0s autopkgtest [21:42:31]: starting date and time: 2024-03-13 21:42:31+0000 0s autopkgtest [21:42:31]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:42:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ys0203_t/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:hdf5,src:openmpi,src:openssl,src:pmix --apt-upgrade pbsuite --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 openssl/3.0.13-0ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-17.secgroup --name adt-noble-arm64-pbsuite-20240313-214231-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 120s autopkgtest [21:44:31]: testbed dpkg architecture: arm64 120s autopkgtest [21:44:31]: testbed apt version: 2.7.12 120s autopkgtest [21:44:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 121s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 121s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 122s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB] 122s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 122s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 122s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 123s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 123s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 123s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 123s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB] 123s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 123s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB] 123s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 128s Fetched 7327 kB in 3s (2439 kB/s) 128s Reading package lists... 129s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 130s Reading package lists... 140s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Calculating upgrade... 143s The following packages will be REMOVED: 143s libssl3 143s The following NEW packages will be installed: 143s libssl3t64 143s The following packages will be upgraded: 143s console-setup console-setup-linux keyboard-configuration openssl 143s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 143s Need to get 4955 kB of archives. 143s After this operation, 74.8 kB of additional disk space will be used. 143s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 144s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 144s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 145s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 145s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 145s Preconfiguring packages ... 146s Fetched 4955 kB in 2s (2707 kB/s) 146s (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 ... 75867 files and directories currently installed.) 146s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 146s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 146s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 146s wget depends on libssl3 (>= 3.0.0). 146s u-boot-tools depends on libssl3 (>= 3.0.0). 146s tnftp depends on libssl3 (>= 3.0.0). 146s tcpdump depends on libssl3 (>= 3.0.0). 146s systemd-resolved depends on libssl3 (>= 3.0.0). 146s systemd depends on libssl3 (>= 3.0.0). 146s sudo depends on libssl3 (>= 3.0.0). 146s sbsigntool depends on libssl3 (>= 3.0.0). 146s rsync depends on libssl3 (>= 3.0.0). 146s python3-cryptography depends on libssl3 (>= 3.0.0). 146s openssh-server depends on libssl3 (>= 3.0.10). 146s openssh-client depends on libssl3 (>= 3.0.10). 146s mtd-utils depends on libssl3 (>= 3.0.0). 146s mokutil depends on libssl3 (>= 3.0.0). 146s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 146s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 146s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 146s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 146s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 146s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 146s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 146s libnvme1 depends on libssl3 (>= 3.0.0). 146s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 146s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 146s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 146s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 146s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 146s kmod depends on libssl3 (>= 3.0.0). 146s dhcpcd-base depends on libssl3 (>= 3.0.0). 146s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 146s 146s (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 ... 75867 files and directories currently installed.) 146s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 146s Selecting previously unselected package libssl3t64:arm64. 147s (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.) 