0s autopkgtest [04:08:16]: starting date and time: 2024-07-13 04:08:16+0000
  0s autopkgtest [04:08:16]: git checkout: fd3bed09 nova: allow more retries for quota issues
  0s autopkgtest [04:08:16]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.32vtgdtn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade porechop --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-41.secgroup --name adt-oracular-arm64-porechop-20240713-040816-juju-7f2275-prod-proposed-migration-environment-3-99479e81-79a1-4073-8365-9e83dab50f08 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
156s autopkgtest [04:10:52]: testbed dpkg architecture: arm64
156s autopkgtest [04:10:52]: testbed apt version: 2.9.6
156s autopkgtest [04:10:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup
157s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB]
158s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [48.2 kB]
158s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B]
158s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [3860 B]
158s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [364 kB]
158s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [109 kB]
158s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2116 B]
158s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB]
158s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B]
158s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [419 kB]
158s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [8752 B]
158s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [8216 B]
158s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B]
160s Fetched 1144 kB in 2s (691 kB/s)
161s Reading package lists...
167s Reading package lists...
167s Building dependency tree...
167s Reading state information...
168s Calculating upgrade...
168s The following packages will be upgraded:
168s   inetutils-telnet libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales
168s   openssh-client openssh-server openssh-sftp-server telnet
169s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
169s Need to get 10.7 MB of archives.
169s After this operation, 28.7 kB disk space will be freed.
169s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-devtools arm64 2.39-3.1ubuntu3 [27.7 kB]
169s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6-dev arm64 2.39-3.1ubuntu3 [1591 kB]
169s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-dev-bin arm64 2.39-3.1ubuntu3 [19.7 kB]
169s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6 arm64 2.39-3.1ubuntu3 [2770 kB]
169s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-bin arm64 2.39-3.1ubuntu3 [579 kB]
169s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-sftp-server arm64 1:9.6p1-3ubuntu17 [36.7 kB]
169s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-server arm64 1:9.6p1-3ubuntu17 [502 kB]
169s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-client arm64 1:9.6p1-3ubuntu17 [888 kB]
169s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 locales all 2.39-3.1ubuntu3 [4220 kB]
170s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 inetutils-telnet arm64 2:2.5-5ubuntu1 [103 kB]
170s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 telnet all 0.17+2.5-5ubuntu1 [3688 B]
171s Preconfiguring packages ...
173s Fetched 10.7 MB in 1s (10.1 MB/s)
173s (Reading database ... 
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173s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_arm64.deb ...
173s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
174s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_arm64.deb ...
174s Unpacking libc6-dev:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
175s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_arm64.deb ...
175s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
175s Preparing to unpack .../libc6_2.39-3.1ubuntu3_arm64.deb ...
176s Unpacking libc6:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
177s Setting up libc6:arm64 (2.39-3.1ubuntu3) ...
177s Error: Could not restart systemd, systemd binary not working
177s (Reading database ... 
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177s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_arm64.deb ...
177s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
178s Setting up libc-bin (2.39-3.1ubuntu3) ...
178s (Reading database ... 
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178s Preparing to unpack .../0-openssh-sftp-server_1%3a9.6p1-3ubuntu17_arm64.deb ...
178s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ...
178s Preparing to unpack .../1-openssh-server_1%3a9.6p1-3ubuntu17_arm64.deb ...
179s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ...
180s Preparing to unpack .../2-openssh-client_1%3a9.6p1-3ubuntu17_arm64.deb ...
180s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ...
180s Preparing to unpack .../3-locales_2.39-3.1ubuntu3_all.deb ...
180s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
181s Preparing to unpack .../4-inetutils-telnet_2%3a2.5-5ubuntu1_arm64.deb ...
181s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ...
181s Preparing to unpack .../5-telnet_0.17+2.5-5ubuntu1_all.deb ...
181s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ...
181s Setting up openssh-client (1:9.6p1-3ubuntu17) ...
181s Setting up inetutils-telnet (2:2.5-5ubuntu1) ...
181s Setting up locales (2.39-3.1ubuntu3) ...
185s Generating locales (this might take a while)...
189s   en_US.UTF-8... done
189s Generation complete.
189s Setting up libc-dev-bin (2.39-3.1ubuntu3) ...
189s Setting up libc-devtools (2.39-3.1ubuntu3) ...
189s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ...
189s Setting up telnet (0.17+2.5-5ubuntu1) ...
189s Setting up openssh-server (1:9.6p1-3ubuntu17) ...
189s Installing new version of config file /etc/pam.d/sshd ...
192s Setting up libc6-dev:arm64 (2.39-3.1ubuntu3) ...
192s Processing triggers for systemd (256-1ubuntu1) ...
194s Processing triggers for man-db (2.12.1-2) ...
