0s autopkgtest [11:17:50]: starting date and time: 2024-11-15 11:17:50+0000 0s autopkgtest [11:17:50]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:17:50]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kguz0i9x/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade macs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-29.secgroup --name adt-plucky-amd64-macs-20241115-111750-juju-7f2275-prod-proposed-migration-environment-15-5b44f5c3-6188-47c1-a147-5eeb662bb820 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 41s autopkgtest [11:18:31]: testbed dpkg architecture: amd64 41s autopkgtest [11:18:31]: testbed apt version: 2.9.8 41s autopkgtest [11:18:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 42s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 42s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1056 kB] 43s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 43s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB] 43s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [297 kB] 43s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [833 kB] 43s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 43s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 43s Fetched 2704 kB in 1s (3267 kB/s) 43s Reading package lists... 45s Reading package lists... 45s Building dependency tree... 45s Reading state information... 45s Calculating upgrade... 45s The following packages will be upgraded: 45s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 45s libexpat1 lxd-installer man-db pastebinit python3-systemd xfsprogs 46s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 46s Need to get 13.6 MB of archives. 46s After this operation, 477 kB of additional disk space will be used. 46s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 46s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 46s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 46s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 46s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 46s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 46s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 46s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 47s Preconfiguring packages ... 47s Fetched 13.6 MB in 1s (13.6 MB/s) 47s (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 ... 75542 files and directories currently installed.) 47s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 47s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 47s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 47s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 47s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 47s (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 ... 75568 files and directories currently installed.) 47s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 47s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 47s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 47s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 47s Preparing to unpack .../2-grub2-common_2.12-5ubuntu7_amd64.deb ... 47s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 48s Preparing to unpack .../3-grub-pc_2.12-5ubuntu7_amd64.deb ... 48s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 48s Preparing to unpack .../4-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 48s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 48s Preparing to unpack .../5-grub-common_2.12-5ubuntu7_amd64.deb ... 48s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 48s Preparing to unpack .../6-lxd-installer_9_all.deb ... 48s Unpacking lxd-installer (9) over (8) ... 48s Preparing to unpack .../7-pastebinit_1.7.1-1_all.deb ... 48s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 48s Preparing to unpack .../8-python3-systemd_235-1build5_amd64.deb ... 48s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 48s Preparing to unpack .../9-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 48s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 48s Setting up libexpat1:amd64 (2.6.4-1) ... 48s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 48s Setting up pastebinit (1.7.1-1) ... 48s Setting up man-db (2.13.0-1) ... 48s Updating database of manual pages ... 50s man-db.service is a disabled or a static unit not running, not starting it. 50s Setting up grub-common (2.12-5ubuntu7) ... 50s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 51s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 51s update-initramfs: deferring update (trigger activated) 51s Setting up lxd-installer (9) ... 52s Setting up python3-systemd (235-1build5) ... 52s Setting up grub2-common (2.12-5ubuntu7) ... 52s Setting up grub-pc-bin (2.12-5ubuntu7) ... 52s Setting up grub-pc (2.12-5ubuntu7) ... 52s Installing for i386-pc platform. 53s Installation finished. No error reported. 53s Sourcing file `/etc/default/grub' 53s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 53s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 53s Generating grub configuration file ... 53s Found linux image: /boot/vmlinuz-6.11.0-8-generic 53s Found initrd image: /boot/initrd.img-6.11.0-8-generic 53s Warning: os-prober will not be executed to detect other bootable partitions. 53s Systems on them will not be added to the GRUB boot configuration. 53s Check GRUB_DISABLE_OS_PROBER documentation entry. 53s Adding boot menu entry for UEFI Firmware Settings ... 53s done 53s Processing triggers for libc-bin (2.40-1ubuntu3) ... 53s Processing triggers for install-info (7.1.1-1) ... 53s Processing triggers for initramfs-tools (0.142ubuntu34) ... 53s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 53s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 62s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 63s Reading package lists... 