147s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 147s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 147s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 147s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 147s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 147s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 147s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 147s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 147s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 147s Setting up keyboard-configuration (1.226ubuntu1) ... 149s Your console font configuration will be updated the next time your system 149s boots. If you want to update it now, run 'setupcon' from a virtual console. 149s update-initramfs: deferring update (trigger activated) 149s Setting up openssl (3.0.13-0ubuntu1) ... 149s Setting up console-setup-linux (1.226ubuntu1) ... 152s Setting up console-setup (1.226ubuntu1) ... 154s update-initramfs: deferring update (trigger activated) 154s Processing triggers for man-db (2.12.0-3) ... 155s Processing triggers for libc-bin (2.39-0ubuntu2) ... 155s Processing triggers for initramfs-tools (0.142ubuntu20) ... 155s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 155s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 175s System running in EFI mode, skipping. 175s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s 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 176s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 178s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 178s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 178s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 178s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 187s Reading package lists... 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s 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 187s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list.d/proposed.list:1 and /etc/apt/sources.list.d/proposed.sources:1 187s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s Calculating upgrade... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 192s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s autopkgtest [21:45:43]: rebooting testbed after setup commands that affected boot 349s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 357s autopkgtest [21:48:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 360s autopkgtest [21:48:31]: @@@@@@@@@@@@@@@@@@@@ apt-source pbsuite 367s Get:1 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (dsc) [2281 B] 367s Get:2 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (tar) [1615 kB] 367s Get:3 http://ftpmaster.internal/ubuntu noble/universe pbsuite 15.8.24+dfsg-7 (diff) [24.5 kB] 367s gpgv: Signature made Mon Feb 8 07:05:55 2021 UTC 367s gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 367s gpgv: issuer "npatra974@gmail.com" 367s gpgv: Can't check signature: No public key 367s dpkg-source: warning: cannot verify inline signature for ./pbsuite_15.8.24+dfsg-7.dsc: no acceptable signature found 368s autopkgtest [21:48:39]: testing package pbsuite version 15.8.24+dfsg-7 368s autopkgtest [21:48:39]: build not needed 371s autopkgtest [21:48:42]: test pbhoney: preparing testbed 374s Reading package lists... 374s Building dependency tree... 374s Reading state information... 375s Starting pkgProblemResolver with broken count: 0 375s Starting 2 pkgProblemResolver with broken count: 0 375s Done 376s The following additional packages will be installed: 376s blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 libgfortran5 376s libhdf5-103-1t64 libhdf5-cpp-103-1 libhdf5-hl-100t64 libhts3 libhtscodecs2 376s liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libsz2 pbdagcon 376s pbhoney pbjelly python3-h5py python3-h5py-serial python3-intervaltree 376s python3-intervaltree-bio python3-networkx python3-numpy python3-pbbanana 376s python3-pbsuite-utils python3-pysam python3-sortedcontainers samtools 376s Suggested packages: 376s python-h5py-doc python-networkx-doc python3-gdal python3-matplotlib 376s python3-pydot python3-pygraphviz python3-scipy gcc gfortran python3-dev 376s python3-pytest python-sortedcontainers-doc cwltool 376s The following NEW packages will be installed: 376s autopkgtest-satdep blasr libaec0 libblas3 libblasr5.3.5 libdeflate0 376s libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1 libhdf5-hl-100t64 libhts3 376s libhtscodecs2 liblapack3 liblzf1 libpbbam2.4.0 libpbcopper2.3.0 libpbseq 376s libsz2 pbdagcon pbhoney pbjelly python3-h5py python3-h5py-serial 376s python3-intervaltree python3-intervaltree-bio python3-networkx python3-numpy 376s python3-pbbanana python3-pbsuite-utils python3-pysam 376s python3-sortedcontainers samtools 376s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 376s Need to get 22.1 MB/22.1 MB of archives. 