195s Processing triggers for ufw (0.36.2-6) ...
196s Reading package lists...
196s Building dependency tree...
196s Reading state information...
197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
198s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease
198s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease
198s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease
198s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
200s Reading package lists...
200s Reading package lists...
200s Building dependency tree...
200s Reading state information...
201s Calculating upgrade...
201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
202s Reading package lists...
202s Building dependency tree...
202s Reading state information...
203s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
203s autopkgtest [04:11:39]: rebooting testbed after setup commands that affected boot
208s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
241s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
248s autopkgtest [04:12:24]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024
252s autopkgtest [04:12:28]: @@@@@@@@@@@@@@@@@@@@ apt-source porechop
254s Get:1 http://ftpmaster.internal/ubuntu oracular/universe porechop 0.2.4+dfsg-4 (dsc) [2067 B]
254s Get:2 http://ftpmaster.internal/ubuntu oracular/universe porechop 0.2.4+dfsg-4 (tar) [726 kB]
254s Get:3 http://ftpmaster.internal/ubuntu oracular/universe porechop 0.2.4+dfsg-4 (diff) [6100 B]
255s gpgv: Signature made Tue Oct 18 09:07:13 2022 UTC
255s gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
255s gpgv: Can't check signature: No public key
255s dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-4.dsc: no acceptable signature found
256s autopkgtest [04:12:32]: testing package porechop version 0.2.4+dfsg-4
257s autopkgtest [04:12:33]: build not needed
257s autopkgtest [04:12:33]: test run-unit-test: preparing testbed
259s Reading package lists...
260s Building dependency tree...
260s Reading state information...
261s Starting pkgProblemResolver with broken count: 0
261s Starting 2 pkgProblemResolver with broken count: 0
261s Done
262s The following additional packages will be installed:
262s   porechop
262s The following NEW packages will be installed:
262s   autopkgtest-satdep porechop
263s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
263s Need to get 56.1 kB/56.8 kB of archives.
263s After this operation, 231 kB of additional disk space will be used.
263s Get:1 /tmp/autopkgtest.xwKVxO/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B]
263s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 porechop arm64 0.2.4+dfsg-4 [56.1 kB]
264s Fetched 56.1 kB in 1s (73.5 kB/s)
264s Selecting previously unselected package porechop.
264s (Reading database ... 
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264s Preparing to unpack .../porechop_0.2.4+dfsg-4_arm64.deb ...
264s Unpacking porechop (0.2.4+dfsg-4) ...
264s Selecting previously unselected package autopkgtest-satdep.
264s Preparing to unpack .../1-autopkgtest-satdep.deb ...
264s Unpacking autopkgtest-satdep (0) ...
265s Setting up porechop (0.2.4+dfsg-4) ...
265s /usr/lib/python3/dist-packages/porechop/misc.py:261: SyntaxWarning: invalid escape sequence '\['
265s   row_str = re.sub('\033\[4m', '', row_str)
265s Setting up autopkgtest-satdep (0) ...
265s Processing triggers for man-db (2.12.1-2) ...
270s (Reading database ... 78412 files and directories currently installed.)
270s Removing autopkgtest-satdep (0) ...
271s autopkgtest [04:12:47]: test run-unit-test: [-----------------------
271s usage: porechop -i INPUT [-o OUTPUT]
271s                 [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]
271s                 [-t THREADS] [-b BARCODE_DIR]
271s                 [--barcode_threshold BARCODE_THRESHOLD]
271s                 [--barcode_diff BARCODE_DIFF] [--require_two_barcodes]
271s                 [--untrimmed] [--discard_unassigned]
271s                 [--adapter_threshold ADAPTER_THRESHOLD]
271s                 [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME]
271s                 [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE]
271s                 [--extra_end_trim EXTRA_END_TRIM]
271s                 [--end_threshold END_THRESHOLD] [--no_split]
271s                 [--discard_middle] [--middle_threshold MIDDLE_THRESHOLD]
271s                 [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]
271s                 [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE]
271s                 [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version]
271s 
271s Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them
271s from the ends and splitting reads with internal adapters
271s 
271s Main options:
271s   -i INPUT, --input INPUT
271s                           FASTA/FASTQ of input reads or a directory which will
271s                           be recursively searched for FASTQ files (required)
271s   -o OUTPUT, --output OUTPUT
271s                           Filename for FASTA or FASTQ of trimmed reads (if not
271s                           set, trimmed reads will be printed to stdout)
271s   --format {auto,fasta,fastq,fasta.gz,fastq.gz}
271s                           Output format for the reads - if auto, the format
271s                           will be chosen based on the output filename or the
271s                           input read format (default: auto)
271s   -v VERBOSITY, --verbosity VERBOSITY
271s                           Level of progress information: 0 = none, 1 = some, 2
271s                           = lots, 3 = full - output will go to stdout if reads
271s                           are saved to a file and stderr if reads are printed
271s                           to stdout (default: 1)
