0s autopkgtest [01:39:39]: starting date and time: 2025-03-16 01:39:39+0000 0s autopkgtest [01:39:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:39:39]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v_kxf1i_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade macs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-9.secgroup --name adt-plucky-s390x-macs-20250316-013939-juju-7f2275-prod-proposed-migration-environment-20-78e53799-4b53-452d-86dc-eb6b0c7e9169 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 96s autopkgtest [01:41:15]: testbed dpkg architecture: s390x 96s autopkgtest [01:41:15]: testbed apt version: 2.9.33 96s autopkgtest [01:41:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 96s autopkgtest [01:41:15]: testbed release detected to be: None 97s autopkgtest [01:41:16]: updating testbed package index (apt update) 97s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 97s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 98s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 98s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 98s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 98s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 98s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 98s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [75.4 kB] 98s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1784 B] 98s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 98s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [294 kB] 98s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [12.3 kB] 98s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [4956 B] 98s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 98s Fetched 940 kB in 1s (1199 kB/s) 99s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s Calculating upgrade... 100s The following packages were automatically installed and are no longer required: 100s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 100s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 100s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 100s linux-tools-6.11.0-8-generic 100s Use 'sudo apt autoremove' to remove them. 100s The following packages will be upgraded: 100s pinentry-curses python3-jinja2 strace 100s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 652 kB of archives. 100s After this operation, 27.6 kB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 100s Fetched 652 kB in 1s (1141 kB/s) 101s (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 ... 81428 files and directories currently installed.) 101s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 101s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 101s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 101s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 101s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 101s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 101s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 101s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 101s Setting up strace (6.13+ds-1ubuntu1) ... 101s Processing triggers for man-db (2.13.0-1) ... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Solving dependencies... 102s The following packages will be REMOVED: 102s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 102s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 102s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 102s linux-tools-6.11.0-8-generic* 102s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 102s After this operation, 167 MB disk space will be freed. 102s (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 ... 81428 files and directories currently installed.) 102s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 102s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 102s Removing libpython3.12t64:s390x (3.12.9-1) ... 102s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 102s Removing libnsl2:s390x (1.3.0-3build3) ... 102s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 102s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 102s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 103s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 103s Processing triggers for libc-bin (2.41-1ubuntu1) ... 103s (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 ... 56328 files and directories currently installed.) 103s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 103s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 103s autopkgtest [01:41:22]: upgrading testbed (apt dist-upgrade and autopurge) 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 103s Starting 2 pkgProblemResolver with broken count: 0 103s Done 104s Entering ResolveByKeep 104s 104s Calculating upgrade... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 104s Solving dependencies... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s autopkgtest [01:41:24]: rebooting testbed after setup commands that affected boot 122s autopkgtest [01:41:41]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 124s autopkgtest [01:41:43]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 137s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1build3 (dsc) [2176 B] 137s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1build3 (tar) [197 MB] 137s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1build3 (diff) [1268 kB] 137s gpgv: Signature made Tue Mar 4 15:51:08 2025 UTC 137s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 137s gpgv: Can't check signature: No public key 137s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1build3.dsc: no acceptable signature found 139s autopkgtest [01:41:58]: testing package macs version 3.0.2-1build3 139s autopkgtest [01:41:58]: build not needed 156s autopkgtest [01:42:15]: test run-unit-test: preparing testbed 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 157s The following NEW packages will be installed: 157s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 157s python3-decorator python3-hmmlearn python3-joblib python3-numpy 157s python3-numpy-dev python3-scipy python3-sklearn python3-sklearn-lib 157s python3-threadpoolctl 157s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 37.2 MB of archives. 