376s After this operation, 121 MB of additional disk space will be used. 376s Get:1 /tmp/autopkgtest.KgePPw/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 376s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 376s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 376s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB] 377s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-cpp-103-1 arm64 1.10.10+repack-3ubuntu2 [120 kB] 377s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 377s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 377s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 377s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbcopper2.3.0 arm64 2.3.0+dfsg-2 [516 kB] 377s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbbam2.4.0 arm64 2.4.0+dfsg-1build1 [634 kB] 377s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libblasr5.3.5 arm64 5.3.5+dfsg-6build3 [1207 kB] 378s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libpbseq arm64 5.3.5+dfsg-6build3 [3068 B] 378s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 blasr arm64 5.3.5+dfsg-6build4 [212 kB] 378s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 378s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 378s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB] 378s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 378s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 378s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 pbdagcon arm64 0.3+git20180411.c14c422+dfsg-8build3 [252 kB] 378s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 378s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbsuite-utils all 15.8.24+dfsg-7 [506 kB] 379s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 379s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 pbjelly all 15.8.24+dfsg-7 [966 kB] 379s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbbanana all 15.8.24+dfsg-7 [16.7 kB] 379s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 379s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB] 380s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B] 380s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 380s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-intervaltree all 3.0.2-1.1 [22.4 kB] 380s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-intervaltree-bio all 1.0.1-4 [8260 B] 380s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 380s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 pbhoney all 15.8.24+dfsg-7 [1051 kB] 381s Fetched 22.1 MB in 4s (5984 kB/s) 381s Selecting previously unselected package libaec0:arm64. 381s (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 ... 75869 files and directories currently installed.) 381s Preparing to unpack .../00-libaec0_1.1.2-1_arm64.deb ... 381s Unpacking libaec0:arm64 (1.1.2-1) ... 381s Selecting previously unselected package libsz2:arm64. 381s Preparing to unpack .../01-libsz2_1.1.2-1_arm64.deb ... 381s Unpacking libsz2:arm64 (1.1.2-1) ... 381s Selecting previously unselected package libhdf5-103-1t64:arm64. 381s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 381s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 381s Selecting previously unselected package libhdf5-cpp-103-1:arm64. 381s Preparing to unpack .../03-libhdf5-cpp-103-1_1.10.10+repack-3ubuntu2_arm64.deb ... 381s Unpacking libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu2) ... 381s Selecting previously unselected package libdeflate0:arm64. 381s Preparing to unpack .../04-libdeflate0_1.19-1_arm64.deb ... 381s Unpacking libdeflate0:arm64 (1.19-1) ... 381s Selecting previously unselected package libhtscodecs2:arm64. 381s Preparing to unpack .../05-libhtscodecs2_1.6.0-1_arm64.deb ... 381s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 381s Selecting previously unselected package libhts3:arm64. 381s Preparing to unpack .../06-libhts3_1.18+ds-1_arm64.deb ... 381s Unpacking libhts3:arm64 (1.18+ds-1) ... 381s Selecting previously unselected package libpbcopper2.3.0:arm64. 381s Preparing to unpack .../07-libpbcopper2.3.0_2.3.0+dfsg-2_arm64.deb ... 381s Unpacking libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 381s Selecting previously unselected package libpbbam2.4.0:arm64. 381s Preparing to unpack .../08-libpbbam2.4.0_2.4.0+dfsg-1build1_arm64.deb ... 381s Unpacking libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... 381s Selecting previously unselected package libblasr5.3.5:arm64. 381s Preparing to unpack .../09-libblasr5.3.5_5.3.5+dfsg-6build3_arm64.deb ... 