntu4) ... 250s Processing triggers for man-db (2.12.0-3) ... 252s Processing triggers for install-info (7.1-3) ... 252s Processing triggers for initramfs-tools (0.142ubuntu19) ... 252s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 252s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 279s System running in EFI mode, skipping. 279s Processing triggers for libc-bin (2.39-0ubuntu2) ... 279s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 279s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 279s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 282s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 283s sh: Attempting to set up Debian/Ubuntu apt sources automatically 283s sh: Distribution appears to be Ubuntu 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 293s eatmydata is already the newest version (131-1). 293s dbus is already the newest version (1.14.10-4ubuntu1). 293s dbus set to manually installed. 293s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 293s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 293s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 295s rng-tools-debian is already the newest version (2.4). 295s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 295s Reading package lists... 296s Building dependency tree... 296s Reading state information... 297s haveged is already the newest version (1.9.14-1ubuntu1). 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 297s Reading package lists... 298s Building dependency tree... 298s Reading state information... 299s The following packages will be REMOVED: 299s cloud-init* python3-configobj* python3-debconf* 300s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 300s After this operation, 3248 kB disk space will be freed. 300s (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 ... 75865 files and directories currently installed.) 300s Removing cloud-init (24.1-0ubuntu1) ... 302s Removing python3-configobj (5.0.8-3) ... 302s Removing python3-debconf (1.5.86) ... 302s Processing triggers for man-db (2.12.0-3) ... 303s (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 ... 75476 files and directories currently installed.) 303s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 304s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 304s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 305s Reading package lists... 306s Building dependency tree... 306s Reading state information... 307s linux-generic is already the newest version (6.8.0-11.11+1). 307s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 308s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 308s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 308s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 308s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 317s Reading package lists... 317s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 317s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 317s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 317s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 318s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 318s Reading package lists... 318s Building dependency tree... 318s Reading state information... 320s Calculating upgrade... 321s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 321s Reading package lists... 321s Building dependency tree... 321s Reading state information... 323s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 323s autopkgtest [21:46:40]: rebooting testbed after setup commands that affected boot 482s autopkgtest [21:49:19]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 482s autopkgtest [21:49:19]: testbed dpkg architecture: arm64 484s autopkgtest [21:49:21]: @@@@@@@@@@@@@@@@@@@@ apt-source prokka 485s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 485s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 485s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 488s Get:1 http://ftpmaster.internal/ubuntu noble/universe prokka 1.14.6+dfsg-6 (dsc) [2068 B] 488s Get:2 http://ftpmaster.internal/ubuntu noble/universe prokka 1.14.6+dfsg-6 (tar) [9927 kB] 488s Get:3 http://ftpmaster.internal/ubuntu noble/universe prokka 1.14.6+dfsg-6 (diff) [5481 kB] 489s gpgv: Signature made Sat Sep 16 16:49:44 2023 UTC 489s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 489s gpgv: Can't check signature: No public key 489s dpkg-source: warning: cannot verify inline signature for ./prokka_1.14.6+dfsg-6.dsc: no acceptable signature found 494s autopkgtest [21:49:31]: testing package prokka version 1.14.6+dfsg-6 494s autopkgtest [21:49:31]: build not needed 599s autopkgtest [21:51:16]: test sample-programs: preparing testbed 602s Reading package lists... 603s Building dependency tree... 603s Reading state information... 603s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 604s Starting 2 pkgProblemResolver with broken count: 0 604s Done 604s Done 605s Starting pkgProblemResolver with broken count: 0 606s Starting 2 pkgProblemResolver with broken count: 0 606s Done 607s The following additional packages will be installed: 607s adwaita-icon-theme aragorn at-spi2-common ca-certificates-java default-jre 607s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 607s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme hmmer 607s humanity-icon-theme infernal java-common libasound2 libasound2-data 607s libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 607s libbio-perl-perl libbio-searchio-hmmer-perl libcairo2 libcups2 607s libdata-stag-perl libdatrie1 libdeflate0 libdivsufsort3 libdrm-amdgpu1 607s libdrm-nouveau2 libdrm-radeon1 libfontconfig1 libgdk-pixbuf-2.0-0 607s libgdk-pixbuf2.0-common libgif7 libgl1 libgl1-mesa-dri libglapi-mesa 607s libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgtk2.0-0 607s libgtk2.0-common libharfbuzz0b libio-string-perl libjbig0 libjpeg-turbo8 607s libjpeg8 liblcms2-2 liblerc4 libllvm17 libmbedcrypto7 libmbedtls14 607s libmbedx509-1 libncbi6 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 607s libpcsclite1 libpixman-1-0 libsharpyuv0 libswiss-perl libthai-data libthai0 607s libtiff6 libvulkan1 libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 607s libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 607s libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1 607s libxfixes3 libxi6 libxinerama1 libxml-libxml-perl 607s libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl 607s libxml-simple-perl libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 607s ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-21-jre openjdk-21-jre-headless 607s parallel prodigal prokka ubuntu-mono x11-common 607s Suggested packages: 607s hmmer-doc libasound2-plugins alsa-utils bioperl libxml-sax-expatxs-perl 607s cups-common gvfs liblcms2-utils pcscd libvibrant6b ncbi-cn3d ncbi-tools-x11 607s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 607s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic csh fish ksh tcsh zsh 607s Recommended packages: 607s librsvg2-common alsa-ucm-conf alsa-topology-conf bioperl-run 607s | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl 607s libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl 607s libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl 607s libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl 607s libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl 607s libset-scalar-perl libsoap-lite-perl libsort-naturally-perl 607s libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl 607s libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl 607s libxml-sax-writer-perl libxml-twig-perl libxml-writer-perl libwww-perl 607s perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl 607s libmldbm-perl libxml-perl libgdk-pixbuf2.0-bin libgl1-amber-dri 607s libgail-common libgtk2.0-bin mesa-vulkan-drivers | vulkan-icd 607s libxml-sax-expat-perl libatk-wrapper-java-jni fonts-dejavu-extra 607s The following NEW packages will be installed: 607s adwaita-icon-theme aragorn at-spi2-common ca-certificates-java default-jre 607s default-jre-headless fontconfig fontconfig-config fonts-dejavu-core 607s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme hmmer 607s humanity-icon-theme infernal java-common libasound2 libasound2-data 607s libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 607s libbio-perl-perl libbio-searchio-hmmer-perl libcairo2 libcups2 607s libdata-stag-perl libdatrie1 libdeflate0 libdivsufsort3 libdrm-amdgpu1 607s libdrm-nouveau2 libdrm-radeon1 libfontconfig1 libgdk-pixbuf-2.0-0 607s libgdk-pixbuf2.0-common libgif7 libgl1 libgl1-mesa-dri libglapi-mesa 607s libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgtk2.0-0 607s libgtk2.0-common libharfbuzz0b libio-string-perl libjbig0 libjpeg-turbo8 607s libjpeg8 liblcms2-2 liblerc4 libllvm17 libmbedcrypto7 libmbedtls14 607s libmbedx509-1 libncbi6 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 607s libpcsclite1 libpixman-1-0 libsharpyuv0 libswiss-perl libthai-data libthai0 607s libtiff6 libvulkan1 libwebp7 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 607s libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 607s libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 libxdamage1 607s libxfixes3 libxi6 libxinerama1 libxml-libxml-perl 607s libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl 607s libxml-simple-perl libxrandr2 libxrender1 libxshmfence1 libxtst6 libxxf86vm1 607s ncbi-blast+ ncbi-data ncbi-tools-bin openjdk-21-jre openjdk-21-jre-headless 607s parallel prodigal prokka ubuntu-mono x11-common 607s 0 upgraded, 107 newly installed, 0 to remove and 0 not upgraded. 607s 1 not fully installed or removed. 