157s After this operation, 153 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 158s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 158s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 159s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 162s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 165s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 165s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 165s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-cykhash s390x 2.0.0-3build3 [504 kB] 165s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 165s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 170s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-joblib all 1.4.2-3 [205 kB] 170s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-threadpoolctl all 3.1.0-1 [21.3 kB] 170s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-sklearn-lib s390x 1.4.2+dfsg-8 [4262 kB] 171s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 171s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-hmmlearn s390x 0.3.2-2build2 [126 kB] 171s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x macs s390x 3.0.2-1build3 [3247 kB] 171s Fetched 37.2 MB in 14s (2646 kB/s) 171s Selecting previously unselected package python3-numpy-dev:s390x. 172s (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 ... 56326 files and directories currently installed.) 172s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 172s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 172s Selecting previously unselected package libblas3:s390x. 172s Preparing to unpack .../01-libblas3_3.12.1-2_s390x.deb ... 172s Unpacking libblas3:s390x (3.12.1-2) ... 172s Selecting previously unselected package libgfortran5:s390x. 172s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 172s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 172s Selecting previously unselected package liblapack3:s390x. 172s Preparing to unpack .../03-liblapack3_3.12.1-2_s390x.deb ... 172s Unpacking liblapack3:s390x (3.12.1-2) ... 172s Selecting previously unselected package python3-numpy. 172s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 172s Unpacking python3-numpy (1:2.2.3+ds-5) ... 172s Selecting previously unselected package libgomp1:s390x. 172s Preparing to unpack .../05-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 172s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 172s Selecting previously unselected package liblbfgsb0:s390x. 172s Preparing to unpack .../06-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 172s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 172s Selecting previously unselected package python3-cykhash. 172s Preparing to unpack .../07-python3-cykhash_2.0.0-3build3_s390x.deb ... 172s Unpacking python3-cykhash (2.0.0-3build3) ... 172s Selecting previously unselected package python3-decorator. 172s Preparing to unpack .../08-python3-decorator_5.1.1-5_all.deb ... 172s Unpacking python3-decorator (5.1.1-5) ... 172s Selecting previously unselected package python3-scipy. 172s Preparing to unpack .../09-python3-scipy_1.14.1-4ubuntu2_s390x.deb ... 172s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 172s Selecting previously unselected package python3-joblib. 172s Preparing to unpack .../10-python3-joblib_1.4.2-3_all.deb ... 172s Unpacking python3-joblib (1.4.2-3) ... 172s Selecting previously unselected package python3-threadpoolctl. 172s Preparing to unpack .../11-python3-threadpoolctl_3.1.0-1_all.deb ... 172s Unpacking python3-threadpoolctl (3.1.0-1) ... 172s Selecting previously unselected package python3-sklearn-lib:s390x. 172s Preparing to unpack .../12-python3-sklearn-lib_1.4.2+dfsg-8_s390x.deb ... 172s Unpacking python3-sklearn-lib:s390x (1.4.2+dfsg-8) ... 172s Selecting previously unselected package python3-sklearn. 172s Preparing to unpack .../13-python3-sklearn_1.4.2+dfsg-8_all.deb ... 172s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 172s Selecting previously unselected package python3-hmmlearn. 172s Preparing to unpack .../14-python3-hmmlearn_0.3.2-2build2_s390x.deb ... 172s Unpacking python3-hmmlearn (0.3.2-2build2) ... 172s Selecting previously unselected package macs. 172s Preparing to unpack .../15-macs_3.0.2-1build3_s390x.deb ... 172s Unpacking macs (3.0.2-1build3) ... 172s Setting up python3-joblib (1.4.2-3) ... 173s Setting up python3-threadpoolctl (3.1.0-1) ... 173s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 173s Setting up python3-cykhash (2.0.0-3build3) ... 173s Setting up python3-decorator (5.1.1-5) ... 173s Setting up libblas3:s390x (3.12.1-2) ... 173s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 173s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 173s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 173s Setting up liblapack3:s390x (3.12.1-2) ... 173s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 173s Setting up python3-numpy (1:2.2.3+ds-5) ... 174s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 174s Setting up python3-scipy (1.14.1-4ubuntu2) ... 176s Setting up python3-sklearn-lib:s390x (1.4.2+dfsg-8) ... 176s Setting up python3-sklearn (1.4.2+dfsg-8) ... 178s Setting up python3-hmmlearn (0.3.2-2build2) ... 178s Setting up macs (3.0.2-1build3) ... 178s Processing triggers for man-db (2.13.0-1) ... 178s Processing triggers for libc-bin (2.41-1ubuntu1) ... 