381s Unpacking libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... 382s Selecting previously unselected package libpbseq:arm64. 382s Preparing to unpack .../10-libpbseq_5.3.5+dfsg-6build3_arm64.deb ... 382s Unpacking libpbseq:arm64 (5.3.5+dfsg-6build3) ... 382s Selecting previously unselected package blasr. 382s Preparing to unpack .../11-blasr_5.3.5+dfsg-6build4_arm64.deb ... 382s Unpacking blasr (5.3.5+dfsg-6build4) ... 382s Selecting previously unselected package libblas3:arm64. 382s Preparing to unpack .../12-libblas3_3.12.0-3_arm64.deb ... 382s Unpacking libblas3:arm64 (3.12.0-3) ... 382s Selecting previously unselected package libgfortran5:arm64. 382s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 382s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 382s Selecting previously unselected package libhdf5-hl-100t64:arm64. 382s Preparing to unpack .../14-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 382s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 382s Selecting previously unselected package liblapack3:arm64. 382s Preparing to unpack .../15-liblapack3_3.12.0-3_arm64.deb ... 382s Unpacking liblapack3:arm64 (3.12.0-3) ... 382s Selecting previously unselected package liblzf1:arm64. 382s Preparing to unpack .../16-liblzf1_3.6-4_arm64.deb ... 382s Unpacking liblzf1:arm64 (3.6-4) ... 382s Selecting previously unselected package pbdagcon. 382s Preparing to unpack .../17-pbdagcon_0.3+git20180411.c14c422+dfsg-8build3_arm64.deb ... 382s Unpacking pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 382s Selecting previously unselected package python3-pysam. 382s Preparing to unpack .../18-python3-pysam_0.22.0+ds-1_arm64.deb ... 382s Unpacking python3-pysam (0.22.0+ds-1) ... 382s Selecting previously unselected package python3-pbsuite-utils. 382s Preparing to unpack .../19-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... 382s Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... 383s Selecting previously unselected package python3-networkx. 383s Preparing to unpack .../20-python3-networkx_2.8.8-1ubuntu1_all.deb ... 383s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 383s Selecting previously unselected package pbjelly. 383s Preparing to unpack .../21-pbjelly_15.8.24+dfsg-7_all.deb ... 383s Unpacking pbjelly (15.8.24+dfsg-7) ... 383s Selecting previously unselected package python3-pbbanana. 383s Preparing to unpack .../22-python3-pbbanana_15.8.24+dfsg-7_all.deb ... 383s Unpacking python3-pbbanana (15.8.24+dfsg-7) ... 383s Selecting previously unselected package python3-numpy. 383s Preparing to unpack .../23-python3-numpy_1%3a1.24.2-2_arm64.deb ... 383s Unpacking python3-numpy (1:1.24.2-2) ... 384s Selecting previously unselected package python3-h5py-serial. 384s Preparing to unpack .../24-python3-h5py-serial_3.10.0-1ubuntu2_arm64.deb ... 384s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 384s Selecting previously unselected package python3-h5py. 384s Preparing to unpack .../25-python3-h5py_3.10.0-1ubuntu2_all.deb ... 384s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 384s Selecting previously unselected package python3-sortedcontainers. 384s Preparing to unpack .../26-python3-sortedcontainers_2.4.0-2_all.deb ... 384s Unpacking python3-sortedcontainers (2.4.0-2) ... 384s Selecting previously unselected package python3-intervaltree. 384s Preparing to unpack .../27-python3-intervaltree_3.0.2-1.1_all.deb ... 384s Unpacking python3-intervaltree (3.0.2-1.1) ... 384s Selecting previously unselected package python3-intervaltree-bio. 384s Preparing to unpack .../28-python3-intervaltree-bio_1.0.1-4_all.deb ... 384s Unpacking python3-intervaltree-bio (1.0.1-4) ... 384s Selecting previously unselected package samtools. 384s Preparing to unpack .../29-samtools_1.19.2-1_arm64.deb ... 384s Unpacking samtools (1.19.2-1) ... 384s Selecting previously unselected package pbhoney. 384s Preparing to unpack .../30-pbhoney_15.8.24+dfsg-7_all.deb ... 384s Unpacking pbhoney (15.8.24+dfsg-7) ... 384s Selecting previously unselected package autopkgtest-satdep. 384s Preparing to unpack .../31-1-autopkgtest-satdep.deb ... 384s Unpacking autopkgtest-satdep (0) ... 384s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 384s Setting up libdeflate0:arm64 (1.19-1) ... 384s Setting up python3-sortedcontainers (2.4.0-2) ... 385s Setting up python3-networkx (2.8.8-1ubuntu1) ... 387s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 387s "graph [edge [ source u'u\4200' target u'u\4200' ] " 387s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 387s + "node [ id u'u\4200' label b ] ]" 387s Setting up libaec0:arm64 (1.1.2-1) ... 387s Setting up libblas3:arm64 (3.12.0-3) ... 