0s autopkgtest [08:50:52]: starting date and time: 2024-11-13 08:50:52+0000 0s autopkgtest [08:50:52]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:50:52]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6a8xh2re/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-27.secgroup --name adt-plucky-amd64-macs-20241113-085051-juju-7f2275-prod-proposed-migration-environment-20-2e2b9a4e-c73f-4d8a-9f3a-54b52bc8239e --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 56s autopkgtest [08:51:48]: testbed dpkg architecture: amd64 56s autopkgtest [08:51:48]: testbed apt version: 2.9.8 56s autopkgtest [08:51:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 57s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 57s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 57s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 57s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 57s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 57s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 57s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 57s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 57s Fetched 2173 kB in 1s (2930 kB/s) 57s Reading package lists... 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s The following NEW packages will be installed: 60s python3.13-gdbm 60s The following packages will be upgraded: 60s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 60s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 253 kB of archives. 60s After this operation, 147 kB of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 60s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 60s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 60s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 61s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 61s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 61s Fetched 253 kB in 0s (583 kB/s) 61s (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 ... 75541 files and directories currently installed.) 61s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 61s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 61s Setting up python3-minimal (3.12.7-1) ... 61s (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 ... 75541 files and directories currently installed.) 61s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 61s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 61s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 61s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 61s Selecting previously unselected package python3.13-gdbm. 61s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 61s Unpacking python3.13-gdbm (3.13.0-2) ... 61s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 61s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 61s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 61s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 61s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 61s Setting up python3.13-gdbm (3.13.0-2) ... 61s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 61s Setting up python3 (3.12.7-1) ... 62s Setting up python3-gdbm:amd64 (3.12.7-1) ... 62s Processing triggers for man-db (2.12.1-3) ... 62s Processing triggers for libc-bin (2.40-1ubuntu3) ... 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 63s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 64s Reading package lists... 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 65s Calculating upgrade... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s autopkgtest [08:52:00]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 68s autopkgtest [08:52:00]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 78s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (dsc) [2152 B] 78s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (tar) [197 MB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (diff) [1268 kB] 78s gpgv: Signature made Sat Sep 7 23:10:03 2024 UTC 78s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1.dsc: no acceptable signature found 81s autopkgtest [08:52:13]: testing package macs version 3.0.2-1 82s autopkgtest [08:52:14]: build not needed 97s autopkgtest [08:52:29]: test run-unit-test: preparing testbed 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Starting pkgProblemResolver with broken count: 0 102s Starting 2 pkgProblemResolver with broken count: 0 102s Done 102s The following additional packages will be installed: 102s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 102s python3-decorator python3-hmmlearn python3-joblib python3-numpy 102s python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl 102s Suggested packages: 102s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 102s python-scipy-doc python3-dap python-sklearn-doc ipython3 102s Recommended packages: 102s python3-pytest python3-simplejson python3-psutil g++ | c++-compiler 102s python3-pil python3-matplotlib 102s The following NEW packages will be installed: 102s autopkgtest-satdep libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs 102s python3-cykhash python3-decorator python3-hmmlearn python3-joblib 102s python3-numpy python3-scipy python3-sklearn python3-sklearn-lib 102s python3-threadpoolctl 102s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 36.9 MB/36.9 MB of archives. 