0s autopkgtest [18:46:35]: starting date and time: 2026-01-22 18:46:35+0000 0s autopkgtest [18:46:35]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:46:35]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p1o8gjgx/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-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-16.secgroup --name adt-resolute-arm64-sniffles-20260122-184634-juju-7f2275-prod-proposed-migration-environment-2-9218cb2f-d822-4cbc-9265-b69e1f4a2544 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-sniffles-20260122-184634-juju-7f2275-prod-proposed-migration-environment-2-9218cb2f-d822-4cbc-9265-b69e1f4a2544 from image adt/ubuntu-resolute-arm64-server-20260122.img (UUID ed27afc7-5f46-4e8b-ad73-864280a0ddbb)... 62s autopkgtest [18:47:37]: testbed dpkg architecture: arm64 62s autopkgtest [18:47:37]: testbed apt version: 3.1.12 62s autopkgtest [18:47:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s autopkgtest [18:47:38]: testbed release detected to be: None 63s autopkgtest [18:47:38]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [19.2 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [815 kB] 65s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 65s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [80.9 kB] 65s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [103 kB] 65s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3316 B] 65s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [7876 B] 65s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 65s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [639 kB] 65s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [16.2 kB] 65s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [4636 B] 65s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [460 B] 68s Fetched 1818 kB in 2s (1210 kB/s) 69s Reading package lists... 70s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Reading package lists... 71s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Calculating upgrade... 72s The following packages were automatically installed and are no longer required: 72s python3.13 python3.13-minimal 72s Use 'sudo apt autoremove' to remove them. 72s The following NEW packages will be installed: 72s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 72s The following packages will be upgraded: 72s libpython3-stdlib python3 python3-gdbm python3-minimal 73s 4 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 73s Need to get 6705 kB of archives. 73s After this operation, 26.0 MB of additional disk space will be used. 73s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 73s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 73s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 73s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 73s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 74s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 74s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 74s dpkg-preconfigure: unable to re-open stdin: No such file or directory 74s Fetched 6705 kB in 1s (5962 kB/s) 74s Selecting previously unselected package libpython3.14-minimal:arm64. 75s (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 ... 135223 files and directories currently installed.) 75s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 75s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 75s Selecting previously unselected package python3.14-minimal. 75s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 75s Unpacking python3.14-minimal (3.14.2-1) ... 75s Preparing to unpack .../python3-gdbm_3.14.2-1_arm64.deb ... 75s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 75s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 75s Setting up python3.14-minimal (3.14.2-1) ... 77s (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 ... 135565 files and directories currently installed.) 77s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 77s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 77s Setting up python3-minimal (3.14.2-1) ... 77s (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 ... 135565 files and directories currently installed.) 77s Preparing to unpack .../python3_3.14.2-1_arm64.deb ... 77s running python pre-rtupdate hooks for python3.14... 77s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 77s Selecting previously unselected package libpython3.14-stdlib:arm64. 77s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_arm64.deb ... 