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s autopkgtest [11:18:54]: rebooting testbed after setup commands that affected boot 68s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 82s autopkgtest [11:19:12]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 84s autopkgtest [11:19:14]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 92s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (dsc) [2152 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (tar) [197 MB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (diff) [1268 kB] 92s gpgv: Signature made Sat Sep 7 23:10:03 2024 UTC 92s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1.dsc: no acceptable signature found 95s autopkgtest [11:19:25]: testing package macs version 3.0.2-1 96s autopkgtest [11:19:26]: build not needed 109s autopkgtest [11:19:39]: test run-unit-test: preparing testbed 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 111s The following additional packages will be installed: 111s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 111s python3-decorator python3-hmmlearn python3-joblib python3-numpy 111s python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl 111s Suggested packages: 111s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 111s python-scipy-doc python3-dap python-sklearn-doc ipython3 111s Recommended packages: 111s python3-pytest python3-simplejson python3-psutil g++ | c++-compiler 111s python3-pil python3-matplotlib 111s The following NEW packages will be installed: 111s autopkgtest-satdep libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs 111s python3-cykhash python3-decorator python3-hmmlearn python3-joblib 111s python3-numpy python3-scipy python3-sklearn python3-sklearn-lib 111s python3-threadpoolctl 111s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 37.7 MB/37.7 MB of archives. 111s After this operation, 172 MB of additional disk space will be used. 111s Get:1 /tmp/autopkgtest.WTiwgy/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 111s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 112s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 112s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 112s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cykhash amd64 2.0.0-3build1 [454 kB] 112s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 112s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 113s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 113s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 113s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 113s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 113s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hmmlearn amd64 0.3.2-2 [127 kB] 113s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 macs amd64 3.0.2-1 [3234 kB] 113s Fetched 37.7 MB in 2s (24.1 MB/s) 113s Selecting previously unselected package libblas3:amd64. 113s (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 ... 75575 files and directories currently installed.) 113s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 113s Unpacking libblas3:amd64 (3.12.0-3build2) ... 113s Selecting previously unselected package libgfortran5:amd64. 113s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 113s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 113s Selecting previously unselected package libgomp1:amd64. 113s Preparing to unpack .../02-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 113s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 113s Selecting previously unselected package liblapack3:amd64. 113s Preparing to unpack .../03-liblapack3_3.12.0-3build2_amd64.deb ... 113s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 114s Selecting previously unselected package liblbfgsb0:amd64. 114s Preparing to unpack .../04-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 114s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 114s Selecting previously unselected package python3-numpy. 114s Preparing to unpack .../05-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 114s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 114s Selecting previously unselected package python3-cykhash. 114s Preparing to unpack .../06-python3-cykhash_2.0.0-3build1_amd64.deb ... 114s Unpacking python3-cykhash (2.0.0-3build1) ... 114s Selecting previously unselected package python3-decorator. 114s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 114s Unpacking python3-decorator (5.1.1-5) ... 114s Selecting previously unselected package python3-scipy. 114s Preparing to unpack .../08-python3-scipy_1.13.1-5_amd64.deb ... 114s Unpacking python3-scipy (1.13.1-5) ... 114s Selecting previously unselected package python3-joblib. 114s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 114s Unpacking python3-joblib (1.3.2-5) ... 114s Selecting previously unselected package python3-threadpoolctl. 114s Preparing to unpack .../10-python3-threadpoolctl_3.1.0-1_all.deb ... 114s Unpacking python3-threadpoolctl (3.1.0-1) ... 114s Selecting previously unselected package python3-sklearn-lib:amd64. 114s Preparing to unpack .../11-python3-sklearn-lib_1.4.2+dfsg-6_amd64.deb ... 114s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 114s Selecting previously unselected package python3-sklearn. 115s Preparing to unpack .../12-python3-sklearn_1.4.2+dfsg-6_all.deb ... 115s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 115s Selecting previously unselected package python3-hmmlearn. 115s Preparing to unpack .../13-python3-hmmlearn_0.3.2-2_amd64.deb ... 115s Unpacking python3-hmmlearn (0.3.2-2) ... 115s Selecting previously unselected package macs. 115s Preparing to unpack .../14-macs_3.0.2-1_amd64.deb ... 115s Unpacking macs (3.0.2-1) ... 115s Selecting previously unselected package autopkgtest-satdep. 115s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 115s Unpacking autopkgtest-satdep (0) ... 115s Setting up python3-joblib (1.3.2-5) ... 115s Setting up python3-threadpoolctl (3.1.0-1) ... 115s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 115s Setting up python3-cykhash (2.0.0-3build1) ... 115s Setting up python3-decorator (5.1.1-5) ... 115s Setting up libblas3:amd64 (3.12.0-3build2) ... 115s 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 115s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 115s Setting up liblapack3:amd64 (3.12.0-3build2) ... 115s 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 115s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 117s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 117s Setting up python3-scipy (1.13.1-5) ... 