607s Need to get 141 MB of archives. 607s After this operation, 691 MB of additional disk space will be used. 607s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 parallel all 20231122+ds-1 [1944 kB] 608s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libio-string-perl all 1.08-4 [11.1 kB] 608s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libdata-stag-perl all 0.14-3 [372 kB] 608s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libbio-perl-perl all 1.7.8-1 [2580 kB] 608s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 609s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 609s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 609s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 609s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 609s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 610s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 610s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 hmmer arm64 3.4+dfsg-2 [1107 kB] 610s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 aragorn arm64 1.2.41-2 [94.8 kB] 610s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB] 610s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libncbi6 arm64 6.1.20170106+dfsg1-10 [4291 kB] 611s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-tools-bin arm64 6.1.20170106+dfsg1-10 [1885 kB] 611s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 infernal arm64 1.1.5-2 [4132 kB] 611s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libswiss-perl all 1.80-1 [813 kB] 611s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxml-namespacesupport-perl all 1.12-2 [13.5 kB] 611s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libxml-sax-base-perl all 1.09-3 [18.9 kB] 611s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libxml-sax-perl all 1.02+dfsg-3 [57.0 kB] 611s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1build2 [296 kB] 611s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libxml-simple-perl all 2.25-2 [64.1 kB] 611s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 611s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 611s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 611s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 611s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 611s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 611s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 611s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 611s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 611s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 611s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 611s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 611s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 611s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 611s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 611s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 611s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 611s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 611s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB] 614s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B] 614s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB] 614s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 at-spi2-common all 2.50.0-1 [7864 B] 614s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libatk1.0-0 arm64 2.50.0-1 [53.8 kB] 614s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 614s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 614s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 614s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 614s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 614s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B] 614s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 614s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 614s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 614s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 614s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 614s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 614s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3 [144 kB] 614s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 614s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 614s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 614s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 614s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 614s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 614s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 614s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxcomposite1 arm64 1:0.4.5-1build2 [7080 B] 614s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB] 614s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1 [21.3 kB] 614s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libxdamage1 arm64 1:1.1.6-1 [6032 B] 614s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libxi6 arm64 2:1.8.1-1 [31.9 kB] 614s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3 [7056 B] 614s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libxrandr2 arm64 2:1.5.2-2 [19.6 kB] 614s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 gtk-update-icon-cache arm64 3.24.40-2ubuntu1 [50.5 kB] 614s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 hicolor-icon-theme all 0.17-2 [9976 B] 614s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 humanity-icon-theme all 0.6.16 [1282 kB] 614s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-mono all 20.10-0ubuntu2 [153 kB] 614s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 adwaita-icon-theme all 46~rc-1 [723 kB] 614s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-0 arm64 2.24.33-2ubuntu2 [1981 kB] 615s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB] 615s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.1-1ubuntu1 [57.8 kB] 615s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B] 615s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B] 615s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B] 615s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB] 615s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B] 615s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB] 615s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B] 615s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB] 615s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B] 615s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB] 615s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB] 615s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 615s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB] 615s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB] 615s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 616s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.1-1ubuntu1 [8226 kB] 617s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.1-1ubuntu1 [166 kB] 617s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB] 617s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB] 617s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB] 617s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 617s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libxtst6 arm64 2:1.2.3-1.1 [13.7 kB] 617s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre arm64 21.0.2+13-2 [226 kB] 617s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre arm64 2:1.21-75+exp1 [922 B] 617s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 libbio-searchio-hmmer-perl all 1.7.3-2 [95.8 kB] 617s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 prokka all 1.14.6+dfsg-6 [15.4 MB] 620s Fetched 141 MB in 11s (13.0 MB/s) 620s Selecting previously unselected package parallel. 620s (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 ... 75421 files and directories currently installed.) 620s Preparing to unpack .../000-parallel_20231122+ds-1_all.deb ... 620s Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' 620s Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' 620s Unpacking parallel (20231122+ds-1) ... 620s Selecting previously unselected package libio-string-perl. 620s Preparing to unpack .../001-libio-string-perl_1.08-4_all.deb ... 620s Unpacking libio-string-perl (1.08-4) ... 620s Selecting previously unselected package libdata-stag-perl. 620s Preparing to unpack .../002-libdata-stag-perl_0.14-3_all.deb ... 620s Unpacking libdata-stag-perl (0.14-3) ... 621s Selecting previously unselected package libbio-perl-perl. 621s Preparing to unpack .../003-libbio-perl-perl_1.7.8-1_all.deb ... 621s Unpacking libbio-perl-perl (1.7.8-1) ... 621s Selecting previously unselected package ncbi-data. 621s Preparing to unpack .../004-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 621s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 622s Selecting previously unselected package libgomp1:arm64. 622s Preparing to unpack .../005-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 622s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 622s Selecting previously unselected package libmbedcrypto7:arm64. 622s Preparing to unpack .../006-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 622s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 622s Selecting previously unselected package libmbedx509-1:arm64. 622s Preparing to unpack .../007-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 622s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 622s Selecting previously unselected package libmbedtls14:arm64. 622s Preparing to unpack .../008-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 622s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 622s Selecting previously unselected package ncbi-blast+. 