0s autopkgtest [02:00:28]: starting date and time: 2025-12-06 02:00:28+0000 0s autopkgtest [02:00:28]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:00:28]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b1x6_004/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade bedtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-ppc64el-5.secgroup --name adt-resolute-ppc64el-bedtools-20251206-020028-juju-7f2275-prod-proposed-migration-environment-20-cadc3c15-9f5f-4dc0-8f9d-1e6ce17fbb71 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-bedtools-20251206-020028-juju-7f2275-prod-proposed-migration-environment-20-cadc3c15-9f5f-4dc0-8f9d-1e6ce17fbb71 from image adt/ubuntu-resolute-ppc64el-server-20251205.img (UUID ec8e7418-51bb-4f88-80fc-4d434bdc97c2)... 52s autopkgtest [02:01:20]: testbed dpkg architecture: ppc64el 52s autopkgtest [02:01:20]: testbed apt version: 3.1.12 52s autopkgtest [02:01:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [02:01:20]: testbed release detected to be: None 53s autopkgtest [02:01:21]: updating testbed package index (apt update) 53s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.4 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [842 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [140 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [226 kB] 54s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [689 kB] 54s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [6928 B] 54s Fetched 2052 kB in 1s (3139 kB/s) 54s Reading package lists... 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages will be upgraded: 56s libnftnl11 libpython3-stdlib lxd-installer python3 python3-attr python3-gdbm 56s python3-minimal 56s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 212 kB of archives. 56s After this operation, 16.4 kB of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.9-2 [28.1 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.9-2 [23.0 kB] 56s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.9-2 [10.8 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libnftnl11 ppc64el 1.3.1-1 [80.0 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-gdbm ppc64el 3.13.9-2 [11.0 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el lxd-installer all 14ubuntu0 [5428 B] 56s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-attr all 25.4.0-1 [53.6 kB] 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory 57s Fetched 212 kB in 0s (13.0 MB/s) 57s (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 ... 81185 files and directories currently installed.) 57s Preparing to unpack .../python3-minimal_3.13.9-2_ppc64el.deb ... 57s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 57s Setting up python3-minimal (3.13.9-2) ... 58s (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 ... 81185 files and directories currently installed.) 58s Preparing to unpack .../0-python3_3.13.9-2_ppc64el.deb ... 58s running python pre-rtupdate hooks for python3.13... 58s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 58s Preparing to unpack .../1-libpython3-stdlib_3.13.9-2_ppc64el.deb ... 58s Unpacking libpython3-stdlib:ppc64el (3.13.9-2) over (3.13.7-1) ... 58s Preparing to unpack .../2-libnftnl11_1.3.1-1_ppc64el.deb ... 58s Unpacking libnftnl11:ppc64el (1.3.1-1) over (1.3.0-1) ... 58s Preparing to unpack .../3-python3-gdbm_3.13.9-2_ppc64el.deb ... 58s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 58s Preparing to unpack .../4-lxd-installer_14ubuntu0_all.deb ... 58s Unpacking lxd-installer (14ubuntu0) over (13ubuntu0) ... 59s Preparing to unpack .../5-python3-attr_25.4.0-1_all.deb ... 59s Unpacking python3-attr (25.4.0-1) over (25.3.0-1) ... 59s Setting up python3-gdbm (3.13.9-2) ... 59s Setting up libnftnl11:ppc64el (1.3.1-1) ... 59s Setting up lxd-installer (14ubuntu0) ... 59s Setting up libpython3-stdlib:ppc64el (3.13.9-2) ... 59s Setting up python3 (3.13.9-2) ... 59s running python rtupdate hooks for python3.13... 59s running python post-rtupdate hooks for python3.13... 59s Setting up python3-attr (25.4.0-1) ... 60s Processing triggers for man-db (2.13.1-1) ... 61s Processing triggers for libc-bin (2.42-2ubuntu2) ... 