179s autopkgtest [01:42:38]: test run-unit-test: [----------------------- 179s + pkg=macs 179s + '[' /tmp/autopkgtest.HKd8Hi/autopkgtest_tmp = '' ']' 179s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.HKd8Hi/autopkgtest_tmp 179s + cd /tmp/autopkgtest.HKd8Hi/autopkgtest_tmp 179s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 179s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] 179s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 179s # ARGUMENTS LIST: 179s # name = test 179s # format = AUTO 179s # ChIP-seq file = ['aluY.chr1.bed'] 179s # control file = None 179s # effective genome size = 2.91e+09 179s # band width = 300 179s # model fold = [5, 50] 179s # qvalue cutoff = 1.00e-02 179s # The maximum gap between significant sites is assigned as the read length/tag size. 179s # The minimum length of peaks is assigned as the predicted fragment length "d". 179s # Larger dataset will be scaled towards smaller dataset. 179s # Range for calculating regional lambda is: 10000 bps 179s # Broad region calling is off 179s # Paired-End mode is off 179s 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] #1 read tag files... 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] #1 read treatment tags... 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] Detected format is: BED 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 tag size is determined as 294 bps 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 tag size = 294.0 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 total tags in treatment: 11628 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 user defined the maximum tags... 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 tags after filtering in treatment: 11628 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 Redundant rate of treatment: 0.00 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #1 finished! 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #2 Build Peak Model... 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #2 Skipped... 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #2 Use 200 as fragment length 179s INFO @ 16 Mar 2025 01:42:38: [33 MB] #3 Call peaks... 179s INFO @ 16 Mar 2025 01:42:38: [34 MB] #3 Pre-compute pvalue-qvalue table... 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #3 In the peak calling step, the following will be performed simultaneously: 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #3 Pileup will be based on sequencing depth in treatment. 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #3 Call peaks for each chromosome... 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #4 Write output xls file... test_peaks.xls 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] #4 Write summits bed file... test_summits.bed 179s INFO @ 16 Mar 2025 01:42:38: [36 MB] Done! 179s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] 179s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 179s # ARGUMENTS LIST: 179s # name = NA 179s # format = AUTO 179s # ChIP-seq file = ['gerp.chr1.bed'] 179s # control file = None 179s # effective genome size = 2.91e+09 179s # band width = 300 179s # model fold = [5, 50] 179s # qvalue cutoff for narrow/strong regions = 5.00e-02 179s # qvalue cutoff for broad/weak regions = 1.00e-01 179s # The maximum gap between significant sites is assigned as the read length/tag size. 179s # The minimum length of peaks is assigned as the predicted fragment length "d". 179s # Larger dataset will be scaled towards smaller dataset. 179s # Range for calculating regional lambda is: 10000 bps 179s # Broad region calling is on 179s # Paired-End mode is off 179s 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] #1 read tag files... 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] #1 read treatment tags... 179s INFO @ 16 Mar 2025 01:42:38: [31 MB] Detected format is: BED 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 tag size is determined as 181 bps 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 tag size = 181.0 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 total tags in treatment: 88292 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 user defined the maximum tags... 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 tags after filtering in treatment: 88292 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 Redundant rate of treatment: 0.00 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #1 finished! 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #2 Build Peak Model... 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #2 Skipped... 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #2 Use 200 as fragment length 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #3 Call peaks... 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 179s INFO @ 16 Mar 2025 01:42:38: [42 MB] #3 Pre-compute pvalue-qvalue table... 180s INFO @ 16 Mar 2025 01:42:39: [59 MB] #3 Call peaks for each chromosome... 180s INFO @ 16 Mar 2025 01:42:39: [61 MB] #4 Write output xls file... NA_peaks.xls 180s INFO @ 16 Mar 2025 01:42:39: [61 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 180s INFO @ 16 Mar 2025 01:42:39: [61 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 180s INFO @ 16 Mar 2025 01:42:39: [61 MB] Done! 180s autopkgtest [01:42:39]: test run-unit-test: -----------------------] 181s autopkgtest [01:42:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 181s run-unit-test PASS 181s autopkgtest [01:42:40]: @@@@@@@@@@@@@@@@@@@@ summary 181s run-unit-test PASS 198s nova [W] Using flock in prodstack6-s390x 198s flock: timeout while waiting to get lock 198s Creating nova instance adt-plucky-s390x-macs-20250316-013939-juju-7f2275-prod-proposed-migration-environment-20-78e53799-4b53-452d-86dc-eb6b0c7e9169 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 198s nova [W] Timed out waiting for 447b00c2-cf2d-4346-b078-0dd637236e45 to get deleted.