0s autopkgtest [19:05:14]: starting date and time: 2024-11-14 19:05:14+0000 0s autopkgtest [19:05:14]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [19:05:14]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rrcyuc9g/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 autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-8.secgroup --name adt-plucky-ppc64el-macs-20241114-190514-juju-7f2275-prod-proposed-migration-environment-15-f59124b3-237d-4691-a939-7582a19dca25 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 424s autopkgtest [19:12:18]: testbed dpkg architecture: ppc64el 424s autopkgtest [19:12:18]: testbed apt version: 2.9.8 424s autopkgtest [19:12:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 425s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 425s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 425s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 425s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 425s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB] 425s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [114 kB] 426s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [697 kB] 426s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 426s Fetched 1957 kB in 1s (1789 kB/s) 426s Reading package lists... 429s Reading package lists... 429s Building dependency tree... 429s Reading state information... 430s Calculating upgrade... 430s The following packages will be upgraded: 430s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 430s libjson-glib-1.0-common libnewt0.52 libutempter0 pastebinit python3-bpfcc 430s python3-newt python3-systemd whiptail 430s 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 430s Need to get 4678 kB of archives. 430s After this operation, 423 kB of additional disk space will be used. 430s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 430s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 430s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 430s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 430s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 430s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 430s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 430s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 430s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 431s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 431s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 431s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 431s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 431s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 431s Fetched 4678 kB in 1s (5749 kB/s) 431s (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.) 431s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 431s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 432s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 432s (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.) 432s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 432s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 432s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 432s (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.) 432s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 432s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 432s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 432s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 432s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 432s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 432s Preparing to unpack .../03-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 432s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 432s Preparing to unpack .../04-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 432s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 432s Preparing to unpack .../05-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 432s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 432s Preparing to unpack .../06-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 432s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 432s Preparing to unpack .../07-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 432s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 432s Preparing to unpack .../08-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 433s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 433s Preparing to unpack .../09-libutempter0_1.2.1-4_ppc64el.deb ... 433s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 433s Preparing to unpack .../10-pastebinit_1.7.1-1_all.deb ... 433s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 433s Preparing to unpack .../11-python3-systemd_235-1build5_ppc64el.deb ... 433s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 433s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 433s Setting up pastebinit (1.7.1-1) ... 433s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 433s Setting up libutempter0:ppc64el (1.2.1-4) ... 433s Setting up whiptail (0.52.24-2ubuntu4) ... 433s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 433s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 433s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 433s Setting up python3-systemd (235-1build5) ... 433s Setting up bpftrace (0.21.2-2ubuntu2) ... 433s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 433s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 433s Processing triggers for man-db (2.12.1-3) ... 435s Processing triggers for libc-bin (2.40-1ubuntu3) ... 435s Reading package lists... 436s Building dependency tree... 436s Reading state information... 436s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 437s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 437s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 437s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 437s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 438s Reading package lists... 438s Reading package lists... 439s Building dependency tree... 439s Reading state information... 439s Calculating upgrade... 439s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 439s Reading package lists... 439s Building dependency tree... 439s Reading state information... 440s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 442s autopkgtest [19:12:36]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 443s autopkgtest [19:12:37]: @@@@@@@@@@@@@@@@@@@@ apt-source macs 455s Get:1 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (dsc) [2152 B] 455s Get:2 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (tar) [197 MB] 455s Get:3 http://ftpmaster.internal/ubuntu plucky/universe macs 3.0.2-1 (diff) [1268 kB] 456s gpgv: Signature made Sat Sep 7 23:10:03 2024 UTC 456s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 456s gpgv: Can't check signature: No public key 456s dpkg-source: warning: cannot verify inline signature for ./macs_3.0.2-1.dsc: no acceptable signature found 462s autopkgtest [19:12:56]: testing package macs version 3.0.2-1 463s autopkgtest [19:12:57]: build not needed 479s autopkgtest [19:13:13]: test run-unit-test: preparing testbed 480s Reading package lists... 