0s autopkgtest [13:01:15]: starting date and time: 2026-01-24 13:01:15+0000 0s autopkgtest [13:01:15]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:01:15]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c46lee0i/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade sniffles --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-11.secgroup --name adt-resolute-amd64-sniffles-20260124-130115-juju-7f2275-prod-proposed-migration-environment-15-e5db8e2d-ea07-478b-b659-9499f790de86 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-sniffles-20260124-130115-juju-7f2275-prod-proposed-migration-environment-15-e5db8e2d-ea07-478b-b659-9499f790de86 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 80s autopkgtest [13:02:35]: testbed dpkg architecture: amd64 80s autopkgtest [13:02:35]: testbed apt version: 3.1.13 81s autopkgtest [13:02:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s autopkgtest [13:02:36]: testbed release detected to be: None 81s autopkgtest [13:02:36]: updating testbed package index (apt update) 82s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 82s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 82s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 82s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 82s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 82s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 82s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 82s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 82s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 82s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 82s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 82s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 82s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 83s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 83s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 83s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 83s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 83s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 83s Fetched 2806 kB in 1s (2519 kB/s) 84s Reading package lists... 84s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 84s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 84s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 84s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 85s Reading package lists... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Calculating upgrade... 85s The following packages were automatically installed and are no longer required: 85s python3.13 python3.13-minimal 85s Use 'sudo apt autoremove' to remove them. 85s The following NEW packages will be installed: 85s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 85s The following packages will be upgraded: 85s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 85s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 10.4 MB of archives. 85s After this operation, 25.2 MB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 85s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 86s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 86s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 86s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 86s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 86s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 86s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 87s dpkg-preconfigure: unable to re-open stdin: No such file or directory 87s Fetched 10.4 MB in 1s (8588 kB/s) 87s Selecting previously unselected package libpython3.14-minimal:amd64. 87s (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 ... 124177 files and directories currently installed.) 87s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 87s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 87s Selecting previously unselected package python3.14-minimal. 87s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 87s Unpacking python3.14-minimal (3.14.2-1) ... 87s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 87s Setting up python3.14-minimal (3.14.2-1) ... 88s (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 ... 124519 files and directories currently installed.) 88s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 88s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 88s Setting up python3-minimal (3.14.2-1) ... 88s (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 ... 124519 files and directories currently installed.) 88s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 88s running python pre-rtupdate hooks for python3.14... 88s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 88s Selecting previously unselected package libpython3.14-stdlib:amd64. 88s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 88s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 88s Selecting previously unselected package python3.14. 88s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 88s Unpacking python3.14 (3.14.2-1) ... 88s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 88s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 88s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 88s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 88s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 88s (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 ... 124980 files and directories currently installed.) 88s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 88s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 88s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 88s Setting up python3.14 (3.14.2-1) ... 89s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 89s Setting up python3-gdbm (3.14.2-1) ... 89s Setting up python3 (3.14.2-1) ... 89s running python rtupdate hooks for python3.14... 89s running python post-rtupdate hooks for python3.14... 89s Processing triggers for man-db (2.13.1-1) ... 89s Processing triggers for systemd (259-1ubuntu2) ... 90s autopkgtest [13:02:45]: upgrading testbed (apt dist-upgrade and autopurge) 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade... 90s The following packages were automatically installed and are no longer required: 90s python3.13 python3.13-minimal 90s Use 'sudo apt autoremove' to remove them. 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Solving dependencies... 90s The following packages will be REMOVED: 90s python3.13* python3.13-minimal* 91s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 91s After this operation, 7860 kB disk space will be freed. 91s (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 ... 124978 files and directories currently installed.) 91s Removing python3.13 (3.13.11-1) ... 91s Removing python3.13-minimal (3.13.11-1) ... 91s Processing triggers for man-db (2.13.1-1) ... 91s Processing triggers for systemd (259-1ubuntu2) ... 92s (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 ... 124951 files and directories currently installed.) 92s Purging configuration files for python3.13-minimal (3.13.11-1) ... 