622s Preparing to unpack .../009-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 622s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 624s Selecting previously unselected package libdivsufsort3:arm64. 624s Preparing to unpack .../010-libdivsufsort3_2.0.1-6_arm64.deb ... 624s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 624s Selecting previously unselected package hmmer. 624s Preparing to unpack .../011-hmmer_3.4+dfsg-2_arm64.deb ... 624s Unpacking hmmer (3.4+dfsg-2) ... 624s Selecting previously unselected package aragorn. 624s Preparing to unpack .../012-aragorn_1.2.41-2_arm64.deb ... 624s Unpacking aragorn (1.2.41-2) ... 624s Selecting previously unselected package prodigal. 624s Preparing to unpack .../013-prodigal_1%3a2.6.3-6_arm64.deb ... 624s Unpacking prodigal (1:2.6.3-6) ... 624s Selecting previously unselected package libncbi6:arm64. 624s Preparing to unpack .../014-libncbi6_6.1.20170106+dfsg1-10_arm64.deb ... 624s Unpacking libncbi6:arm64 (6.1.20170106+dfsg1-10) ... 625s Selecting previously unselected package ncbi-tools-bin. 625s Preparing to unpack .../015-ncbi-tools-bin_6.1.20170106+dfsg1-10_arm64.deb ... 625s Unpacking ncbi-tools-bin (6.1.20170106+dfsg1-10) ... 625s Selecting previously unselected package infernal. 625s Preparing to unpack .../016-infernal_1.1.5-2_arm64.deb ... 625s Unpacking infernal (1.1.5-2) ... 626s Selecting previously unselected package libswiss-perl. 626s Preparing to unpack .../017-libswiss-perl_1.80-1_all.deb ... 626s Unpacking libswiss-perl (1.80-1) ... 626s Selecting previously unselected package libxml-namespacesupport-perl. 626s Preparing to unpack .../018-libxml-namespacesupport-perl_1.12-2_all.deb ... 626s Unpacking libxml-namespacesupport-perl (1.12-2) ... 626s Selecting previously unselected package libxml-sax-base-perl. 626s Preparing to unpack .../019-libxml-sax-base-perl_1.09-3_all.deb ... 626s Unpacking libxml-sax-base-perl (1.09-3) ... 626s Selecting previously unselected package libxml-sax-perl. 626s Preparing to unpack .../020-libxml-sax-perl_1.02+dfsg-3_all.deb ... 626s Unpacking libxml-sax-perl (1.02+dfsg-3) ... 626s Selecting previously unselected package libxml-libxml-perl. 626s Preparing to unpack .../021-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1build2_arm64.deb ... 626s Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1build2) ... 626s Selecting previously unselected package libxml-simple-perl. 626s Preparing to unpack .../022-libxml-simple-perl_2.25-2_all.deb ... 626s Unpacking libxml-simple-perl (2.25-2) ... 626s Selecting previously unselected package ca-certificates-java. 626s Preparing to unpack .../023-ca-certificates-java_20240118_all.deb ... 626s Unpacking ca-certificates-java (20240118) ... 626s Selecting previously unselected package java-common. 626s Preparing to unpack .../024-java-common_0.75+exp1_all.deb ... 626s Unpacking java-common (0.75+exp1) ... 626s Selecting previously unselected package libavahi-common-data:arm64. 626s Preparing to unpack .../025-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 626s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 626s Selecting previously unselected package libavahi-common3:arm64. 626s Preparing to unpack .../026-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 626s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 626s Selecting previously unselected package libavahi-client3:arm64. 626s Preparing to unpack .../027-libavahi-client3_0.8-13ubuntu2_arm64.deb ... 626s Unpacking libavahi-client3:arm64 (0.8-13ubuntu2) ... 626s Selecting previously unselected package libcups2:arm64. 626s Preparing to unpack .../028-libcups2_2.4.6-0ubuntu3_arm64.deb ... 626s Unpacking libcups2:arm64 (2.4.6-0ubuntu3) ... 626s Selecting previously unselected package liblcms2-2:arm64. 626s Preparing to unpack .../029-liblcms2-2_2.14-2_arm64.deb ... 626s Unpacking liblcms2-2:arm64 (2.14-2) ... 626s Selecting previously unselected package libjpeg-turbo8:arm64. 626s Preparing to unpack .../030-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 627s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 627s Selecting previously unselected package libjpeg8:arm64. 627s Preparing to unpack .../031-libjpeg8_8c-2ubuntu11_arm64.deb ... 627s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 627s Selecting previously unselected package fonts-dejavu-mono. 627s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8_all.deb ... 627s Unpacking fonts-dejavu-mono (2.37-8) ... 627s Selecting previously unselected package fonts-dejavu-core. 627s Preparing to unpack .../033-fonts-dejavu-core_2.37-8_all.deb ... 627s Unpacking fonts-dejavu-core (2.37-8) ... 627s Selecting previously unselected package fontconfig-config. 627s Preparing to unpack .../034-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 627s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 627s Selecting previously unselected package libfontconfig1:arm64. 627s Preparing to unpack .../035-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 627s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 627s Selecting previously unselected package libasound2-data. 627s Preparing to unpack .../036-libasound2-data_1.2.10-3build1_all.deb ... 627s Unpacking libasound2-data (1.2.10-3build1) ... 628s Selecting previously unselected package libasound2:arm64. 628s Preparing to unpack .../037-libasound2_1.2.10-3build1_arm64.deb ... 628s Unpacking libasound2:arm64 (1.2.10-3build1) ... 628s Selecting previously unselected package libgraphite2-3:arm64. 628s Preparing to unpack .../038-libgraphite2-3_1.3.14-2_arm64.deb ... 628s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 628s Selecting previously unselected package libharfbuzz0b:arm64. 628s Preparing to unpack .../039-libharfbuzz0b_8.3.0-2_arm64.deb ... 628s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 628s Selecting previously unselected package libpcsclite1:arm64. 628s Preparing to unpack .../040-libpcsclite1_2.0.0-1_arm64.deb ... 628s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 628s Selecting previously unselected package openjdk-21-jre-headless:arm64. 628s Preparing to unpack .../041-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ... 628s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 632s Selecting previously unselected package default-jre-headless. 632s Preparing to unpack .../042-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ... 632s Unpacking default-jre-headless (2:1.21-75+exp1) ... 632s Selecting previously unselected package libgtk2.0-common. 632s Preparing to unpack .../043-libgtk2.0-common_2.24.33-2ubuntu2_all.deb ... 632s Unpacking libgtk2.0-common (2.24.33-2ubuntu2) ... 632s Selecting previously unselected package at-spi2-common. 632s Preparing to unpack .../044-at-spi2-common_2.50.0-1_all.deb ... 632s Unpacking at-spi2-common (2.50.0-1) ... 632s Selecting previously unselected package libatk1.0-0:arm64. 632s Preparing to unpack .../045-libatk1.0-0_2.50.0-1_arm64.deb ... 632s Unpacking libatk1.0-0:arm64 (2.50.0-1) ... 632s Selecting previously unselected package libpixman-1-0:arm64. 632s Preparing to unpack .../046-libpixman-1-0_0.42.2-1_arm64.deb ... 632s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 632s Selecting previously unselected package libxcb-render0:arm64. 632s Preparing to unpack .../047-libxcb-render0_1.15-1_arm64.deb ... 632s Unpacking libxcb-render0:arm64 (1.15-1) ... 632s Selecting previously unselected package libxcb-shm0:arm64. 632s Preparing to unpack .../048-libxcb-shm0_1.15-1_arm64.deb ... 632s Unpacking libxcb-shm0:arm64 (1.15-1) ... 632s Selecting previously unselected package libxrender1:arm64. 632s Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 632s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 632s Selecting previously unselected package libcairo2:arm64. 632s Preparing to unpack .../050-libcairo2_1.18.0-1_arm64.deb ... 632s Unpacking libcairo2:arm64 (1.18.0-1) ... 632s Selecting previously unselected package libgdk-pixbuf2.0-common. 632s Preparing to unpack .../051-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... 632s Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 633s Selecting previously unselected package libdeflate0:arm64. 633s Preparing to unpack .../052-libdeflate0_1.19-1_arm64.deb ... 633s Unpacking libdeflate0:arm64 (1.19-1) ... 633s Selecting previously unselected package libjbig0:arm64. 633s Preparing to unpack .../053-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 633s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 633s Selecting previously unselected package liblerc4:arm64. 633s Preparing to unpack .../054-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 633s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 633s Selecting previously unselected package libsharpyuv0:arm64. 633s Preparing to unpack .../055-libsharpyuv0_1.3.2-0.4_arm64.deb ... 633s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 633s Selecting previously unselected package libwebp7:arm64. 633s Preparing to unpack .../056-libwebp7_1.3.2-0.4_arm64.deb ... 633s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 633s Selecting previously unselected package libtiff6:arm64. 633s Preparing to unpack .../057-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 633s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 633s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 633s Preparing to unpack .../058-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3_arm64.deb ... 633s Unpacking libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 633s Selecting previously unselected package fontconfig. 