387s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 387s Setting up liblzf1:arm64 (3.6-4) ... 387s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 387s Setting up libsz2:arm64 (1.1.2-1) ... 387s Setting up libpbcopper2.3.0:arm64 (2.3.0+dfsg-2) ... 387s Setting up liblapack3:arm64 (3.12.0-3) ... 387s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 387s Setting up libhts3:arm64 (1.18+ds-1) ... 387s Setting up python3-pysam (0.22.0+ds-1) ... 387s Setting up python3-intervaltree (3.0.2-1.1) ... 388s Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... 388s /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' 388s for i in re.findall("\d+|\^?[ATCGN]+", md): 388s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' 388s splRE = re.compile("\s+") 388s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' 388s splRE = re.compile("\s+") 388s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' 388s self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) 388s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' 388s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 388s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' 388s data = re.split("\s+",line) 388s /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' 388s data = re.split("\s+",line) 388s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' 388s METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' 388s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' 388s ',\s*(Number\s*=\s*(?P[0-9.])\s*,' 388s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' 388s '\s*Type\s*=\s*(?P\w+)\s*,)?' 388s /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' 388s '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ 388s /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' 388s regex = re.compile("ref\d{7}") 388s Setting up libpbbam2.4.0:arm64 (2.4.0+dfsg-1build1) ... 388s Setting up samtools (1.19.2-1) ... 388s Setting up python3-numpy (1:1.24.2-2) ... 392s Setting up python3-intervaltree-bio (1.0.1-4) ... 392s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 392s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 393s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 393s Setting up python3-h5py (3.10.0-1ubuntu2) ... 393s Setting up libhdf5-cpp-103-1:arm64 (1.10.10+repack-3ubuntu2) ... 393s Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-6build3) ... 393s Setting up libpbseq:arm64 (5.3.5+dfsg-6build3) ... 393s Setting up blasr (5.3.5+dfsg-6build4) ... 393s Setting up pbdagcon (0.3+git20180411.c14c422+dfsg-8build3) ... 393s Setting up pbjelly (15.8.24+dfsg-7) ... 394s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' 394s getSub = re.compile("(.*)##(\d+)#(\d+)##$") 394s /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' 394s splRE = re.compile("\s+") 394s /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' 394s refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") 394s /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' 394s nprocRe = re.compile("--nproc (\d+)") 394s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' 394s """ 394s /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' 394s datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") 394s Setting up python3-pbbanana (15.8.24+dfsg-7) ... 394s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' 394s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 394s /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' 394s data = re.split("\s+",line) 394s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' 394s subreadGrab = re.compile(".*/(\d+)_(\d+)$") 394s /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' 394s data = re.split("\s+",line) 394s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' 394s _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") 394s /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' 394s getContigName = re.compile("(\d+)_contig") 394s /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' 394s "awk -F\ '{{if ($1 < 500) print $2}}' | " 394s Setting up pbhoney (15.8.24+dfsg-7) ... 394s /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' 394s forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") 394s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' 394s """ 394s /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' 394s datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") 394s /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' 394s for i in re.findall("\d+|\^?[ATCGN]+", md): 394s Setting up autopkgtest-satdep (0) ... 394s Processing triggers for man-db (2.12.0-3) ... 395s Processing triggers for libc-bin (2.39-0ubuntu2) ... 402s (Reading database ... 78576 files and directories currently installed.) 