61s autopkgtest [02:01:29]: upgrading testbed (apt dist-upgrade and autopurge) 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Solving dependencies... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [02:01:30]: rebooting testbed after setup commands that affected boot 101s autopkgtest [02:02:09]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:47:32 UTC 2025 103s autopkgtest [02:02:11]: @@@@@@@@@@@@@@@@@@@@ apt-source bedtools 106s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (dsc) [2230 B] 106s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (tar) [14.5 MB] 106s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (diff) [14.5 kB] 106s gpgv: Signature made Mon Dec 4 19:20:23 2023 UTC 106s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 106s gpgv: issuer "emollier@debian.org" 106s gpgv: Can't check signature: No public key 106s dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found 107s autopkgtest [02:02:15]: testing package bedtools version 2.31.1+dfsg-2 107s autopkgtest [02:02:15]: build not needed 109s autopkgtest [02:02:17]: test run-unit-test: preparing testbed 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 109s The following NEW packages will be installed: 109s bedtools bedtools-test libdeflate0 libhtscodecs2 tabix 109s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 20.0 MB of archives. 109s After this operation, 54.1 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bedtools ppc64el 2.31.1+dfsg-2 [782 kB] 110s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el bedtools-test all 2.31.1+dfsg-2 [18.2 MB] 110s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 110s Get:4 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 111s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el tabix ppc64el 1.22.1+ds2-1 [771 kB] 111s Fetched 20.0 MB in 1s (17.5 MB/s) 111s Selecting previously unselected package bedtools. 111s (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 ... 81185 files and directories currently installed.) 111s Preparing to unpack .../bedtools_2.31.1+dfsg-2_ppc64el.deb ... 111s Unpacking bedtools (2.31.1+dfsg-2) ... 111s Selecting previously unselected package bedtools-test. 111s Preparing to unpack .../bedtools-test_2.31.1+dfsg-2_all.deb ... 111s Unpacking bedtools-test (2.31.1+dfsg-2) ... 112s Selecting previously unselected package libdeflate0:ppc64el. 112s Preparing to unpack .../libdeflate0_1.23-2_ppc64el.deb ... 112s Unpacking libdeflate0:ppc64el (1.23-2) ... 112s Selecting previously unselected package libhtscodecs2:ppc64el. 112s Preparing to unpack .../libhtscodecs2_1.6.1-2_ppc64el.deb ... 112s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 112s Selecting previously unselected package tabix. 112s Preparing to unpack .../tabix_1.22.1+ds2-1_ppc64el.deb ... 112s Unpacking tabix (1.22.1+ds2-1) ... 112s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 112s Setting up libdeflate0:ppc64el (1.23-2) ... 112s Setting up bedtools-test (2.31.1+dfsg-2) ... 112s Setting up tabix (1.22.1+ds2-1) ... 112s Setting up bedtools (2.31.1+dfsg-2) ... 112s Processing triggers for man-db (2.13.1-1) ... 113s Processing triggers for libc-bin (2.42-2ubuntu2) ... 114s autopkgtest [02:02:22]: test run-unit-test: [----------------------- 114s Testing bedtools bamtobed: 114s bamtobed.t1...ok 114s bamtobed.t2...ok 114s bamtobed.t3...ok 114s bamtobed.t4...ok 114s bamtobed.t5...ok 114s bamtobed.t6...ok 114s bamtobed.t7...ok 114s bamtobed.t8...ok 114s bamtobed.t9...ok 114s bamtobed.t10...ok 114s bamtobed.t9...ok 114s bamtobed.t11...ok 114s bamtobed.t12..ok 114s bamtobed.t13..ok 115s Testing bedtools bamtofastq: 115s ok 115s ok 115s Testing bedtools bed12tobed6: 115s bed12tobed6.t1...ok 115s bed12tobed6.t2...ok 115s bed12tobed6.t3...ok 115s bed12tobed6.t4...ok 115s bed12tobed6.t5...ok 115s Testing bedtools bedtobam: 115s bedtobam.t1...ok 115s Testing bedtools bigchroms: 115s bigchroms.t01...ok 115s bigchroms.t02...ok 115s bigchroms.t03... skip set env var 'BT_NO_BIG_FILES' to run this test 115s bigchroms.t04... merge ok 115s bigchroms.t05... closest ok 115s Testing bedtools closest: 