102s After this operation, 157 MB of additional disk space will be used. 102s Get:1 /tmp/autopkgtest.8AieVo/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cykhash amd64 2.0.0-3build1 [454 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 104s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 104s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 104s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 104s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 104s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hmmlearn amd64 0.3.2-2 [127 kB] 104s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 macs amd64 3.0.2-1 [3234 kB] 104s Fetched 36.9 MB in 2s (21.0 MB/s) 104s Selecting previously unselected package libblas3:amd64. 104s (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 ... 75548 files and directories currently installed.) 104s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 104s Unpacking libblas3:amd64 (3.12.0-3build2) ... 104s Selecting previously unselected package libgfortran5:amd64. 104s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 104s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 104s Selecting previously unselected package libgomp1:amd64. 104s Preparing to unpack .../02-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 104s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 104s Selecting previously unselected package liblapack3:amd64. 104s Preparing to unpack .../03-liblapack3_3.12.0-3build2_amd64.deb ... 104s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 104s Selecting previously unselected package liblbfgsb0:amd64. 104s Preparing to unpack .../04-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 104s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 104s Selecting previously unselected package python3-numpy. 104s Preparing to unpack .../05-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 104s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 105s Selecting previously unselected package python3-cykhash. 105s Preparing to unpack .../06-python3-cykhash_2.0.0-3build1_amd64.deb ... 105s Unpacking python3-cykhash (2.0.0-3build1) ... 105s Selecting previously unselected package python3-decorator. 105s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 105s Unpacking python3-decorator (5.1.1-5) ... 105s Selecting previously unselected package python3-scipy. 105s Preparing to unpack .../08-python3-scipy_1.13.1-5_amd64.deb ... 105s Unpacking python3-scipy (1.13.1-5) ... 105s Selecting previously unselected package python3-joblib. 105s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 105s Unpacking python3-joblib (1.3.2-5) ... 105s Selecting previously unselected package python3-threadpoolctl. 105s Preparing to unpack .../10-python3-threadpoolctl_3.1.0-1_all.deb ... 105s Unpacking python3-threadpoolctl (3.1.0-1) ... 105s Selecting previously unselected package python3-sklearn-lib:amd64. 105s Preparing to unpack .../11-python3-sklearn-lib_1.4.2+dfsg-6_amd64.deb ... 105s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 105s Selecting previously unselected package python3-sklearn. 105s Preparing to unpack .../12-python3-sklearn_1.4.2+dfsg-6_all.deb ... 105s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 105s Selecting previously unselected package python3-hmmlearn. 105s Preparing to unpack .../13-python3-hmmlearn_0.3.2-2_amd64.deb ... 105s Unpacking python3-hmmlearn (0.3.2-2) ... 105s Selecting previously unselected package macs. 105s Preparing to unpack .../14-macs_3.0.2-1_amd64.deb ... 105s Unpacking macs (3.0.2-1) ... 105s Selecting previously unselected package autopkgtest-satdep. 105s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 105s Unpacking autopkgtest-satdep (0) ... 105s Setting up python3-joblib (1.3.2-5) ... 106s Setting up python3-threadpoolctl (3.1.0-1) ... 106s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 106s Setting up python3-cykhash (2.0.0-3build1) ... 106s Setting up python3-decorator (5.1.1-5) ... 106s Setting up libblas3:amd64 (3.12.0-3build2) ... 106s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 106s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 106s Setting up liblapack3:amd64 (3.12.0-3build2) ... 106s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 106s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 107s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 107s Setting up python3-scipy (1.13.1-5) ... 110s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 110s Setting up python3-sklearn (1.4.2+dfsg-6) ... 111s Setting up python3-hmmlearn (0.3.2-2) ... 111s Setting up macs (3.0.2-1) ... 112s Setting up autopkgtest-satdep (0) ... 112s Processing triggers for man-db (2.12.1-3) ... 112s Processing triggers for libc-bin (2.40-1ubuntu3) ... 114s (Reading database ... 79106 files and directories currently installed.) 114s Removing autopkgtest-satdep (0) ... 114s autopkgtest [08:52:46]: test run-unit-test: [----------------------- 115s + pkg=macs 115s + '[' /tmp/autopkgtest.8AieVo/autopkgtest_tmp = '' ']' 115s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.8AieVo/autopkgtest_tmp 115s + cd /tmp/autopkgtest.8AieVo/autopkgtest_tmp 115s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 115s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] 115s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 115s # ARGUMENTS LIST: 115s # name = test 115s # format = AUTO 115s # ChIP-seq file = ['aluY.chr1.bed'] 115s # control file = None 115s # effective genome size = 2.91e+09 115s # band width = 300 115s # model fold = [5, 50] 115s # qvalue cutoff = 1.00e-02 115s # The maximum gap between significant sites is assigned as the read length/tag size. 115s # The minimum length of peaks is assigned as the predicted fragment length "d". 