77s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 78s Selecting previously unselected package python3.14. 78s Preparing to unpack .../python3.14_3.14.2-1_arm64.deb ... 78s Unpacking python3.14 (3.14.2-1) ... 78s Preparing to unpack .../libpython3-stdlib_3.14.2-1_arm64.deb ... 78s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.7-1) ... 78s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 78s Setting up python3.14 (3.14.2-1) ... 79s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 79s Setting up python3-gdbm (3.14.2-1) ... 79s Setting up python3 (3.14.2-1) ... 79s running python rtupdate hooks for python3.14... 79s running python post-rtupdate hooks for python3.14... 79s Processing triggers for man-db (2.13.1-1) ... 80s Processing triggers for systemd (259-1ubuntu2) ... 81s autopkgtest [18:47:56]: upgrading testbed (apt dist-upgrade and autopurge) 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Calculating upgrade... 83s The following packages were automatically installed and are no longer required: 83s python3.13 python3.13-minimal 83s Use 'sudo apt autoremove' to remove them. 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Solving dependencies... 84s The following packages will be REMOVED: 84s python3.13* python3.13-minimal* 84s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 84s After this operation, 7766 kB disk space will be freed. 84s (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 ... 135995 files and directories currently installed.) 84s Removing python3.13 (3.13.11-1) ... 84s Removing python3.13-minimal (3.13.11-1) ... 86s Processing triggers for man-db (2.13.1-1) ... 86s Processing triggers for systemd (259-1ubuntu2) ... 86s (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 ... 135968 files and directories currently installed.) 86s Purging configuration files for python3.13-minimal (3.13.11-1) ... 89s autopkgtest [18:48:04]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 89s autopkgtest [18:48:04]: @@@@@@@@@@@@@@@@@@@@ apt-source sniffles 92s Get:1 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (dsc) [2056 B] 92s Get:2 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (tar) [2917 kB] 92s Get:3 http://ftpmaster.internal/ubuntu resolute/universe sniffles 2.6.0-1 (diff) [8416 B] 92s gpgv: Signature made Sat Feb 15 22:05:44 2025 UTC 92s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 92s gpgv: issuer "tille@debian.org" 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./sniffles_2.6.0-1.dsc: no acceptable signature found 93s autopkgtest [18:48:08]: testing package sniffles version 2.6.0-1 93s autopkgtest [18:48:08]: build not needed 94s autopkgtest [18:48:09]: test run-unit-test: preparing testbed 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Solving dependencies... 95s The following NEW packages will be installed: 95s libdeflate0 libhts3t64 libhtscodecs2 python3-edlib python3-psutil 95s python3-pysam sniffles 95s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 5266 kB of archives. 95s After this operation, 47.0 MB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 95s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 95s Get:3 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.22.1+ds2-1 [442 kB] 95s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-edlib arm64 1.2.7-7 [97.8 kB] 95s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-psutil arm64 7.1.0-1ubuntu1 [191 kB] 95s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pysam arm64 0.23.3+ds-2 [4348 kB] 95s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 sniffles all 2.6.0-1 [58.5 kB] 96s Fetched 5266 kB in 1s (9893 kB/s) 96s Selecting previously unselected package libdeflate0:arm64. 96s (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 ... 135970 files and directories currently installed.) 96s Preparing to unpack .../0-libdeflate0_1.23-2_arm64.deb ... 96s Unpacking libdeflate0:arm64 (1.23-2) ... 96s Selecting previously unselected package libhtscodecs2:arm64. 96s Preparing to unpack .../1-libhtscodecs2_1.6.1-2_arm64.deb ... 96s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 96s Selecting previously unselected package libhts3t64:arm64. 96s Preparing to unpack .../2-libhts3t64_1.22.1+ds2-1_arm64.deb ... 96s Unpacking libhts3t64:arm64 (1.22.1+ds2-1) ... 96s Selecting previously unselected package python3-edlib:arm64. 96s Preparing to unpack .../3-python3-edlib_1.2.7-7_arm64.deb ... 96s Unpacking python3-edlib:arm64 (1.2.7-7) ... 96s Selecting previously unselected package python3-psutil. 