0s autopkgtest [18:50:46]: starting date and time: 2024-11-13 18:50:46+0000 0s autopkgtest [18:50:46]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:50:46]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hx6bxrmx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade macs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-4.secgroup --name adt-plucky-ppc64el-macs-20241113-180305-juju-7f2275-prod-proposed-migration-environment-20-b19e60b7-c682-4d22-95b0-54d46ee11870 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/ 116s autopkgtest [18:52:42]: testbed dpkg architecture: ppc64el 116s autopkgtest [18:52:42]: testbed apt version: 2.9.8 116s autopkgtest [18:52:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 117s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 117s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 117s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 118s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 118s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 118s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [113 kB] 118s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [672 kB] 118s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 118s Fetched 1978 kB in 1s (1895 kB/s) 118s Reading package lists... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following NEW packages will be installed: 121s python3.13-gdbm 121s The following packages will be upgraded: 121s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libpython3-stdlib 121s libutempter0 python3 python3-gdbm python3-minimal 121s 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 1265 kB of archives. 121s After this operation, 141 kB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 121s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 121s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 121s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 122s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 122s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 122s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 122s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 122s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 122s Fetched 1265 kB in 1s (2056 kB/s) 122s (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 ... 73767 files and directories currently installed.) 122s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 122s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 123s Setting up python3-minimal (3.12.7-1) ... 123s (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 ... 73767 files and directories currently installed.) 123s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 123s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 123s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 123s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 123s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 123s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 123s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 123s Selecting previously unselected package python3.13-gdbm. 123s (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 ... 73767 files and directories currently installed.) 123s Preparing to unpack .../python3.13-gdbm_3.13.0-2_ppc64el.deb ... 123s Unpacking python3.13-gdbm (3.13.0-2) ... 123s Preparing to unpack .../python3-gdbm_3.12.7-1_ppc64el.deb ... 123s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 123s Preparing to unpack .../libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 123s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 123s Preparing to unpack .../libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 123s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 123s Preparing to unpack .../libutempter0_1.2.1-4_ppc64el.deb ... 123s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 123s Setting up libutempter0:ppc64el (1.2.1-4) ... 123s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 123s Setting up python3.13-gdbm (3.13.0-2) ... 123s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 123s Setting up python3 (3.12.7-1) ... 123s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 123s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 123s Processing triggers for man-db (2.12.1-3) ... 125s Processing triggers for libc-bin (2.40-1ubuntu3) ... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 126s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 127s Reading package lists... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 128s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [18:52:57]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 131s autopkgtest [18:52:57]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 147s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (dsc) [2152 B] 147s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (tar) [197 MB] 147s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (diff) [1268 kB] 147s gpgv: Signature made Sat Sep 7 23:10:03 2024 UTC 147s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1.dsc: no acceptable signature found 152s autopkgtest [18:53:18]: testing package macs version 3.0.2-1 153s autopkgtest [18:53:19]: build not needed 170s autopkgtest [18:53:36]: test run-unit-test: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 174s The following additional packages will be installed: 174s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 174s python3-decorator python3-hmmlearn python3-joblib python3-numpy 174s python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl 174s Suggested packages: 174s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 174s python-scipy-doc python3-dap python-sklearn-doc ipython3 174s Recommended packages: 174s python3-pytest python3-simplejson python3-psutil g++ | c++-compiler 174s python3-pil python3-matplotlib 174s The following NEW packages will be installed: 174s autopkgtest-satdep libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs 174s python3-cykhash python3-decorator python3-hmmlearn python3-joblib 174s python3-numpy python3-scipy python3-sklearn python3-sklearn-lib 174s python3-threadpoolctl 174s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 36.8 MB/36.8 MB of archives. 