115s closest.t1...ok 115s closest.t2...ok 115s closest.t3...ok 115s closest.t4...ok 115s closest.t5...ok 115s closest.t6...ok 115s closest.t7...ok 115s closest.t8...ok 115s closest.t9...ok 115s closest.t10...ok 115s closest.t11...ok 115s closest.t13...ok 115s closest.t14...ok 115s closest.t15...ok 115s closest.t16...ok 115s closest.t17...ok 115s closest.t18...ok 115s closest.t19...ok 115s closest.t20...ok 115s closest.t21...ok 115s closest.t22...ok 115s closest.t23...ok 115s closest.t24...ok 115s closest.t25...ok 115s closest.t26...ok 115s closest.t27...ok 115s closest.t28...ok 115s closest.t29...ok 115s closest.t30...ok 115s closest.t31...ok 115s closest.t32...ok 115s closest.t33...ok 115s closest.t34...ok 115s closest.t35...ok 115s closest.t36...ok 115s closest.t37...ok 115s closest.t38...ok 115s closest.t39...ok 115s closest.t40...ok 115s closest.t41...ok 115s closest.t42...ok 115s closest.t43...ok 115s closest.t44...ok 115s closest.t45...ok 115s closest.t46...ok 115s closest.t47...ok 115s closest.t48...ok 115s closest.t49...ok 115s closest.t50...ok 115s closest.t51...ok 115s closest.t52...ok 115s closest.t53...ok 115s closest.t54...ok 115s closest.t55...ok 115s closest.t56...ok 115s closest.t57...ok 115s closest.t58...ok 115s closest.t59...ok 115s closest.t60...ok 115s closest.t61...ok 115s closest.t62...ok 115s closest.t63...ok 115s closest.t64...ok 115s closest.t65...ok 115s closest.t66...ok 115s closest.t67...ok 115s closest.t68...ok 115s closest.t69...ok 115s closest.t70...ok 115s closest.t71...ok 115s 115s ########################################################### 115s # 115s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 115s # 115s ########################################################### 115s 115s closest.t01...ok 115s closest.t02...ok 115s closest.t03...ok 115s closest.t04...ok 115s closest.t05...ok 115s closest.t06...ok 115s closest.t07...ok 115s closest.t08...ok 115s closest.t09...ok 115s closest.t10...ok 115s closest.t11...ok 115s closest.t12...ok 115s closest.t13...ok 115s closest.t14...ok 115s closest.t15...ok 115s closest.t16...ok 115s closest.t17...ok 115s closest.t18...ok 115s closest.t19...ok 115s closest.20...ok 115s closest.21...ok 115s closest.22...ok 115s closest.23...ok 115s 115s ########################################################### 115s # 115s # K CLOSEST HITS TESTS 115s # 115s ########################################################### 115s 115s kclosest.t1...ok 115s kclosest.t2...ok 115s kclosest.t3...ok 115s kclosest.t4...ok 115s kclosest.t5...ok 115s kclosest.t6...ok 115s kclosest.t7...ok 115s kclosest.t8...ok 115s kclosest.t9...ok 115s kclosest.t10...ok 115s kclosest.t11...Warning: Fewer hits (5) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t12...Warning: Fewer hits (5) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s Warning: Fewer hits (3) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. 115s kclosest.t13...ok 115s kclosest.t14...Warning: Fewer hits (1) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t15...Warning: Fewer hits (11) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t16...ok 115s kclosest.t17...Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t18...Warning: Fewer hits (11) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t19...Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t20...Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t21...Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t22...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t23...Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s kclosest.t24...ok 115s kclosest.t25...ok 115s kclosest.t26...Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t27...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s ok 115s kclosest.t28...Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 115s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 117s ok 117s kclosest.t29...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 117s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 117s ok 117s kclosest.t30...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. 