119s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 119s Setting up python3-sklearn (1.4.2+dfsg-6) ... 121s Setting up python3-hmmlearn (0.3.2-2) ... 121s Setting up macs (3.0.2-1) ... 121s Setting up autopkgtest-satdep (0) ... 121s Processing triggers for man-db (2.13.0-1) ... 121s Processing triggers for libc-bin (2.40-1ubuntu3) ... 124s (Reading database ... 79153 files and directories currently installed.) 124s Removing autopkgtest-satdep (0) ... 124s autopkgtest [11:19:54]: test run-unit-test: [----------------------- 124s + pkg=macs 124s + '[' /tmp/autopkgtest.WTiwgy/autopkgtest_tmp = '' ']' 124s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.WTiwgy/autopkgtest_tmp 124s + cd /tmp/autopkgtest.WTiwgy/autopkgtest_tmp 124s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 124s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] 125s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 125s # ARGUMENTS LIST: 125s # name = test 125s # format = AUTO 125s # ChIP-seq file = ['aluY.chr1.bed'] 125s # control file = None 125s # effective genome size = 2.91e+09 125s # band width = 300 125s # model fold = [5, 50] 125s # qvalue cutoff = 1.00e-02 125s # The maximum gap between significant sites is assigned as the read length/tag size. 125s # The minimum length of peaks is assigned as the predicted fragment length "d". 125s # Larger dataset will be scaled towards smaller dataset. 125s # Range for calculating regional lambda is: 10000 bps 125s # Broad region calling is off 125s # Paired-End mode is off 125s 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] #1 read tag files... 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] #1 read treatment tags... 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] Detected format is: BED 125s INFO @ 15 Nov 2024 11:19:55: [41 MB] #1 tag size is determined as 294 bps 125s INFO @ 15 Nov 2024 11:19:55: [41 MB] #1 tag size = 294.0 125s INFO @ 15 Nov 2024 11:19:55: [41 MB] #1 total tags in treatment: 11628 125s INFO @ 15 Nov 2024 11:19:55: [41 MB] #1 user defined the maximum tags... 125s INFO @ 15 Nov 2024 11:19:55: [41 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #1 tags after filtering in treatment: 11628 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #1 Redundant rate of treatment: 0.00 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #1 finished! 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #2 Build Peak Model... 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #2 Skipped... 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #2 Use 200 as fragment length 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #3 Call peaks... 125s INFO @ 15 Nov 2024 11:19:55: [42 MB] #3 Pre-compute pvalue-qvalue table... 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #3 In the peak calling step, the following will be performed simultaneously: 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #3 Pileup will be based on sequencing depth in treatment. 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #3 Call peaks for each chromosome... 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #4 Write output xls file... test_peaks.xls 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] #4 Write summits bed file... test_summits.bed 125s INFO @ 15 Nov 2024 11:19:55: [45 MB] Done! 125s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] 125s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 125s # ARGUMENTS LIST: 125s # name = NA 125s # format = AUTO 125s # ChIP-seq file = ['gerp.chr1.bed'] 125s # control file = None 125s # effective genome size = 2.91e+09 125s # band width = 300 125s # model fold = [5, 50] 125s # qvalue cutoff for narrow/strong regions = 5.00e-02 125s # qvalue cutoff for broad/weak regions = 1.00e-01 125s # The maximum gap between significant sites is assigned as the read length/tag size. 125s # The minimum length of peaks is assigned as the predicted fragment length "d". 125s # Larger dataset will be scaled towards smaller dataset. 125s # Range for calculating regional lambda is: 10000 bps 125s # Broad region calling is on 125s # Paired-End mode is off 125s 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] #1 read tag files... 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] #1 read treatment tags... 125s INFO @ 15 Nov 2024 11:19:55: [40 MB] Detected format is: BED 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 tag size is determined as 181 bps 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 tag size = 181.0 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 total tags in treatment: 88292 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 user defined the maximum tags... 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 tags after filtering in treatment: 88292 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 Redundant rate of treatment: 0.00 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #1 finished! 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #2 Build Peak Model... 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #2 Skipped... 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #2 Use 200 as fragment length 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #3 Call peaks... 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 125s INFO @ 15 Nov 2024 11:19:55: [51 MB] #3 Pre-compute pvalue-qvalue table... 125s INFO @ 15 Nov 2024 11:19:55: [68 MB] #3 Call peaks for each chromosome... 125s INFO @ 15 Nov 2024 11:19:55: [71 MB] #4 Write output xls file... NA_peaks.xls 125s INFO @ 15 Nov 2024 11:19:55: [71 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 125s INFO @ 15 Nov 2024 11:19:55: [71 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 125s INFO @ 15 Nov 2024 11:19:55: [71 MB] Done! 125s autopkgtest [11:19:55]: test run-unit-test: -----------------------] 126s autopkgtest [11:19:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 126s run-unit-test PASS 126s autopkgtest [11:19:56]: @@@@@@@@@@@@@@@@@@@@ summary 126s run-unit-test PASS 138s nova [W] Skipping flock for amd64 138s Creating nova instance adt-plucky-amd64-macs-20241115-111750-juju-7f2275-prod-proposed-migration-environment-15-5b44f5c3-6188-47c1-a147-5eeb662bb820 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...