174s After this operation, 169 MB of additional disk space will be used. 174s Get:1 /tmp/autopkgtest.EfuYlr/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 174s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 174s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 175s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 175s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 175s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cykhash ppc64el 2.0.0-3build1 [506 kB] 175s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 175s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 176s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB] 176s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB] 176s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6 [3838 kB] 176s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 177s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-hmmlearn ppc64el 0.3.2-2 [130 kB] 177s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el macs ppc64el 3.0.2-1 [3238 kB] 177s Fetched 36.8 MB in 3s (12.5 MB/s) 177s Selecting previously unselected package libblas3:ppc64el. 177s (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 ... 73774 files and directories currently installed.) 177s Preparing to unpack .../00-libblas3_3.12.0-3build2_ppc64el.deb ... 177s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 177s Selecting previously unselected package libgfortran5:ppc64el. 177s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 177s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 177s Selecting previously unselected package libgomp1:ppc64el. 177s Preparing to unpack .../02-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 177s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 177s Selecting previously unselected package liblapack3:ppc64el. 177s Preparing to unpack .../03-liblapack3_3.12.0-3build2_ppc64el.deb ... 177s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 177s Selecting previously unselected package liblbfgsb0:ppc64el. 177s Preparing to unpack .../04-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 177s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 177s Selecting previously unselected package python3-numpy. 177s Preparing to unpack .../05-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 177s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 177s Selecting previously unselected package python3-cykhash. 177s Preparing to unpack .../06-python3-cykhash_2.0.0-3build1_ppc64el.deb ... 177s Unpacking python3-cykhash (2.0.0-3build1) ... 177s Selecting previously unselected package python3-decorator. 177s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 177s Unpacking python3-decorator (5.1.1-5) ... 177s Selecting previously unselected package python3-scipy. 177s Preparing to unpack .../08-python3-scipy_1.13.1-5_ppc64el.deb ... 177s Unpacking python3-scipy (1.13.1-5) ... 178s Selecting previously unselected package python3-joblib. 178s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 178s Unpacking python3-joblib (1.3.2-5) ... 178s Selecting previously unselected package python3-threadpoolctl. 178s Preparing to unpack .../10-python3-threadpoolctl_3.1.0-1_all.deb ... 178s Unpacking python3-threadpoolctl (3.1.0-1) ... 178s Selecting previously unselected package python3-sklearn-lib:ppc64el. 178s Preparing to unpack .../11-python3-sklearn-lib_1.4.2+dfsg-6_ppc64el.deb ... 178s Unpacking python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 179s Selecting previously unselected package python3-sklearn. 179s Preparing to unpack .../12-python3-sklearn_1.4.2+dfsg-6_all.deb ... 179s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 179s Selecting previously unselected package python3-hmmlearn. 179s Preparing to unpack .../13-python3-hmmlearn_0.3.2-2_ppc64el.deb ... 179s Unpacking python3-hmmlearn (0.3.2-2) ... 179s Selecting previously unselected package macs. 179s Preparing to unpack .../14-macs_3.0.2-1_ppc64el.deb ... 179s Unpacking macs (3.0.2-1) ... 179s Selecting previously unselected package autopkgtest-satdep. 179s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 179s Unpacking autopkgtest-satdep (0) ... 179s Setting up python3-joblib (1.3.2-5) ... 179s Setting up python3-threadpoolctl (3.1.0-1) ... 180s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 180s Setting up python3-cykhash (2.0.0-3build1) ... 180s Setting up python3-decorator (5.1.1-5) ... 180s Setting up libblas3:ppc64el (3.12.0-3build2) ... 180s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 180s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 180s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 180s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 180s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 183s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 183s Setting up python3-scipy (1.13.1-5) ... 187s Setting up python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 187s Setting up python3-sklearn (1.4.2+dfsg-6) ... 190s Setting up python3-hmmlearn (0.3.2-2) ... 190s Setting up macs (3.0.2-1) ... 191s Setting up autopkgtest-satdep (0) ... 191s Processing triggers for man-db (2.12.1-3) ... 191s Processing triggers for libc-bin (2.40-1ubuntu3) ... 193s (Reading database ... 77332 files and directories currently installed.) 193s Removing autopkgtest-satdep (0) ... 