96s Preparing to unpack .../4-python3-psutil_7.1.0-1ubuntu1_arm64.deb ... 96s Unpacking python3-psutil (7.1.0-1ubuntu1) ... 96s Selecting previously unselected package python3-pysam. 96s Preparing to unpack .../5-python3-pysam_0.23.3+ds-2_arm64.deb ... 96s Unpacking python3-pysam (0.23.3+ds-2) ... 96s 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:arm64 (1.6.1-2) ... 97s Setting up libdeflate0:arm64 (1.23-2) ... 97s Setting up python3-psutil (7.1.0-1ubuntu1) ... 97s Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... 97s Setting up python3-edlib:arm64 (1.2.7-7) ... 97s Setting up python3-pysam (0.23.3+ds-2) ... 97s Setting up sniffles (2.6.0-1) ... 97s Processing triggers for man-db (2.13.1-1) ... 98s Processing triggers for libc-bin (2.42-2ubuntu4) ... 99s autopkgtest [18:48:14]: test run-unit-test: [----------------------- 100s 2026-01-22 18:48:15,379 INFO sniffles.main (2164): Running Sniffles2, build 2.6.0 100s 2026-01-22 18:48:15,379 INFO sniffles.main (2164): Run Mode: call_sample 100s 2026-01-22 18:48:15,379 INFO sniffles.main (2164): Start on: 2026/01/22 18:48:15 100s 2026-01-22 18:48:15,379 INFO sniffles.main (2164): Working dir: /tmp/autopkgtest.x8q8j8/autopkgtest_tmp 100s 2026-01-22 18:48:15,379 INFO sniffles.main (2164): Used command: /usr/bin/sniffles --input test.bam --snf test.snf 100s 2026-01-22 18:48:15,379 INFO sniffles.main (2164): ============================== 100s 2026-01-22 18:48:15,397 INFO sniffles.main (2164): Opening for reading: test.bam 100s 2026-01-22 18:48:15,399 INFO sniffles.main (2164): Opening for writing: test.snf 100s 2026-01-22 18:48:15,403 INFO sniffles.main (2164): 100s 2026-01-22 18:48:15,403 INFO sniffles.main (2164): Analyzing 1 alignments total... 100s 2026-01-22 18:48:15,404 INFO sniffles.main (2164): 100s 2026-01-22 18:48:15,404 INFO sniffles.worker (2164): Starting worker 0 100s 2026-01-22 18:48:15,408 ERROR sniffles.main (2164): Unhandled error while running sniffles. 100s Traceback (most recent call last): 100s File "/usr/bin/sniffles", line 580, in 100s Sniffles2_Main(processes) 100s ~~~~~~~~~~~~~~^^^^^^^^^^^ 100s File "/usr/bin/sniffles", line 492, in Sniffles2_Main 100s p.start() 100s ~~~~~~~^^ 100s File "/usr/lib/python3/dist-packages/sniffles/parallel.py", line 522, in start 100s self.process.start() 100s ~~~~~~~~~~~~~~~~~~^^ 100s File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start 100s self._popen = self._Popen(self) 100s ~~~~~~~~~~~^^^^^^ 100s File "/usr/lib/python3.14/multiprocessing/context.py", line 224, in _Popen 100s return _default_context.get_context().Process._Popen(process_obj) 100s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 100s File "/usr/lib/python3.14/multiprocessing/context.py", line 300, in _Popen 100s return Popen(process_obj) 100s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ 100s super().__init__(process_obj) 100s ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ 100s File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ 100s self._launch(process_obj) 100s ~~~~~~~~~~~~^^^^^^^^^^^^^ 100s File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 47, in _launch 100s reduction.dump(process_obj, buf) 100s ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ 100s File "/usr/lib/python3.14/multiprocessing/reduction.py", line 60, in dump 100s ForkingPickler(file, protocol).dump(obj) 100s ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^ 100s TypeError: cannot pickle '_thread.RLock' object 100s when serializing dict item '_lock' 100s when serializing psutil.Process state 100s when serializing psutil.Process object 100s when serializing dict item '_process' 100s when serializing sniffles.utils.resmon.ResourceMonitor state 100s when serializing sniffles.utils.resmon.ResourceMonitor object 100s when serializing dict item 'recycle' 100s when serializing sniffles.parallel.SnifflesWorker state 100s when serializing sniffles.parallel.SnifflesWorker object 100s when serializing tuple item 0 100s when serializing method reconstructor arguments 100s when serializing method object 100s when serializing dict item '_target' 100s when serializing multiprocessing.context.Process state 100s when serializing multiprocessing.context.Process object 100s autopkgtest [18:48:15]: test run-unit-test: -----------------------] 100s autopkgtest [18:48:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 100s run-unit-test FAIL non-zero exit status 1 101s autopkgtest [18:48:16]: @@@@@@@@@@@@@@@@@@@@ summary 101s run-unit-test FAIL non-zero exit status 1