480s Building dependency tree... 480s Reading state information... 481s Starting pkgProblemResolver with broken count: 0 481s Starting 2 pkgProblemResolver with broken count: 0 481s Done 481s The following additional packages will be installed: 481s libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs python3-cykhash 481s python3-decorator python3-hmmlearn python3-joblib python3-numpy 481s python3-scipy python3-sklearn python3-sklearn-lib python3-threadpoolctl 481s Suggested packages: 481s python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 481s python-scipy-doc python3-dap python-sklearn-doc ipython3 481s Recommended packages: 481s python3-pytest python3-simplejson python3-psutil g++ | c++-compiler 481s python3-pil python3-matplotlib 481s The following NEW packages will be installed: 481s autopkgtest-satdep libblas3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 macs 481s python3-cykhash python3-decorator python3-hmmlearn python3-joblib 481s python3-numpy python3-scipy python3-sklearn python3-sklearn-lib 482s python3-threadpoolctl 482s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 482s Need to get 37.5 MB/37.5 MB of archives. 482s After this operation, 182 MB of additional disk space will be used. 482s Get:1 /tmp/autopkgtest.emx0IA/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 482s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 482s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 482s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 482s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 482s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 482s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 482s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cykhash ppc64el 2.0.0-3build1 [506 kB] 482s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 482s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 483s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB] 483s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB] 483s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6 [3838 kB] 483s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 483s Get:15 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-hmmlearn ppc64el 0.3.2-2 [130 kB] 483s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el macs ppc64el 3.0.2-1 [3238 kB] 484s Fetched 37.5 MB in 2s (22.8 MB/s) 484s Selecting previously unselected package libblas3:ppc64el. 484s (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 ... 73773 files and directories currently installed.) 484s Preparing to unpack .../00-libblas3_3.12.0-3build2_ppc64el.deb ... 484s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 484s Selecting previously unselected package libgfortran5:ppc64el. 484s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 484s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 484s Selecting previously unselected package libgomp1:ppc64el. 484s Preparing to unpack .../02-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 484s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 484s Selecting previously unselected package liblapack3:ppc64el. 484s Preparing to unpack .../03-liblapack3_3.12.0-3build2_ppc64el.deb ... 484s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 484s Selecting previously unselected package liblbfgsb0:ppc64el. 484s Preparing to unpack .../04-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 484s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 484s Selecting previously unselected package python3-numpy. 484s Preparing to unpack .../05-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 484s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 484s Selecting previously unselected package python3-cykhash. 484s Preparing to unpack .../06-python3-cykhash_2.0.0-3build1_ppc64el.deb ... 484s Unpacking python3-cykhash (2.0.0-3build1) ... 484s Selecting previously unselected package python3-decorator. 484s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 484s Unpacking python3-decorator (5.1.1-5) ... 484s Selecting previously unselected package python3-scipy. 484s Preparing to unpack .../08-python3-scipy_1.13.1-5_ppc64el.deb ... 484s Unpacking python3-scipy (1.13.1-5) ... 485s Selecting previously unselected package python3-joblib. 485s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 485s Unpacking python3-joblib (1.3.2-5) ... 485s Selecting previously unselected package python3-threadpoolctl. 485s Preparing to unpack .../10-python3-threadpoolctl_3.1.0-1_all.deb ... 485s Unpacking python3-threadpoolctl (3.1.0-1) ... 485s Selecting previously unselected package python3-sklearn-lib:ppc64el. 485s Preparing to unpack .../11-python3-sklearn-lib_1.4.2+dfsg-6_ppc64el.deb ... 485s Unpacking python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 486s Selecting previously unselected package python3-sklearn. 486s Preparing to unpack .../12-python3-sklearn_1.4.2+dfsg-6_all.deb ... 486s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 486s Selecting previously unselected package python3-hmmlearn. 486s Preparing to unpack .../13-python3-hmmlearn_0.3.2-2_ppc64el.deb ... 486s Unpacking python3-hmmlearn (0.3.2-2) ... 486s Selecting previously unselected package macs. 486s Preparing to unpack .../14-macs_3.0.2-1_ppc64el.deb ... 486s Unpacking macs (3.0.2-1) ... 486s Selecting previously unselected package autopkgtest-satdep. 486s Preparing to unpack .../15-1-autopkgtest-satdep.deb ... 486s Unpacking autopkgtest-satdep (0) ... 486s Setting up python3-joblib (1.3.2-5) ... 486s Setting up python3-threadpoolctl (3.1.0-1) ... 487s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 487s Setting up python3-cykhash (2.0.0-3build1) ... 487s Setting up python3-decorator (5.1.1-5) ... 487s Setting up libblas3:ppc64el (3.12.0-3build2) ... 487s 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 487s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 487s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 487s 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 487s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 490s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 490s Setting up python3-scipy (1.13.1-5) ... 495s Setting up python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 495s Setting up python3-sklearn (1.4.2+dfsg-6) ... 498s Setting up python3-hmmlearn (0.3.2-2) ... 