115s # Larger dataset will be scaled towards smaller dataset. 115s # Range for calculating regional lambda is: 10000 bps 115s # Broad region calling is off 115s # Paired-End mode is off 115s 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] #1 read tag files... 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] #1 read treatment tags... 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] Detected format is: BED 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 tag size is determined as 294 bps 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 tag size = 294.0 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 total tags in treatment: 11628 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 user defined the maximum tags... 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 tags after filtering in treatment: 11628 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 Redundant rate of treatment: 0.00 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #1 finished! 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #2 Build Peak Model... 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #2 Skipped... 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #2 Use 200 as fragment length 115s INFO @ 13 Nov 2024 08:52:47: [41 MB] #3 Call peaks... 115s INFO @ 13 Nov 2024 08:52:47: [42 MB] #3 Pre-compute pvalue-qvalue table... 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #3 In the peak calling step, the following will be performed simultaneously: 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #3 Pileup will be based on sequencing depth in treatment. 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #3 Call peaks for each chromosome... 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #4 Write output xls file... test_peaks.xls 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] #4 Write summits bed file... test_summits.bed 115s INFO @ 13 Nov 2024 08:52:47: [44 MB] Done! 115s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] 115s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 115s # ARGUMENTS LIST: 115s # name = NA 115s # format = AUTO 115s # ChIP-seq file = ['gerp.chr1.bed'] 115s # control file = None 115s # effective genome size = 2.91e+09 115s # band width = 300 115s # model fold = [5, 50] 115s # qvalue cutoff for narrow/strong regions = 5.00e-02 115s # qvalue cutoff for broad/weak regions = 1.00e-01 115s # The maximum gap between significant sites is assigned as the read length/tag size. 115s # The minimum length of peaks is assigned as the predicted fragment length "d". 115s # Larger dataset will be scaled towards smaller dataset. 115s # Range for calculating regional lambda is: 10000 bps 115s # Broad region calling is on 115s # Paired-End mode is off 115s 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] #1 read tag files... 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] #1 read treatment tags... 115s INFO @ 13 Nov 2024 08:52:47: [39 MB] Detected format is: BED 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 tag size is determined as 181 bps 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 tag size = 181.0 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 total tags in treatment: 88292 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 user defined the maximum tags... 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 tags after filtering in treatment: 88292 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 Redundant rate of treatment: 0.00 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #1 finished! 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #2 Build Peak Model... 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #2 Skipped... 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #2 Use 200 as fragment length 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #3 Call peaks... 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 115s INFO @ 13 Nov 2024 08:52:47: [50 MB] #3 Pre-compute pvalue-qvalue table... 115s INFO @ 13 Nov 2024 08:52:47: [68 MB] #3 Call peaks for each chromosome... 115s INFO @ 13 Nov 2024 08:52:47: [70 MB] #4 Write output xls file... NA_peaks.xls 115s INFO @ 13 Nov 2024 08:52:47: [70 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 115s INFO @ 13 Nov 2024 08:52:47: [70 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 115s INFO @ 13 Nov 2024 08:52:47: [70 MB] Done! 116s autopkgtest [08:52:48]: test run-unit-test: -----------------------] 116s autopkgtest [08:52:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 116s run-unit-test PASS 117s autopkgtest [08:52:49]: @@@@@@@@@@@@@@@@@@@@ summary 117s run-unit-test PASS 135s nova [W] Skipping flock for amd64 135s Creating nova instance adt-plucky-amd64-macs-20241113-085051-juju-7f2275-prod-proposed-migration-environment-20-2e2b9a4e-c73f-4d8a-9f3a-54b52bc8239e from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...