271s   -t THREADS, --threads THREADS
271s                           Number of threads to use for adapter alignment
271s                           (default: 2)
271s 
271s Barcode binning settings:
271s   Control the binning of reads based on barcodes (i.e. barcode
271s   demultiplexing)
271s 
271s   -b BARCODE_DIR, --barcode_dir BARCODE_DIR
271s                           Reads will be binned based on their barcode and
271s                           saved to separate files in this directory
271s                           (incompatible with --output)
271s   --barcode_threshold BARCODE_THRESHOLD
271s                           A read must have at least this percent identity to a
271s                           barcode to be binned (default: 75.0)
271s   --barcode_diff BARCODE_DIFF
271s                           If the difference between a read's best barcode
271s                           identity and its second-best barcode identity is
271s                           less than this value, it will not be put in a
271s                           barcode bin (to exclude cases which are too close to
271s                           call) (default: 5.0)
271s   --require_two_barcodes  Reads will only be put in barcode bins if they have
271s                           a strong match for the barcode on both their start
271s                           and end (default: a read can be binned with a match
271s                           at its start or end)
271s   --untrimmed             Bin reads but do not trim them (default: trim the
271s                           reads)
271s   --discard_unassigned    Discard unassigned reads (instead of creating a
271s                           "none" bin) (default: False)
271s 
271s Adapter search settings:
271s   Control how the program determines which adapter sets are present
271s 
271s   --adapter_threshold ADAPTER_THRESHOLD
271s                           An adapter set has to have at least this percent
271s                           identity to be labelled as present and trimmed off
271s                           (0 to 100) (default: 90.0)
271s   --check_reads CHECK_READS
271s                           This many reads will be aligned to all possible
271s                           adapters to determine which adapter sets are present
271s                           (default: 10000)
271s   --scoring_scheme SCORING_SCHEME
271s                           Comma-delimited string of alignment scores: match,
271s                           mismatch, gap open, gap extend (default: 3,-6,-5,-2)
271s 
271s End adapter settings:
271s   Control the trimming of adapters from read ends
271s 
271s   --end_size END_SIZE     The number of base pairs at each end of the read
271s                           which will be searched for adapter sequences
271s                           (default: 150)
271s   --min_trim_size MIN_TRIM_SIZE
271s                           Adapter alignments smaller than this will be ignored
271s                           (default: 4)
271s   --extra_end_trim EXTRA_END_TRIM
271s                           This many additional bases will be removed next to
271s                           adapters found at the ends of reads (default: 2)
271s   --end_threshold END_THRESHOLD
271s                           Adapters at the ends of reads must have at least
271s                           this percent identity to be removed (0 to 100)
271s                           (default: 75.0)
271s 
271s Middle adapter settings:
271s   Control the splitting of read from middle adapters
271s 
271s   --no_split              Skip splitting reads based on middle adapters
271s                           (default: split reads when an adapter is found in
271s                           the middle)
271s   --discard_middle        Reads with middle adapters will be discarded
271s                           (default: reads with middle adapters are split)
271s                           (required for reads to be used with Nanopolish, this
271s                           option is on by default when outputting reads into
271s                           barcode bins)
271s   --middle_threshold MIDDLE_THRESHOLD
271s                           Adapters in the middle of reads must have at least
271s                           this percent identity to be found (0 to 100)
271s                           (default: 90.0)
271s   --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE
271s                           This many additional bases will be removed next to
271s                           middle adapters on their "good" side (default: 10)
271s   --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE
271s                           This many additional bases will be removed next to
271s                           middle adapters on their "bad" side (default: 100)
271s   --min_split_read_size MIN_SPLIT_READ_SIZE
271s                           Post-split read pieces smaller than this many base
271s                           pairs will not be outputted (default: 1000)
271s 
271s Help:
271s   -h, --help              Show this help message and exit
271s   --version               Show program's version number and exit
272s autopkgtest [04:12:48]: test run-unit-test: -----------------------]
272s autopkgtest [04:12:48]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
272s run-unit-test        PASS (superficial)
272s autopkgtest [04:12:48]: @@@@@@@@@@@@@@@@@@@@ summary
272s run-unit-test        PASS (superficial)
291s nova [W] Skipping flock in bos03-arm64
291s Creating nova instance adt-oracular-arm64-porechop-20240713-040816-juju-7f2275-prod-proposed-migration-environment-3-99479e81-79a1-4073-8365-9e83dab50f08 from image adt/ubuntu-oracular-arm64-server-20240712.img (UUID a9c53646-2a41-49d7-a14b-d40262a2cb6c)...