633s Preparing to unpack .../059-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 633s Unpacking fontconfig (2.15.0-1ubuntu1) ... 633s Selecting previously unselected package libthai-data. 633s Preparing to unpack .../060-libthai-data_0.1.29-2_all.deb ... 633s Unpacking libthai-data (0.1.29-2) ... 633s Selecting previously unselected package libdatrie1:arm64. 633s Preparing to unpack .../061-libdatrie1_0.2.13-3_arm64.deb ... 633s Unpacking libdatrie1:arm64 (0.2.13-3) ... 633s Selecting previously unselected package libthai0:arm64. 633s Preparing to unpack .../062-libthai0_0.1.29-2_arm64.deb ... 633s Unpacking libthai0:arm64 (0.1.29-2) ... 633s Selecting previously unselected package libpango-1.0-0:arm64. 633s Preparing to unpack .../063-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 633s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 633s Selecting previously unselected package libpangoft2-1.0-0:arm64. 633s Preparing to unpack .../064-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 633s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 633s Selecting previously unselected package libpangocairo-1.0-0:arm64. 633s Preparing to unpack .../065-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 633s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 633s Selecting previously unselected package libxcomposite1:arm64. 633s Preparing to unpack .../066-libxcomposite1_1%3a0.4.5-1build2_arm64.deb ... 633s Unpacking libxcomposite1:arm64 (1:0.4.5-1build2) ... 633s Selecting previously unselected package libxfixes3:arm64. 634s Preparing to unpack .../067-libxfixes3_1%3a6.0.0-2_arm64.deb ... 634s Unpacking libxfixes3:arm64 (1:6.0.0-2) ... 634s Selecting previously unselected package libxcursor1:arm64. 634s Preparing to unpack .../068-libxcursor1_1%3a1.2.1-1_arm64.deb ... 634s Unpacking libxcursor1:arm64 (1:1.2.1-1) ... 634s Selecting previously unselected package libxdamage1:arm64. 634s Preparing to unpack .../069-libxdamage1_1%3a1.1.6-1_arm64.deb ... 634s Unpacking libxdamage1:arm64 (1:1.1.6-1) ... 634s Selecting previously unselected package libxi6:arm64. 634s Preparing to unpack .../070-libxi6_2%3a1.8.1-1_arm64.deb ... 634s Unpacking libxi6:arm64 (2:1.8.1-1) ... 634s Selecting previously unselected package libxinerama1:arm64. 634s Preparing to unpack .../071-libxinerama1_2%3a1.1.4-3_arm64.deb ... 634s Unpacking libxinerama1:arm64 (2:1.1.4-3) ... 634s Selecting previously unselected package libxrandr2:arm64. 634s Preparing to unpack .../072-libxrandr2_2%3a1.5.2-2_arm64.deb ... 634s Unpacking libxrandr2:arm64 (2:1.5.2-2) ... 634s Selecting previously unselected package gtk-update-icon-cache. 634s Preparing to unpack .../073-gtk-update-icon-cache_3.24.40-2ubuntu1_arm64.deb ... 634s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ... 634s Selecting previously unselected package hicolor-icon-theme. 634s Preparing to unpack .../074-hicolor-icon-theme_0.17-2_all.deb ... 634s Unpacking hicolor-icon-theme (0.17-2) ... 634s Selecting previously unselected package humanity-icon-theme. 634s Preparing to unpack .../075-humanity-icon-theme_0.6.16_all.deb ... 634s Unpacking humanity-icon-theme (0.6.16) ... 637s Selecting previously unselected package ubuntu-mono. 637s Preparing to unpack .../076-ubuntu-mono_20.10-0ubuntu2_all.deb ... 637s Unpacking ubuntu-mono (20.10-0ubuntu2) ... 638s Selecting previously unselected package adwaita-icon-theme. 638s Preparing to unpack .../077-adwaita-icon-theme_46~rc-1_all.deb ... 638s Unpacking adwaita-icon-theme (46~rc-1) ... 639s Selecting previously unselected package libgtk2.0-0:arm64. 639s Preparing to unpack .../078-libgtk2.0-0_2.24.33-2ubuntu2_arm64.deb ... 639s Unpacking libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 639s Selecting previously unselected package libglvnd0:arm64. 639s Preparing to unpack .../079-libglvnd0_1.7.0-1_arm64.deb ... 639s Unpacking libglvnd0:arm64 (1.7.0-1) ... 639s Selecting previously unselected package libglapi-mesa:arm64. 639s Preparing to unpack .../080-libglapi-mesa_24.0.1-1ubuntu1_arm64.deb ... 639s Unpacking libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 639s Selecting previously unselected package libx11-xcb1:arm64. 639s Preparing to unpack .../081-libx11-xcb1_2%3a1.8.7-1_arm64.deb ... 639s Unpacking libx11-xcb1:arm64 (2:1.8.7-1) ... 639s Selecting previously unselected package libxcb-dri2-0:arm64. 639s Preparing to unpack .../082-libxcb-dri2-0_1.15-1_arm64.deb ... 639s Unpacking libxcb-dri2-0:arm64 (1.15-1) ... 639s Selecting previously unselected package libxcb-dri3-0:arm64. 639s Preparing to unpack .../083-libxcb-dri3-0_1.15-1_arm64.deb ... 639s Unpacking libxcb-dri3-0:arm64 (1.15-1) ... 639s Selecting previously unselected package libxcb-glx0:arm64. 639s Preparing to unpack .../084-libxcb-glx0_1.15-1_arm64.deb ... 639s Unpacking libxcb-glx0:arm64 (1.15-1) ... 639s Selecting previously unselected package libxcb-present0:arm64. 639s Preparing to unpack .../085-libxcb-present0_1.15-1_arm64.deb ... 639s Unpacking libxcb-present0:arm64 (1.15-1) ... 639s Selecting previously unselected package libxcb-randr0:arm64. 639s Preparing to unpack .../086-libxcb-randr0_1.15-1_arm64.deb ... 639s Unpacking libxcb-randr0:arm64 (1.15-1) ... 639s Selecting previously unselected package libxcb-sync1:arm64. 640s Preparing to unpack .../087-libxcb-sync1_1.15-1_arm64.deb ... 640s Unpacking libxcb-sync1:arm64 (1.15-1) ... 640s Selecting previously unselected package libxcb-xfixes0:arm64. 640s Preparing to unpack .../088-libxcb-xfixes0_1.15-1_arm64.deb ... 640s Unpacking libxcb-xfixes0:arm64 (1.15-1) ... 640s Selecting previously unselected package libxshmfence1:arm64. 640s Preparing to unpack .../089-libxshmfence1_1.3-1build4_arm64.deb ... 640s Unpacking libxshmfence1:arm64 (1.3-1build4) ... 640s Selecting previously unselected package libxxf86vm1:arm64. 640s Preparing to unpack .../090-libxxf86vm1_1%3a1.1.4-1build3_arm64.deb ... 640s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build3) ... 640s Selecting previously unselected package libvulkan1:arm64. 640s Preparing to unpack .../091-libvulkan1_1.3.275.0-1_arm64.deb ... 640s Unpacking libvulkan1:arm64 (1.3.275.0-1) ... 640s Selecting previously unselected package libdrm-amdgpu1:arm64. 640s Preparing to unpack .../092-libdrm-amdgpu1_2.4.120-2_arm64.deb ... 640s Unpacking libdrm-amdgpu1:arm64 (2.4.120-2) ... 640s Selecting previously unselected package libdrm-nouveau2:arm64. 640s Preparing to unpack .../093-libdrm-nouveau2_2.4.120-2_arm64.deb ... 640s Unpacking libdrm-nouveau2:arm64 (2.4.120-2) ... 640s Selecting previously unselected package libdrm-radeon1:arm64. 640s Preparing to unpack .../094-libdrm-radeon1_2.4.120-2_arm64.deb ... 640s Unpacking libdrm-radeon1:arm64 (2.4.120-2) ... 640s Selecting previously unselected package libllvm17:arm64. 640s Preparing to unpack .../095-libllvm17_1%3a17.0.6-5build1_arm64.deb ... 640s Unpacking libllvm17:arm64 (1:17.0.6-5build1) ... 642s Selecting previously unselected package libgl1-mesa-dri:arm64. 642s Preparing to unpack .../096-libgl1-mesa-dri_24.0.1-1ubuntu1_arm64.deb ... 642s Unpacking libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 642s Selecting previously unselected package libglx-mesa0:arm64. 642s Preparing to unpack .../097-libglx-mesa0_24.0.1-1ubuntu1_arm64.deb ... 642s Unpacking libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 642s Selecting previously unselected package libglx0:arm64. 642s Preparing to unpack .../098-libglx0_1.7.0-1_arm64.deb ... 642s Unpacking libglx0:arm64 (1.7.0-1) ... 642s Selecting previously unselected package libgl1:arm64. 642s Preparing to unpack .../099-libgl1_1.7.0-1_arm64.deb ... 642s Unpacking libgl1:arm64 (1.7.0-1) ... 642s Selecting previously unselected package libgif7:arm64. 642s Preparing to unpack .../100-libgif7_5.2.1-2.5_arm64.deb ... 642s Unpacking libgif7:arm64 (5.2.1-2.5) ... 642s Selecting previously unselected package x11-common. 642s Preparing to unpack .../101-x11-common_1%3a7.7+23ubuntu2_all.deb ... 642s Unpacking x11-common (1:7.7+23ubuntu2) ... 642s Selecting previously unselected package libxtst6:arm64. 643s Preparing to unpack .../102-libxtst6_2%3a1.2.3-1.1_arm64.deb ... 643s Unpacking libxtst6:arm64 (2:1.2.3-1.1) ... 643s Selecting previously unselected package openjdk-21-jre:arm64. 643s Preparing to unpack .../103-openjdk-21-jre_21.0.2+13-2_arm64.deb ... 643s Unpacking openjdk-21-jre:arm64 (21.0.2+13-2) ... 643s Selecting previously unselected package default-jre. 643s Preparing to unpack .../104-default-jre_2%3a1.21-75+exp1_arm64.deb ... 643s Unpacking default-jre (2:1.21-75+exp1) ... 643s Selecting previously unselected package libbio-searchio-hmmer-perl. 643s Preparing to unpack .../105-libbio-searchio-hmmer-perl_1.7.3-2_all.deb ... 643s Unpacking libbio-searchio-hmmer-perl (1.7.3-2) ... 643s Selecting previously unselected package prokka. 643s Preparing to unpack .../106-prokka_1.14.6+dfsg-6_all.deb ... 643s Unpacking prokka (1.14.6+dfsg-6) ... 644s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 644s Setting up aragorn (1.2.41-2) ... 644s Setting up libxcb-dri3-0:arm64 (1.15-1) ... 644s Setting up liblcms2-2:arm64 (2.14-2) ... 644s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 644s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 644s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 644s Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... 644s Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... 644s Setting up libxdamage1:arm64 (1:1.1.6-1) ... 644s Setting up libxcb-xfixes0:arm64 (1.15-1) ... 644s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 644s Setting up hicolor-icon-theme (0.17-2) ... 