402s Removing autopkgtest-satdep (0) ... 403s autopkgtest [21:49:14]: test pbhoney: [----------------------- 403s PIEMapping 403s 403s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 403s Reid. "PBHoney: identyfying genomic variants via 403s long-read discordance and interrupted mapping." 403s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 403s doi:10.1186/1471-2105-15-180 403s 403s 2024-03-13 21:49:14,793 [INFO] Running /usr/bin/Honey pie filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam 403s 2024-03-13 21:49:14,793 [INFO] Running Blasr 451s 2024-03-13 21:50:02,405 [INFO] [0, b'[INFO] 2024-03-13T21:49:14 [blasr] started.\n[INFO] 2024-03-13T21:50:02 [blasr] ended.\n', None] 451s 2024-03-13 21:50:02,405 [INFO] Mapping Tails 451s 2024-03-13 21:50:02,406 [INFO] Extracting tails 451s 2024-03-13 21:50:02,807 [INFO] Parsed 433 reads 451s 2024-03-13 21:50:02,807 [INFO] Found 278 tails 451s 2024-03-13 21:50:02,807 [INFO] 21 reads had double tails 451s 2024-03-13 21:50:02,808 [INFO] Running Blasr 461s 2024-03-13 21:50:12,523 [INFO] [0, b'[INFO] 2024-03-13T21:50:02 [blasr] started.\n[INFO] 2024-03-13T21:50:12 [blasr] ended.\n', None] 461s 2024-03-13 21:50:12,524 [INFO] Consolidating alignments 461s 2024-03-13 21:50:12,586 [INFO] 172 tails mapped 461s Sam To Bam 461s Calling Tails 462s 462s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 462s Reid. "PBHoney: identyfying genomic variants via 462s long-read discordance and interrupted mapping." 462s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 462s doi:10.1186/1471-2105-15-180 462s 462s 2024-03-13 21:50:13,499 [INFO] Running /usr/bin/Honey tails mappingFinal.bam 462s 2024-03-13 21:50:13,500 [INFO] Parsing lambda_NEB3011 462s 2024-03-13 21:50:13,537 [INFO] Parsing lambda_NEB3011_lambda_NEB3011 462s 2024-03-13 21:50:13,558 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 56 pre-filter clusters 462s 2024-03-13 21:50:13,561 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 10 post-filter clusters 462s 2024-03-13 21:50:13,561 [INFO] Finished 462s Calling Spots 463s 463s Please Cite: English, Adam C., William J. Salerno, Jeffery G. 463s Reid. "PBHoney: identyfying genomic variants via 463s long-read discordance and interrupted mapping." 463s BMC Bioinformatics 2014, 15:180 (June 10, 2014). 463s doi:10.1186/1471-2105-15-180 463s 463s 2024-03-13 21:50:14,196 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 463s 2024-03-13 21:50:14,218 [INFO] Starting lambda_NEB3011:ErrorCounter 463s 2024-03-13 21:50:14,230 [INFO] 605 reads to parse in lambda_NEB3011 463s 2024-03-13 21:50:14,236 [INFO] 5% complete 463s 2024-03-13 21:50:14,237 [INFO] 10% complete 463s 2024-03-13 21:50:14,243 [INFO] 15% complete 463s 2024-03-13 21:50:14,247 [INFO] 20% complete 463s 2024-03-13 21:50:14,249 [INFO] 25% complete 463s 2024-03-13 21:50:14,253 [INFO] 30% complete 463s 2024-03-13 21:50:14,258 [INFO] 35% complete 463s 2024-03-13 21:50:14,261 [INFO] 40% complete 463s 2024-03-13 21:50:14,263 [INFO] 45% complete 463s 2024-03-13 21:50:14,267 [INFO] 50% complete 463s 2024-03-13 21:50:14,269 [INFO] 55% complete 463s 2024-03-13 21:50:14,273 [INFO] 60% complete 463s 2024-03-13 21:50:14,277 [INFO] 65% complete 463s 2024-03-13 21:50:14,280 [INFO] 70% complete 463s 2024-03-13 21:50:14,283 [INFO] 75% complete 463s 2024-03-13 21:50:14,287 [INFO] 80% complete 463s 2024-03-13 21:50:14,290 [INFO] 85% complete 463s 2024-03-13 21:50:14,294 [INFO] 90% complete 463s 2024-03-13 21:50:14,296 [INFO] 95% complete 463s 2024-03-13 21:50:14,324 [INFO] lambda_NEB3011:ErrorCounter -> spot 463s 2024-03-13 21:50:14,325 [INFO] Starting lambda_NEB3011:SpotCaller 463s 2024-03-13 21:50:14,340 [INFO] |lambda_NEB3011:SpotCaller|COV processing 463s 2024-03-13 21:50:14,340 [INFO] |lambda_NEB3011:SpotCaller|MaxCov:32 MeanCov:16 StdCov:5 MinCov:5 463s 2024-03-13 21:50:14,340 [INFO] |lambda_NEB3011:SpotCaller|INS processing 463s 2024-03-13 21:50:14,348 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.032458 -- RateStd 0.177212 463s 2024-03-13 21:50:14,349 [INFO] |lambda_NEB3011:SpotCaller|DEL processing 463s 2024-03-13 21:50:14,357 [INFO] |lambda_NEB3011:SpotCaller|RateMean 0.104832 -- RateStd 0.306337 463s 2024-03-13 21:50:14,361 [INFO] Finished 463s 2024-03-13 21:50:14,362 [INFO] Thread Consumer-1: Exiting 463s autopkgtest [21:50:14]: test pbhoney: -----------------------] 464s autopkgtest [21:50:15]: test pbhoney: - - - - - - - - - - results - - - - - - - - - - 464s pbhoney PASS 464s autopkgtest [21:50:15]: @@@@@@@@@@@@@@@@@@@@ summary 464s pbhoney PASS 479s Creating nova instance adt-noble-arm64-pbsuite-20240313-214231-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID a0e860fd-0684-417f-821d-d8092ab02621)...