94s autopkgtest [13:02:49]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 94s autopkgtest [13:02:49]: @@@@@@@@@@@@@@@@@@@@ apt-source sniffles 95s Get:1 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (dsc) [2056 B] 95s Get:2 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (tar) [2917 kB] 95s Get:3 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (diff) [8416 B] 95s gpgv: Signature made Sat Feb 15 22:05:44 2025 UTC 95s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 95s gpgv: issuer "tille@debian.org" 95s gpgv: Can't check signature: No public key 95s dpkg-source: warning: cannot verify inline signature for ./sniffles_2.6.0-1.dsc: no acceptable signature found 95s autopkgtest [13:02:50]: testing package sniffles version 2.6.0-1 95s autopkgtest [13:02:50]: build not needed 96s autopkgtest [13:02:51]: test run-unit-test: preparing testbed 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Solving dependencies... 97s The following NEW packages will be installed: 97s libdeflate0 libhts3t64 libhtscodecs2 python3-edlib python3-psutil 97s python3-pysam sniffles 97s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 5504 kB of archives. 97s After this operation, 46.7 MB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 97s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2build1 [108 kB] 97s Get:3 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 97s Get:4 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-edlib amd64 1.2.7-7 [99.4 kB] 97s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-psutil amd64 7.1.0-1ubuntu1 [191 kB] 97s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.3+ds-2 [4536 kB] 97s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 sniffles all 2.6.0-1 [58.5 kB] 97s Fetched 5504 kB in 0s (13.0 MB/s) 97s Selecting previously unselected package libdeflate0:amd64. 97s (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 ... 124953 files and directories currently installed.) 97s Preparing to unpack .../0-libdeflate0_1.23-2_amd64.deb ... 97s Unpacking libdeflate0:amd64 (1.23-2) ... 97s Selecting previously unselected package libhtscodecs2:amd64. 97s Preparing to unpack .../1-libhtscodecs2_1.6.1-2build1_amd64.deb ... 97s Unpacking libhtscodecs2:amd64 (1.6.1-2build1) ... 97s Selecting previously unselected package libhts3t64:amd64. 97s Preparing to unpack .../2-libhts3t64_1.22.1+ds2-1_amd64.deb ... 97s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 97s Selecting previously unselected package python3-edlib:amd64. 97s Preparing to unpack .../3-python3-edlib_1.2.7-7_amd64.deb ... 97s Unpacking python3-edlib:amd64 (1.2.7-7) ... 97s Selecting previously unselected package python3-psutil. 97s Preparing to unpack .../4-python3-psutil_7.1.0-1ubuntu1_amd64.deb ... 97s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 97s Selecting previously unselected package python3-pysam. 97s Preparing to unpack .../5-python3-pysam_0.23.3+ds-2_amd64.deb ... 97s Unpacking python3-pysam (0.23.3+ds-2) ... 97s Selecting previously unselected package sniffles. 97s Preparing to unpack .../6-sniffles_2.6.0-1_all.deb ... 97s Unpacking sniffles (2.6.0-1) ... 97s Setting up libhtscodecs2:amd64 (1.6.1-2build1) ... 97s Setting up libdeflate0:amd64 (1.23-2) ... 97s Setting up python3-psutil (7.1.0-1ubuntu1) ... 98s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 98s Setting up python3-edlib:amd64 (1.2.7-7) ... 98s Setting up python3-pysam (0.23.3+ds-2) ... 98s Setting up sniffles (2.6.0-1) ... 98s Processing triggers for man-db (2.13.1-1) ... 98s Processing triggers for libc-bin (2.42-2ubuntu4) ... 99s autopkgtest [13:02:54]: test run-unit-test: [----------------------- 99s 2026-01-24 13:02:54,442 INFO sniffles.main (2216): Running Sniffles2, build 2.6.0 99s 2026-01-24 13:02:54,443 INFO sniffles.main (2216): Run Mode: call_sample 99s 2026-01-24 13:02:54,443 INFO sniffles.main (2216): Start on: 2026/01/24 13:02:54 99s 2026-01-24 13:02:54,443 INFO sniffles.main (2216): Working dir: /tmp/autopkgtest.uBA8UV/autopkgtest_tmp 99s 2026-01-24 13:02:54,443 INFO sniffles.main (2216): Used command: /usr/bin/sniffles --input test.bam --snf test.snf 99s 2026-01-24 13:02:54,443 INFO sniffles.main (2216): ============================== 99s 2026-01-24 13:02:54,450 INFO sniffles.main (2216): Opening for reading: test.bam 99s 2026-01-24 13:02:54,451 INFO sniffles.main (2216): Opening for writing: test.snf 99s 2026-01-24 13:02:54,452 INFO sniffles.main (2216): 99s 2026-01-24 13:02:54,452 INFO sniffles.main (2216): Analyzing 1 alignments total... 99s 2026-01-24 13:02:54,452 INFO sniffles.main (2216): 99s 2026-01-24 13:02:54,452 INFO sniffles.worker (2216): Starting worker 0 99s 2026-01-24 13:02:54,454 ERROR sniffles.main (2216): Unhandled error while running sniffles. 99s Traceback (most recent call last): 99s File "/usr/bin/sniffles", line 580, in 99s Sniffles2_Main(processes) 99s ~~~~~~~~~~~~~~^^^^^^^^^^^ 99s File "/usr/bin/sniffles", line 492, in Sniffles2_Main 99s p.start() 99s ~~~~~~~^^ 99s File "/usr/lib/python3/dist-packages/sniffles/parallel.py", line 522, in start 99s self.process.start() 99s ~~~~~~~~~~~~~~~~~~^^ 99s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start 99s self._popen = self._Popen(self) 99s ~~~~~~~~~~~^^^^^^ 99s File "/usr/lib/python3.14/multiprocessing/context.py", line 224, in _Popen 99s return _default_context.get_context().Process._Popen(process_obj) 99s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 99s File "/usr/lib/python3.14/multiprocessing/context.py", line 300, in _Popen 99s return Popen(process_obj) 99s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ 99s super().__init__(process_obj) 99s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 99s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ 99s self._launch(process_obj) 99s ~~~~~~~~~~~~^^^^^^^^^^^^^ 99s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 47, in _launch 99s reduction.dump(process_obj, buf) 99s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 99s File "/usr/lib/python3.14/multiprocessing/reduction.py", line 60, in dump 99s ForkingPickler(file, protocol).dump(obj) 99s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^ 99s TypeError: cannot pickle '_thread.RLock' object 99s when serializing dict item '_lock' 99s when serializing psutil.Process state 99s when serializing psutil.Process object 99s when serializing dict item '_process' 99s when serializing sniffles.utils.resmon.ResourceMonitor state 99s when serializing sniffles.utils.resmon.ResourceMonitor object 99s when serializing dict item 'recycle' 99s when serializing sniffles.parallel.SnifflesWorker state 99s when serializing sniffles.parallel.SnifflesWorker object 99s when serializing tuple item 0 99s when serializing method reconstructor arguments 99s when serializing method object 99s when serializing dict item '_target' 99s when serializing multiprocessing.context.Process state 99s when serializing multiprocessing.context.Process object 99s autopkgtest [13:02:54]: test run-unit-test: -----------------------] 100s autopkgtest [13:02:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 100s run-unit-test FAIL non-zero exit status 1 100s autopkgtest [13:02:55]: @@@@@@@@@@@@@@@@@@@@ summary 100s run-unit-test FAIL non-zero exit status 1