644s Setting up libxi6:arm64 (2:1.8.1-1) ... 644s Setting up java-common (0.75+exp1) ... 644s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 644s Setting up libdatrie1:arm64 (0.2.13-3) ... 644s Setting up libxcb-render0:arm64 (1.15-1) ... 644s Setting up prodigal (1:2.6.3-6) ... 644s Setting up libdrm-radeon1:arm64 (2.4.120-2) ... 644s Setting up libglvnd0:arm64 (1.7.0-1) ... 644s Setting up libxcb-glx0:arm64 (1.15-1) ... 644s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 644s Setting up x11-common (1:7.7+23ubuntu2) ... 646s Setting up libdeflate0:arm64 (1.19-1) ... 646s Setting up libxml-namespacesupport-perl (1.12-2) ... 646s Setting up libxcb-shm0:arm64 (1.15-1) ... 646s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 646s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 646s Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ... 646s Setting up libxcb-present0:arm64 (1.15-1) ... 646s Setting up libasound2-data (1.2.10-3build1) ... 646s Setting up infernal (1.1.5-2) ... 646s Setting up libxml-sax-base-perl (1.09-3) ... 646s Setting up libio-string-perl (1.08-4) ... 646s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 646s Setting up libxfixes3:arm64 (1:6.0.0-2) ... 646s Setting up libxcb-sync1:arm64 (1.15-1) ... 646s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 646s Setting up libxinerama1:arm64 (2:1.1.4-3) ... 646s Setting up fonts-dejavu-mono (2.37-8) ... 646s Setting up libxrandr2:arm64 (2:1.5.2-2) ... 646s Setting up fonts-dejavu-core (2.37-8) ... 646s Setting up libpcsclite1:arm64 (2.0.0-1) ... 646s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 646s Setting up libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 646s Setting up parallel (20231122+ds-1) ... 646s Setting up libvulkan1:arm64 (1.3.275.0-1) ... 646s Setting up libwebp7:arm64 (1.3.2-0.4) ... 646s Setting up libxcb-dri2-0:arm64 (1.15-1) ... 646s Setting up libgif7:arm64 (5.2.1-2.5) ... 646s Setting up libdata-stag-perl (0.14-3) ... 646s Setting up libxshmfence1:arm64 (1.3-1build4) ... 646s Setting up at-spi2-common (2.50.0-1) ... 646s Setting up libxcb-randr0:arm64 (1.15-1) ... 646s Setting up libasound2:arm64 (1.2.10-3build1) ... 646s Setting up libswiss-perl (1.80-1) ... 646s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 646s Setting up libthai-data (0.1.29-2) ... 646s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ... 646s Setting up libatk1.0-0:arm64 (2.50.0-1) ... 646s Setting up libbio-perl-perl (1.7.8-1) ... 646s Setting up ca-certificates-java (20240118) ... 646s No JRE found. Skipping Java certificates setup. 646s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 646s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 646s Setting up libxcomposite1:arm64 (1:0.4.5-1build2) ... 646s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 646s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 646s Setting up libncbi6:arm64 (6.1.20170106+dfsg1-10) ... 646s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 646s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 646s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 646s Setting up libxtst6:arm64 (2:1.2.3-1.1) ... 646s Setting up libxcursor1:arm64 (1:1.2.1-1) ... 646s Setting up libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 646s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 646s Setting up libxml-sax-perl (1.02+dfsg-3) ... 647s update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... 647s update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... 647s 647s Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version 648s Setting up ncbi-blast+ (2.12.0+ds-4) ... 648s Setting up libthai0:arm64 (0.1.29-2) ... 648s Setting up libbio-searchio-hmmer-perl (1.7.3-2) ... 648s Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1build2) ... 648s update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... 648s update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... 648s update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... 649s Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version 649s Setting up ncbi-tools-bin (6.1.20170106+dfsg1-10) ... 649s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 649s Setting up hmmer (3.4+dfsg-2) ... 649s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 649s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 649s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 649s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ... 649s Setting up fontconfig (2.15.0-1ubuntu1) ... 651s Regenerating fonts cache... done. 651s Setting up libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 651s Setting up libglx0:arm64 (1.7.0-1) ... 651s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 651s Setting up libcairo2:arm64 (1.18.0-1) ... 651s Setting up libgl1:arm64 (1.7.0-1) ... 651s Setting up libxml-simple-perl (2.25-2) ... 651s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 651s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 651s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 651s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 651s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 651s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 651s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 651s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 651s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 651s Setting up adwaita-icon-theme (46~rc-1) ... 651s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 651s Setting up libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 651s Setting up humanity-icon-theme (0.6.16) ... 652s Setting up ubuntu-mono (20.10-0ubuntu2) ... 652s Processing triggers for man-db (2.12.0-3) ... 655s Processing triggers for libc-bin (2.39-0ubuntu2) ... 655s Processing triggers for ca-certificates-java (20240118) ... 656s Adding debian:ACCVRAIZ1.pem 656s Adding debian:AC_RAIZ_FNMT-RCM.pem 656s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 656s Adding debian:ANF_Secure_Server_Root_CA.pem 656s Adding debian:Actalis_Authentication_Root_CA.pem 656s Adding debian:AffirmTrust_Commercial.pem 656s Adding debian:AffirmTrust_Networking.pem 656s Adding debian:AffirmTrust_Premium.pem 656s Adding debian:AffirmTrust_Premium_ECC.pem 656s Adding debian:Amazon_Root_CA_1.pem 656s Adding debian:Amazon_Root_CA_2.pem 656s Adding debian:Amazon_Root_CA_3.pem 656s Adding debian:Amazon_Root_CA_4.pem 656s Adding debian:Atos_TrustedRoot_2011.pem 656s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 656s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 656s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 656s Adding debian:BJCA_Global_Root_CA1.pem 656s Adding debian:BJCA_Global_Root_CA2.pem 656s Adding debian:Baltimore_CyberTrust_Root.pem 656s Adding debian:Buypass_Class_2_Root_CA.pem 656s Adding debian:Buypass_Class_3_Root_CA.pem 656s Adding debian:CA_Disig_Root_R2.pem 656s Adding debian:CFCA_EV_ROOT.pem 656s Adding debian:COMODO_Certification_Authority.pem 656s Adding debian:COMODO_ECC_Certification_Authority.pem 656s Adding debian:COMODO_RSA_Certification_Authority.pem 656s Adding debian:Certainly_Root_E1.pem 656s Adding debian:Certainly_Root_R1.pem 656s Adding debian:Certigna.pem 656s Adding debian:Certigna_Root_CA.pem 656s Adding debian:Certum_EC-384_CA.pem 656s Adding debian:Certum_Trusted_Network_CA.pem 656s Adding debian:Certum_Trusted_Network_CA_2.pem 656s Adding debian:Certum_Trusted_Root_CA.pem 656s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 656s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 656s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 656s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 656s Adding debian:Comodo_AAA_Services_root.pem 656s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 656s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 656s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 656s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 656s Adding debian:DigiCert_Assured_ID_Root_CA.pem 656s Adding debian:DigiCert_Assured_ID_Root_G2.pem 656s Adding debian:DigiCert_Assured_ID_Root_G3.pem 656s Adding debian:DigiCert_Global_Root_CA.pem 656s Adding debian:DigiCert_Global_Root_G2.pem 656s Adding debian:DigiCert_Global_Root_G3.pem 656s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 656s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 656s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 656s Adding debian:DigiCert_Trusted_Root_G4.pem 656s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 656s Adding debian:Entrust_Root_Certification_Authority.pem 656s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 656s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 656s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 656s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 656s Adding debian:GLOBALTRUST_2020.pem 656s Adding debian:GTS_Root_R1.pem 656s Adding debian:GTS_Root_R2.pem 656s Adding debian:GTS_Root_R3.pem 656s Adding debian:GTS_Root_R4.pem 656s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 656s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 656s Adding debian:GlobalSign_Root_CA.pem 656s Adding debian:GlobalSign_Root_CA_-_R3.pem 656s Adding debian:GlobalSign_Root_CA_-_R6.pem 656s Adding debian:GlobalSign_Root_E46.pem 656s Adding debian:GlobalSign_Root_R46.pem 656s Adding debian:Go_Daddy_Class_2_CA.pem 656s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 656s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 656s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 656s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 