498s Setting up macs (3.0.2-1) ... 498s Setting up autopkgtest-satdep (0) ... 498s Processing triggers for man-db (2.12.1-3) ... 499s Processing triggers for libc-bin (2.40-1ubuntu3) ... 502s (Reading database ... 77351 files and directories currently installed.) 502s Removing autopkgtest-satdep (0) ... 503s autopkgtest [19:13:37]: test run-unit-test: [----------------------- 503s + pkg=macs 503s + '[' /tmp/autopkgtest.emx0IA/autopkgtest_tmp = '' ']' 503s + cp -a /usr/share/doc/macs/examples/aluY.chr1.bed.gz /usr/share/doc/macs/examples/gerp.chr1.bed.gz /tmp/autopkgtest.emx0IA/autopkgtest_tmp 503s + cd /tmp/autopkgtest.emx0IA/autopkgtest_tmp 503s + gunzip aluY.chr1.bed.gz gerp.chr1.bed.gz 503s + macs3 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 503s INFO @ 14 Nov 2024 19:13:37: [46 MB] 503s # Command line: callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01 503s # ARGUMENTS LIST: 503s # name = test 503s # format = AUTO 503s # ChIP-seq file = ['aluY.chr1.bed'] 503s # control file = None 503s # effective genome size = 2.91e+09 503s # band width = 300 503s # model fold = [5, 50] 503s # qvalue cutoff = 1.00e-02 503s # The maximum gap between significant sites is assigned as the read length/tag size. 503s # The minimum length of peaks is assigned as the predicted fragment length "d". 503s # Larger dataset will be scaled towards smaller dataset. 503s # Range for calculating regional lambda is: 10000 bps 503s # Broad region calling is off 503s # Paired-End mode is off 503s 503s INFO @ 14 Nov 2024 19:13:37: [46 MB] #1 read tag files... 503s INFO @ 14 Nov 2024 19:13:37: [46 MB] #1 read treatment tags... 503s INFO @ 14 Nov 2024 19:13:37: [46 MB] Detected format is: BED 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 tag size is determined as 294 bps 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 tag size = 294.0 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 total tags in treatment: 11628 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 user defined the maximum tags... 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 tags after filtering in treatment: 11628 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 Redundant rate of treatment: 0.00 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #1 finished! 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #2 Build Peak Model... 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #2 Skipped... 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #2 Use 200 as fragment length 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 Call peaks... 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 Pre-compute pvalue-qvalue table... 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 In the peak calling step, the following will be performed simultaneously: 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 Write bedGraph files for treatment pileup (after scaling if necessary)... test_treat_pileup.bdg 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 Write bedGraph files for control lambda (after scaling if necessary)... test_control_lambda.bdg 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 Pileup will be based on sequencing depth in treatment. 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #3 Call peaks for each chromosome... 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #4 Write output xls file... test_peaks.xls 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #4 Write peak in narrowPeak format file... test_peaks.narrowPeak 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] #4 Write summits bed file... test_summits.bed 503s INFO @ 14 Nov 2024 19:13:37: [49 MB] Done! 503s + macs3 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 504s INFO @ 14 Nov 2024 19:13:38: [48 MB] 504s # Command line: callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1 504s # ARGUMENTS LIST: 504s # name = NA 504s # format = AUTO 504s # ChIP-seq file = ['gerp.chr1.bed'] 504s # control file = None 504s # effective genome size = 2.91e+09 504s # band width = 300 504s # model fold = [5, 50] 504s # qvalue cutoff for narrow/strong regions = 5.00e-02 504s # qvalue cutoff for broad/weak regions = 1.00e-01 504s # The maximum gap between significant sites is assigned as the read length/tag size. 504s # The minimum length of peaks is assigned as the predicted fragment length "d". 504s # Larger dataset will be scaled towards smaller dataset. 504s # Range for calculating regional lambda is: 10000 bps 504s # Broad region calling is on 504s # Paired-End mode is off 504s 504s INFO @ 14 Nov 2024 19:13:38: [48 MB] #1 read tag files... 504s INFO @ 14 Nov 2024 19:13:38: [48 MB] #1 read treatment tags... 504s INFO @ 14 Nov 2024 19:13:38: [48 MB] Detected format is: BED 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 tag size is determined as 181 bps 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 tag size = 181.0 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 total tags in treatment: 88292 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 user defined the maximum tags... 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 tags after filtering in treatment: 88292 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 Redundant rate of treatment: 0.00 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #1 finished! 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #2 Build Peak Model... 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #2 Skipped... 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #2 Use 200 as fragment length 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #3 Call peaks... 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000... 504s INFO @ 14 Nov 2024 19:13:38: [58 MB] #3 Pre-compute pvalue-qvalue table... 504s INFO @ 14 Nov 2024 19:13:38: [74 MB] #3 Call peaks for each chromosome... 504s INFO @ 14 Nov 2024 19:13:38: [78 MB] #4 Write output xls file... NA_peaks.xls 504s INFO @ 14 Nov 2024 19:13:38: [78 MB] #4 Write broad peak in broadPeak format file... NA_peaks.broadPeak 504s INFO @ 14 Nov 2024 19:13:38: [78 MB] #4 Write broad peak in bed12/gappedPeak format file... NA_peaks.gappedPeak 504s INFO @ 14 Nov 2024 19:13:38: [78 MB] Done! 505s autopkgtest [19:13:39]: test run-unit-test: -----------------------] 505s run-unit-test PASS 505s autopkgtest [19:13:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 505s autopkgtest [19:13:39]: @@@@@@@@@@@@@@@@@@@@ summary 505s run-unit-test PASS 510s nova [W] Using flock in prodstack6-ppc64el 510s Creating nova instance adt-plucky-ppc64el-macs-20241114-190514-juju-7f2275-prod-proposed-migration-environment-15-f59124b3-237d-4691-a939-7582a19dca25 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)... 510s nova [W] nova quota exceeded (attempt #0)