194s autopkgtest [18:54:00]: test run-unit-test: [----------------------- 194s + pkg=macs 194s + '[' /tmp/autopkgtest.EfuYlr/autopkgtest_tmp = '' ']' 194s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.EfuYlr/autopkgtest_tmp 194s + cd /tmp/autopkgtest.EfuYlr/autopkgtest_tmp 194s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 194s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 194s INFO @ 13 Nov 2024 18:54:00: [48 MB] 194s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 194s # ARGUMENTS LIST: 194s # name = test 194s # format = AUTO 194s # ChIP-seq file = ['aluY.chr1.bed'] 194s # control file = None 194s # effective genome size = 2.91e+09 194s # band width = 300 194s # model fold = [5, 50] 194s # qvalue cutoff = 1.00e-02 194s # The maximum gap between significant sites is assigned as the read length/tag size. 194s # The minimum length of peaks is assigned as the predicted fragment length "d". 194s # Larger dataset will be scaled towards smaller dataset. 194s # Range for calculating regional lambda is: 10000 bps 194s # Broad region calling is off 194s # Paired-End mode is off 194s 194s INFO @ 13 Nov 2024 18:54:00: [48 MB] #1 read tag files... 194s INFO @ 13 Nov 2024 18:54:00: [48 MB] #1 read treatment tags... 194s INFO @ 13 Nov 2024 18:54:00: [48 MB] Detected format is: BED 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 tag size is determined as 294 bps 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 tag size = 294.0 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 total tags in treatment: 11628 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 user defined the maximum tags... 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 tags after filtering in treatment: 11628 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 Redundant rate of treatment: 0.00 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #1 finished! 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #2 Build Peak Model... 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #2 Skipped... 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #2 Use 200 as fragment length 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 Call peaks... 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 Pre-compute pvalue-qvalue table... 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 In the peak calling step, the following will be performed simultaneously: 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 Pileup will be based on sequencing depth in treatment. 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #3 Call peaks for each chromosome... 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #4 Write output xls file... test_peaks.xls 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] #4 Write summits bed file... test_summits.bed 194s INFO @ 13 Nov 2024 18:54:00: [50 MB] Done! 194s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 195s INFO @ 13 Nov 2024 18:54:01: [48 MB] 195s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 195s # ARGUMENTS LIST: 195s # name = NA 195s # format = AUTO 195s # ChIP-seq file = ['gerp.chr1.bed'] 195s # control file = None 195s # effective genome size = 2.91e+09 195s # band width = 300 195s # model fold = [5, 50] 195s # qvalue cutoff for narrow/strong regions = 5.00e-02 195s # qvalue cutoff for broad/weak regions = 1.00e-01 195s # The maximum gap between significant sites is assigned as the read length/tag size. 195s # The minimum length of peaks is assigned as the predicted fragment length "d". 195s # Larger dataset will be scaled towards smaller dataset. 195s # Range for calculating regional lambda is: 10000 bps 195s # Broad region calling is on 195s # Paired-End mode is off 195s 195s INFO @ 13 Nov 2024 18:54:01: [48 MB] #1 read tag files... 195s INFO @ 13 Nov 2024 18:54:01: [48 MB] #1 read treatment tags... 195s INFO @ 13 Nov 2024 18:54:01: [48 MB] Detected format is: BED 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 tag size is determined as 181 bps 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 tag size = 181.0 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 total tags in treatment: 88292 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 user defined the maximum tags... 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 tags after filtering in treatment: 88292 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 Redundant rate of treatment: 0.00 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #1 finished! 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #2 Build Peak Model... 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #2 Skipped... 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #2 Use 200 as fragment length 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #3 Call peaks... 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 195s INFO @ 13 Nov 2024 18:54:01: [59 MB] #3 Pre-compute pvalue-qvalue table... 195s INFO @ 13 Nov 2024 18:54:01: [77 MB] #3 Call peaks for each chromosome... 195s INFO @ 13 Nov 2024 18:54:01: [77 MB] #4 Write output xls file... NA_peaks.xls 195s INFO @ 13 Nov 2024 18:54:01: [77 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 195s INFO @ 13 Nov 2024 18:54:01: [77 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 195s INFO @ 13 Nov 2024 18:54:01: [77 MB] Done! 196s autopkgtest [18:54:02]: test run-unit-test: -----------------------] 196s run-unit-test PASS 196s autopkgtest [18:54:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 196s autopkgtest [18:54:02]: @@@@@@@@@@@@@@@@@@@@ summary 196s run-unit-test PASS 208s nova [W] Using flock in prodstack6-ppc64el 208s flock: timeout while waiting to get lock 208s Creating nova instance adt-plucky-ppc64el-macs-20241113-180305-juju-7f2275-prod-proposed-migration-environment-20-b19e60b7-c682-4d22-95b0-54d46ee11870 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...