656s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 656s Adding debian:HiPKI_Root_CA_-_G1.pem 656s Adding debian:Hongkong_Post_Root_CA_3.pem 656s Adding debian:ISRG_Root_X1.pem 656s Adding debian:ISRG_Root_X2.pem 656s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 656s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 656s Adding debian:Izenpe.com.pem 656s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 656s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 656s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 656s Adding debian:NAVER_Global_Root_Certification_Authority.pem 656s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 656s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 656s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 656s Adding debian:QuoVadis_Root_CA_1_G3.pem 656s Adding debian:QuoVadis_Root_CA_2.pem 657s Adding debian:QuoVadis_Root_CA_2_G3.pem 657s Adding debian:QuoVadis_Root_CA_3.pem 657s Adding debian:QuoVadis_Root_CA_3_G3.pem 657s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 657s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 657s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 657s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 657s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 657s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 657s Adding debian:SZAFIR_ROOT_CA2.pem 657s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 657s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 657s Adding debian:SecureSign_RootCA11.pem 657s Adding debian:SecureTrust_CA.pem 657s Adding debian:Secure_Global_CA.pem 657s Adding debian:Security_Communication_ECC_RootCA1.pem 657s Adding debian:Security_Communication_RootCA2.pem 657s Adding debian:Security_Communication_RootCA3.pem 657s Adding debian:Security_Communication_Root_CA.pem 657s Adding debian:Starfield_Class_2_CA.pem 657s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 657s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 657s Adding debian:SwissSign_Gold_CA_-_G2.pem 657s Adding debian:SwissSign_Silver_CA_-_G2.pem 657s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 657s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 657s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 657s Adding debian:TWCA_Global_Root_CA.pem 657s Adding debian:TWCA_Root_Certification_Authority.pem 657s Adding debian:TeliaSonera_Root_CA_v1.pem 657s Adding debian:Telia_Root_CA_v2.pem 657s Adding debian:TrustAsia_Global_Root_CA_G3.pem 657s Adding debian:TrustAsia_Global_Root_CA_G4.pem 657s Adding debian:Trustwave_Global_Certification_Authority.pem 657s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 657s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 657s Adding debian:TunTrust_Root_CA.pem 657s Adding debian:UCA_Extended_Validation_Root.pem 657s Adding debian:UCA_Global_G2_Root.pem 657s Adding debian:USERTrust_ECC_Certification_Authority.pem 657s Adding debian:USERTrust_RSA_Certification_Authority.pem 657s Adding debian:XRamp_Global_CA_Root.pem 657s Adding debian:certSIGN_ROOT_CA.pem 657s Adding debian:certSIGN_Root_CA_G2.pem 657s Adding debian:e-Szigno_Root_CA_2017.pem 657s Adding debian:ePKI_Root_Certification_Authority.pem 657s Adding debian:emSign_ECC_Root_CA_-_C3.pem 657s Adding debian:emSign_ECC_Root_CA_-_G3.pem 657s Adding debian:emSign_Root_CA_-_C1.pem 657s Adding debian:emSign_Root_CA_-_G1.pem 657s Adding debian:vTrus_ECC_Root_CA.pem 657s Adding debian:vTrus_Root_CA.pem 657s done. 657s Setting up openjdk-21-jre:arm64 (21.0.2+13-2) ... 657s Setting up default-jre-headless (2:1.21-75+exp1) ... 657s Setting up default-jre (2:1.21-75+exp1) ... 657s Setting up prokka (1.14.6+dfsg-6) ... 657s Setting up autopkgtest-satdep (0) ... 670s (Reading database ... 91502 files and directories currently installed.) 670s Removing autopkgtest-satdep (0) ... 671s autopkgtest [21:52:28]: test sample-programs: [----------------------- 671s + pkg=prokka 671s + '[' /tmp/autopkgtest.ppmBFH/autopkgtest_tmp = '' ']' 671s + sh /usr/share/doc/prokka/get-additional-data 671s + wget -np -N https://github.com/tseemann/prokka/archive/v1.14.6.tar.gz 671s --2024-03-07 21:52:28-- https://github.com/tseemann/prokka/archive/v1.14.6.tar.gz 672s Resolving squid.internal (squid.internal)... 185.125.188.86, 185.125.188.85 672s Connecting to squid.internal (squid.internal)|185.125.188.86|:3128... connected. 672s Proxy request sent, awaiting response... 302 Found 672s Location: https://codeload.github.com/tseemann/prokka/tar.gz/refs/tags/v1.14.6 [following] 672s --2024-03-07 21:52:29-- https://codeload.github.com/tseemann/prokka/tar.gz/refs/tags/v1.14.6 672s Connecting to squid.internal (squid.internal)|185.125.188.86|:3128... connected. 673s Proxy request sent, awaiting response... 200 OK 673s Length: unspecified [application/x-gzip] 673s Saving to: ‘v1.14.6.tar.gz’ 673s 673s 0K .......... .......... .......... .......... .......... 383K 673s 50K .......... .......... .......... .......... .......... 917K 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.......... .......... .......... .......... .......... 2.22M 674s 9150K .......... .......... .......... .......... .......... 6.91M 674s 9200K .......... .......... .......... .......... .......... 6.59M 674s 9250K .......... .......... .......... .......... .......... 3.83M 674s 9300K .......... .......... .......... .......... .......... 8.85M 674s 9350K .......... .......... .......... .......... .......... 8.42M 674s 9400K .......... .......... .......... .......... .......... 36.8M 674s 9450K .......... .......... .......... .......... .......... 19.7M 674s 9500K .......... .......... .......... .......... .......... 13.2M 674s 9550K .......... .......... .......... .......... .......... 7.03M 674s 9600K .......... .......... .......... .......... .......... 14.0M 674s 9650K .......... .......... .......... .......... .......... 11.1M 674s 9700K .......... .......... .......... .......... .......... 6.84M 674s 9750K .......... .......... .......... .......... .......... 4.83M 674s 9800K .......... .......... .......... .......... .......... 22.8M 674s 9850K .......... .......... .......... .......... .......... 22.0M 674s 9900K .......... .......... .......... .......... .......... 7.55M 674s 9950K .......... .......... .......... .......... .......... 7.45M 674s 10000K .......... .......... .......... .......... .......... 6.28M 674s 10050K .......... .......... .......... .......... .......... 40.7M 674s 10100K .......... .......... .......... .......... .......... 5.28M 674s 10150K .......... .......... .......... .......... .......... 5.26M 674s 10200K .......... .......... .......... .......... .......... 15.3M 674s 10250K .......... .......... .......... .......... .......... 23.1M 674s 10300K .......... .......... .......... .......... .......... 2.54M 674s 10350K .......... .......... .......... .......... .......... 10.7M 674s 10400K .......... .......... .......... .......... .......... 5.93M 674s 10450K .......... .......... .......... .......... 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686s 108100K .......... .......... .......... .......... .......... 45.6M 686s 108150K .......... .......... .......... .......... .......... 21.3M 686s 108200K .......... .......... .......... .......... .......... 10.3M 686s 108250K .......... .......... .......... .......... .......... 39.5M 686s 108300K .......... .......... .......... .......... .......... 34.7M 686s 108350K .......... .......... .......... .......... .......... 8.34M 686s 108400K .......... .......... .......... .......... .......... 43.7M 686s 108450K .......... .......... .......... .......... .......... 21.5M 686s 108500K .......... .......... .......... .......... .......... 37.1M 686s 108550K .......... .......... .......... .......... .......... 49.3M 686s 108600K .......... .......... .......... .......... .......... 8.37M 686s 108650K .......... .......... .......... .......... .......... 41.9M 686s 108700K .......... .......... .......... .......... .......... 48.1M 686s 108750K .......... .......... 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686s 109450K .......... .......... .......... .......... .......... 6.44M 686s 109500K .......... .......... .......... .......... .......... 13.5M 686s 109550K .......... .......... .......... .......... .......... 47.3M 686s 109600K .......... .......... .......... .......... .......... 47.9M 686s 109650K .......... .......... .......... .......... .......... 8.92M 686s 109700K .......... .......... .......... .......... .......... 38.7M 686s 109750K .......... .......... .......... .......... .......... 30.8M 686s 109800K .......... .......... .......... .......... .......... 22.9M 686s 109850K .......... .......... .......... .......... .......... 52.7M 686s 109900K .......... .......... .......... .......... .......... 48.3M 686s 109950K .......... .......... .......... .. 12.6M=13s 686s 686s Last-modified header missing -- time-stamps turned off. 686s 2024-03-07 21:52:43 (8.06 MB/s) - ‘v1.14.6.tar.gz’ saved [112621657] 686s 686s + tar -xaf v1.14.6.tar.gz --no-anchored hmm 690s + rm -rf /home/ubuntu/.local/lib/prokka/db/hmm 690s + mv prokka-1.14.6/db/hmm /home/ubuntu/.local/lib/prokka/db 690s + tar -xaf v1.14.6.tar.gz --no-anchored kingdom 694s + rm -rf /home/ubuntu/.local/lib/prokka/db/kingdom 694s + mv prokka-1.14.6/db/kingdom /home/ubuntu/.local/lib/prokka/db 694s + cp -rf /usr/share/prokka/db/cm /home/ubuntu/.local/lib/prokka/db/ 694s + cp -rf /usr/share/prokka/db/genus /home/ubuntu/.local/lib/prokka/db/ 694s + prokka --setupdb 695s [21:52:51] Appending to PATH: /usr/bin 695s [21:52:51] Cleaning databases in /home/ubuntu/.local/lib/prokka/db 695s [21:52:51] Cleaning complete. 695s [21:52:51] Looking for 'makeblastdb' - found /usr/bin/makeblastdb 695s [21:52:52] Determined makeblastdb version is 002012 from 'makeblastdb: 2.12.0+' 695s [21:52:52] Making kingdom BLASTP database: /home/ubuntu/.local/lib/prokka/db/kingdom/Archaea/sprot 695s [21:52:52] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/kingdom\/Archaea\/sprot -logfile /dev/null 695s [21:52:52] Making kingdom BLASTP database: /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/sprot 695s [21:52:52] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/kingdom\/Bacteria\/sprot -logfile /dev/null 698s [21:52:55] Making kingdom BLASTP database: /home/ubuntu/.local/lib/prokka/db/kingdom/Mitochondria/sprot 698s [21:52:55] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/kingdom\/Mitochondria\/sprot -logfile /dev/null 698s [21:52:55] Making kingdom BLASTP database: /home/ubuntu/.local/lib/prokka/db/kingdom/Viruses/sprot 698s [21:52:55] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/kingdom\/Viruses\/sprot -logfile /dev/null 699s [21:52:56] Making kingdom BLASTP database: /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/IS 699s [21:52:56] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/kingdom\/Bacteria\/IS -logfile /dev/null 699s [21:52:56] Making kingdom BLASTP database: /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/AMR 699s [21:52:56] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/kingdom\/Bacteria\/AMR -logfile /dev/null 700s [21:52:57] Making genus BLASTP database: /home/ubuntu/.local/lib/prokka/db/genus/Enterococcus 700s [21:52:57] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/genus\/Enterococcus -logfile /dev/null 701s [21:52:58] Making genus BLASTP database: /home/ubuntu/.local/lib/prokka/db/genus/Escherichia 701s [21:52:58] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/genus\/Escherichia -logfile /dev/null 701s [21:52:58] Making genus BLASTP database: /home/ubuntu/.local/lib/prokka/db/genus/Staphylococcus 701s [21:52:58] Running: makeblastdb -hash_index -dbtype prot -in \/home\/ubuntu\/\.local\/lib\/prokka\/db\/genus\/Staphylococcus -logfile /dev/null 702s [21:52:59] Looking for 'hmmpress' - found /usr/bin/hmmpress 702s [21:52:59] Determined hmmpress version is 003004 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/' 702s [21:52:59] Pressing HMM database: /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm 702s [21:52:59] Running: hmmpress \/home\/ubuntu\/\.local\/lib\/prokka\/db\/hmm\/HAMAP\.hmm 705s Working... done. 705s Pressed and indexed 1536 HMMs (1536 names). 705s Models pressed into binary file: /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm.h3m 705s SSI index for binary model file: /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm.h3i 705s Profiles (MSV part) pressed into: /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm.h3f 705s Profiles (remainder) pressed into: /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm.h3p 705s [21:53:02] Looking for 'cmpress' - found /usr/bin/cmpress 705s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 705s [21:53:02] Determined cmpress version is 001001 from '# INFERNAL 1.1.5 (Sep 2023)' 705s [21:53:02] Pressing CM database: /home/ubuntu/.local/lib/prokka/db/cm/Viruses 705s [21:53:02] Running: cmpress \/home\/ubuntu\/\.local\/lib\/prokka\/db\/cm\/Viruses 705s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 705s Working... done. 705s Pressed and indexed 239 CMs and p7 HMM filters (239 names and 239 accessions). 705s Covariance models and p7 filters pressed into binary file: /home/ubuntu/.local/lib/prokka/db/cm/Viruses.i1m 705s SSI index for binary covariance model file: /home/ubuntu/.local/lib/prokka/db/cm/Viruses.i1i 705s Optimized p7 filter profiles (MSV part) pressed into: /home/ubuntu/.local/lib/prokka/db/cm/Viruses.i1f 705s Optimized p7 filter profiles (remainder) pressed into: /home/ubuntu/.local/lib/prokka/db/cm/Viruses.i1p 705s [21:53:02] Pressing CM database: /home/ubuntu/.local/lib/prokka/db/cm/Bacteria 705s [21:53:02] Running: cmpress \/home\/ubuntu\/\.local\/lib\/prokka\/db\/cm\/Bacteria 705s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 707s Working... done. 707s Pressed and indexed 1127 CMs and p7 HMM filters (1127 names and 1127 accessions). 707s Covariance models and p7 filters pressed into binary file: /home/ubuntu/.local/lib/prokka/db/cm/Bacteria.i1m 707s SSI index for binary covariance model file: /home/ubuntu/.local/lib/prokka/db/cm/Bacteria.i1i 707s Optimized p7 filter profiles (MSV part) pressed into: /home/ubuntu/.local/lib/prokka/db/cm/Bacteria.i1f 707s Optimized p7 filter profiles (remainder) pressed into: /home/ubuntu/.local/lib/prokka/db/cm/Bacteria.i1p 707s [21:53:04] Pressing CM database: /home/ubuntu/.local/lib/prokka/db/cm/Archaea 707s [21:53:04] Running: cmpress \/home\/ubuntu\/\.local\/lib\/prokka\/db\/cm\/Archaea 707s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 707s Working... done. 707s Pressed and indexed 152 CMs and p7 HMM filters (152 names and 152 accessions). 707s Covariance models and p7 filters pressed into binary file: /home/ubuntu/.local/lib/prokka/db/cm/Archaea.i1m 707s SSI index for binary covariance model file: /home/ubuntu/.local/lib/prokka/db/cm/Archaea.i1i 707s Optimized p7 filter profiles (MSV part) pressed into: /home/ubuntu/.local/lib/prokka/db/cm/Archaea.i1f 707s Optimized p7 filter profiles (remainder) pressed into: /home/ubuntu/.local/lib/prokka/db/cm/Archaea.i1p 707s [21:53:04] Looking for databases in: /home/ubuntu/.local/lib/prokka/db 707s [21:53:04] * Kingdoms: Archaea Bacteria Mitochondria Viruses 707s [21:53:04] * Genera: Enterococcus Escherichia Staphylococcus 707s [21:53:04] * HMMs: HAMAP 707s [21:53:04] * CMs: Archaea Bacteria Viruses 707s + prokka --version 707s prokka 1.14.6 707s + prokka --help 708s --help This help 708s --version Print version and exit 708s --citation Print citation for referencing Prokka 708s --quiet No screen output (default OFF) 708s --debug Debug mode: keep all temporary files (default OFF) 708s --dbdir [X] Prokka database root folders (default '/home/ubuntu/.local/lib/prokka/db') 708s --listdb List all configured databases 708s --setupdb Index all installed databases 708s --cleandb Remove all database indices 708s --depends List all software dependencies 708s --outdir [X] Output folder [auto] (default '') 708s --force Force overwriting existing output folder (default OFF) 708s --prefix [X] Filename output prefix [auto] (default '') 708s Name: 708s Prokka 1.14.6 by Torsten Seemann 708s Synopsis: 708s rapid bacterial genome annotation 708s Usage: 708s prokka [options] 708s General: 708s Setup: 708s Outputs: 708s Organism details: 708s Annotations: 708s Matching: 708s Computation: 708s --addgenes Add 'gene' features for each 'CDS' feature (default OFF) 708s --addmrna Add 'mRNA' features for each 'CDS' feature (default OFF) 708s --locustag [X] Locus tag prefix [auto] (default '') 708s --increment [N] Locus tag counter increment (default '1') 708s --gffver [N] GFF version (default '3') 708s --compliant Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF) 708s --centre [X] Sequencing centre ID. (default '') 708s --accver [N] Version to put in Genbank file (default '1') 708s --genus [X] Genus name (default 'Genus') 708s --species [X] Species name (default 'species') 708s --strain [X] Strain name (default 'strain') 708s --plasmid [X] Plasmid name or identifier (default '') 708s --kingdom [X] Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria') 708s --gcode [N] Genetic code / Translation table (set if --kingdom is set) (default '0') 708s --prodigaltf [X] Prodigal training file (default '') 708s --gram [X] Gram: -/neg +/pos (default '') 708s --usegenus Use genus-specific BLAST databases (needs --genus) (default OFF) 708s --proteins [X] FASTA or GBK file to use as 1st priority (default '') 708s --hmms [X] Trusted HMM to first annotate from (default '') 708s --metagenome Improve gene predictions for highly fragmented genomes (default OFF) 708s --rawproduct Do not clean up /product annotation (default OFF) 708s --cdsrnaolap Allow [tr]RNA to overlap CDS (default OFF) 708s --evalue [n.n] Similarity e-value cut-off (default '1e-09') 708s --coverage [n.n] Minimum coverage on query protein (default '80') 708s --cpus [N] Number of CPUs to use [0=all] (default '8') 708s --fast Fast mode - only use basic BLASTP databases (default OFF) 708s --noanno For CDS just set /product="unannotated protein" (default OFF) 708s --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1') 708s --rfam Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0') 708s --norrna Don't run rRNA search (default OFF) 708s --notrna Don't run tRNA search (default OFF) 708s --rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF) 708s + prokka --listdb 708s [21:53:05] Looking for databases in: /home/ubuntu/.local/lib/prokka/db 708s [21:53:05] * Kingdoms: Archaea Bacteria Mitochondria Viruses 708s [21:53:05] * Genera: Enterococcus Escherichia Staphylococcus 708s [21:53:05] * HMMs: HAMAP 708s [21:53:05] * CMs: Archaea Bacteria Viruses 708s ++ nproc 708s + prokka --cpus 1 --outdir /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm --prefix asm test/plasmid.fna 708s [21:53:05] This is prokka 1.14.6 708s [21:53:05] Written by Torsten Seemann 708s [21:53:05] Homepage is https://github.com/tseemann/prokka 708s [21:53:05] Local time is Thu Mar 7 21:53:05 2024 708s [21:53:05] You are ubuntu 708s [21:53:05] Operating system is linux 708s [21:53:05] You have BioPerl 1.7.8 708s Argument "1.7.8" isn't numeric in numeric lt (<) at /usr/bin/prokka line 259. 708s [21:53:05] System has 1 cores. 708s [21:53:05] Will use maximum of 1 cores. 708s [21:53:05] Annotating as >>> Bacteria <<< 708s [21:53:05] Generating locus_tag from 'test/plasmid.fna' contents. 708s [21:53:05] Setting --locustag KCKEPNKI from MD5 4c4e9742af5bddec0d5d78a498415fb0 708s [21:53:05] Creating new output folder: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm 708s [21:53:05] Running: mkdir -p \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm 708s [21:53:05] Using filename prefix: asm.XXX 708s [21:53:05] Setting HMMER_NCPU=1 708s [21:53:05] Writing log to: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.log 709s [21:53:05] Command: /usr/bin/prokka --cpus 1 --outdir /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm --prefix asm test/plasmid.fna 709s [21:53:05] Appending to PATH: /usr/bin 709s [21:53:05] Looking for 'aragorn' - found /usr/bin/aragorn 709s [21:53:05] Determined aragorn version is 001002 from 'ARAGORN v1.2.41 Dean Laslett' 709s [21:53:05] Looking for 'blastp' - found /usr/bin/blastp 709s [21:53:06] Determined blastp version is 002012 from 'blastp: 2.12.0+' 709s [21:53:06] Looking for 'cmpress' - found /usr/bin/cmpress 709s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 709s [21:53:06] Determined cmpress version is 001001 from '# INFERNAL 1.1.5 (Sep 2023)' 709s [21:53:06] Looking for 'cmscan' - found /usr/bin/cmscan 709s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 709s [21:53:06] Determined cmscan version is 001001 from '# INFERNAL 1.1.5 (Sep 2023)' 709s [21:53:06] Looking for 'egrep' - found /usr/bin/egrep 709s [21:53:06] Looking for 'find' - found /usr/bin/find 709s [21:53:06] Looking for 'grep' - found /usr/bin/grep 709s [21:53:06] Looking for 'hmmpress' - found /usr/bin/hmmpress 709s [21:53:06] Determined hmmpress version is 003004 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/' 709s [21:53:06] Looking for 'hmmscan' - found /usr/bin/hmmscan 709s [21:53:06] Determined hmmscan version is 003004 from '# HMMER 3.4 (Aug 2023); http://hmmer.org/' 709s [21:53:06] Looking for 'java' - found /usr/bin/java 709s [21:53:06] Looking for 'makeblastdb' - found /usr/bin/makeblastdb 709s [21:53:06] Determined makeblastdb version is 002012 from 'makeblastdb: 2.12.0+' 709s [21:53:06] Looking for 'parallel' - found /usr/bin/parallel 710s [21:53:07] Determined parallel version is 20231122 from 'GNU parallel 20231122' 710s [21:53:07] Looking for 'prodigal' - found /usr/bin/prodigal 710s [21:53:07] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016' 710s [21:53:07] Looking for 'prokka-genbank_to_fasta_db' - found /usr/bin/prokka-genbank_to_fasta_db 710s [21:53:07] Looking for 'sed' - found /usr/bin/sed 710s [21:53:07] Looking for 'tbl2asn' - found /usr/bin/tbl2asn 710s [21:53:07] Determined tbl2asn version is 025003 from 'tbl2asn 25.3 arguments:' 710s [21:53:07] Using genetic code table 11. 710s [21:53:07] Loading and checking input file: test/plasmid.fna 710s [21:53:07] Wrote 1 contigs totalling 56520 bp. 710s [21:53:07] Predicting tRNAs and tmRNAs 710s [21:53:07] Running: aragorn -l -gc11 -w \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.fna 710s [21:53:07] Found 0 tRNAs 710s [21:53:07] Predicting Ribosomal RNAs 710s [21:53:07] You need either Barrnap or RNAmmer installed to predict rRNAs! 710s [21:53:07] Skipping ncRNA search, enable with --rfam if desired. 710s [21:53:07] Total of 0 tRNA + rRNA features 710s [21:53:07] Predicting coding sequences 710s [21:53:07] Contigs total 56520 bp, so using meta mode 710s [21:53:07] Running: prodigal -i \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.fna -c -m -g 11 -p meta -f sco -q 710s [21:53:07] Found 63 CDS 710s [21:53:07] Connecting features back to sequences 710s [21:53:07] Not using genus-specific database. Try --usegenus to enable it. 710s [21:53:07] Annotating CDS, please be patient. 710s [21:53:07] Will use 1 CPUs for similarity searching. 710s [21:53:07] There are still 63 unannotated CDS left (started with 63) 710s [21:53:07] Will use blast to search against /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/IS with 1 CPUs 710s [21:53:07] Running: cat \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.IS\.tmp\.3017\.faa | parallel --gnu --plain -j 1 --block 8370 --recstart '>' --pipe blastp -query - -db /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.IS\.tmp\.3017\.blast 2> /dev/null 714s [21:53:11] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.IS.tmp.3017.faa 714s [21:53:11] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.IS.tmp.3017.blast 714s [21:53:11] There are still 62 unannotated CDS left (started with 63) 714s [21:53:11] Will use blast to search against /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/AMR with 1 CPUs 714s [21:53:11] Running: cat \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.AMR\.tmp\.3017\.faa | parallel --gnu --plain -j 1 --block 8175 --recstart '>' --pipe blastp -query - -db /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.AMR\.tmp\.3017\.blast 2> /dev/null 716s [21:53:13] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.AMR.tmp.3017.faa 716s [21:53:13] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.AMR.tmp.3017.blast 716s [21:53:13] There are still 62 unannotated CDS left (started with 63) 716s [21:53:13] Will use blast to search against /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/sprot with 1 CPUs 716s [21:53:13] Running: cat \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.sprot\.tmp\.3017\.faa | parallel --gnu --plain -j 1 --block 8175 --recstart '>' --pipe blastp -query - -db /home/ubuntu/.local/lib/prokka/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.sprot\.tmp\.3017\.blast 2> /dev/null 725s [21:53:22] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.sprot.tmp.3017.faa 725s [21:53:22] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.sprot.tmp.3017.blast 725s [21:53:22] There are still 54 unannotated CDS left (started with 63) 725s [21:53:22] Will use hmmer to search against /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm with 1 CPUs 725s [21:53:22] Running: cat \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.HAMAP\.hmm\.tmp\.3017\.faa | parallel --gnu --plain -j 1 --block 6980 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /home/ubuntu/.local/lib/prokka/db/hmm/HAMAP.hmm /dev/stdin > \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.HAMAP\.hmm\.tmp\.3017\.hmmer 2> /dev/null 735s [21:53:32] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.HAMAP.hmm.tmp.3017.faa 735s [21:53:32] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.HAMAP.hmm.tmp.3017.hmmer 735s [21:53:32] Labelling remaining 54 proteins as 'hypothetical protein' 735s [21:53:32] Found 8 unique /gene codes. 735s [21:53:32] Fixed 0 colliding /gene names. 735s [21:53:32] Adding /locus_tag identifiers 735s [21:53:32] Assigned 63 locus_tags to CDS and RNA features. 735s [21:53:32] Writing outputs to /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/ 735s [21:53:32] Generating annotation statistics file 735s [21:53:32] Generating Genbank and Sequin files 735s [21:53:32] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.err -i \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.fsa 2> /dev/null 736s [21:53:33] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/errorsummary.val 736s [21:53:33] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.dr 736s [21:53:33] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.fixedproducts 736s [21:53:33] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.ecn 736s [21:53:33] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.val 736s [21:53:33] Repairing broken .GBK output that tbl2asn produces... 736s [21:53:33] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.gbf > \/tmp\/autopkgtest\.ppmBFH\/autopkgtest_tmp\/asm\/asm\.gbk 736s [21:53:33] Deleting unwanted file: /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.gbf 736s [21:53:33] Output files: 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.sqn 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.gbk 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.fna 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.err 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.log 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.ffn 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.faa 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.gff 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.txt 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.fsa 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.tbl 736s [21:53:33] /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.tsv 736s [21:53:33] Annotation finished successfully. 736s [21:53:33] Walltime used: 0.47 minutes 736s [21:53:33] If you use this result please cite the Prokka paper: 736s [21:53:33] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. 736s [21:53:33] Type 'prokka --citation' for more details. 736s [21:53:33] Thank you, come again. 736s >NC_017032.1 736s + grep '>' /tmp/autopkgtest.ppmBFH/autopkgtest_tmp/asm/asm.fna 736s autopkgtest [21:53:33]: test sample-programs: -----------------------] 737s sample-programs PASS 737s autopkgtest [21:53:34]: test sample-programs: - - - - - - - - - - results - - - - - - - - - - 737s autopkgtest [21:53:34]: @@@@@@@@@@@@@@@@@@@@ summary 737s sample-programs PASS 773s Creating nova instance adt-noble-arm64-prokka-20240307-214117-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240306.img (UUID fe83f9af-4e32-48b1-9e6a-30d9e6eedf79)...