117s ok 117s kclosest.t31...ok 117s kclosest.t32...ok 117s kclosest.t33...ok 117s kclosest.t34...ok 117s kclosest.t35...ok 117s kclosest.t36...ok 117s kclosest.t37...ok 117s kclosest.t38...ok 117s kclosest.t39...ok 117s kclosest.t40...ok 117s kclosest.t41...ok 117s kclosest.t42...ok 117s kclosest.t43...ok 117s kclosest.t44...ok 117s kclosest.t45...ok 117s Testing bedtools cluster: 117s cluster.t1...ok 117s cluster.t2...ok 117s Testing bedtools complement: 117s complement.t1...ok 117s complement.t2...ok 117s complement.t3...ok 117s complement.t4...ok 117s complement.t5...ok 117s complement.t6...ok 117s complement.t7...ok 117s complement.t8...ok 117s complement.t9...ok 117s complement.t9...ok 117s complement.t10...ok 117s Testing bedtools coverage: 117s coverage.t1...ok 117s coverage.t1b...ok 117s coverage.t2...ok 117s coverage.t2b...ok 117s coverage.t3...ok 117s coverage.t3b...ok 117s coverage.t4...ok 117s coverage.t4b...ok 117s coverage.t5...ok 117s coverage.t5b...ok 117s coverage.t6...ok 117s coverage.t6b...ok 117s coverage.t7...ok 117s coverage.t7b...ok 117s coverage.t8...ok 117s coverage.t8b...ok 117s coverage.t9...ok 117s coverage.t9b...ok 117s coverage.t10...ok 117s coverage.t10b...ok 117s coverage.t11...ok 117s coverage.t11b...ok 117s coverage.t12...ok 117s coverage.t12b...ok 117s coverage.t13...ok 117s coverage.t13b...ok 117s coverage.t14...ok 117s coverage.t14b...ok 117s coverage.t15...ok 117s coverage.t15b...ok 117s coverage.t16...ok 117s coverage.t16b...ok 117s coverage.t17...ok 117s coverage.t17b...ok 117s coverage.t18...ok 117s coverage.t18b...ok 117s coverage.t19...ok 117s coverage.t19b...ok 117s coverage.t20...ok 117s Testing bedtools expand: 117s expand.t1...ok 117s expand.t2...ok 117s expand.t3...ok 117s Testing bedtools fisher: 117s fisher.t1...ok 117s fisher.t2...ok 117s fisher.t3...ok 117s fisher.t4...ok 117s fisher.t5...ok 117s fisher.t6...ok 117s Testing bedtools flank: 117s flank.t1...ok 117s flank.t2...ok 117s flank.t3...ok 117s flank.t4...ok 117s flank.t5...ok 117s flank.t6...ok 117s flank.t7...ok 117s flank.t8...ok 117s flank.t9...ok 117s flank.t10...ok 117s flank.t11...ok 117s Testing bedtools general: 117s general.t01...ok 117s general.t02...ok 117s general.t03...ok 117s general.t05...ok 117s general.t06...ok 117s general.t07...ok 117s general.t08...ok 117s general.t09...ok 117s general.t10...ok 117s general.t11...ok 117s general.t12...ok 117s general.t13...ok 117s general.t14...ok 117s general.15...ok 117s general.t16...ok 117s general.t17...ok 117s general.t18...ok 117s general.t19...ok 117s general.t20...ok 117s general.t21...ok 117s general.22...ok 117s general.t23...ok 117s general.t24...ok 117s general.t25...ok 117s general.t26...ok 117s general.t27...ok 117s general.t28...ok 117s general.29...ok 117s general.t30...ok 117s general.t31...ok 117s general.t32...ok 117s general.t33...ok 117s general.t34...ok 117s general.t35...ok 117s general.36...ok 117s general.t37...ok 117s general.t38...ok 117s general.t39...ok 117s general.t40...ok 117s general.t41...ok 117s general.t42...ok 117s general.t43...ok 117s general.t44...ok 117s general.t45...ok 117s general.t46...ok 117s Testing bedtools genomecov: 117s genomecov.t1...ok 117s genomecov.t2...ok 117s genomecov.t3...ok 117s genomecov.t4...ok 117s genomecov.t5...ok 117s genomecov.t6...ok 117s genomecov.t7...ok 117s genomecov.t8...ok 117s genomecov.t9...ok 117s genomecov.t10...ok 117s genomecov.t11...ok 117s genomecov.t12...ok 117s genomecov.t13...ok 117s genomecov.t14...ok 117s genomecov.t15...ok 117s genomecov.t16...ok 117s genomecov.t17...ok 117s genomecov.t18...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. 118s ok 118s Testing bedtools getfasta: 118s getfasta.t01...ok 118s getfasta.t02...ok 118s getfasta.t03...ok 118s getfasta.t04...ok 118s getfasta.t05...ok 118s getfasta.t06...ok 118s getfasta.t07...ok 118s getfasta.t08...ok 118s getfasta.t09...ok 119s getfasta.t10...ok 119s getfasta.t11...ok 119s getfasta.t12a...ok 119s getfasta.t12a...ok 119s getfasta.t12b...ok 119s getfasta.t13a...ok 119s getfasta.t13b...ok 119s getfasta.t13c...ok 119s getfasta.t14...ok 119s getfasta.t15...ok 119s getfasta.t134..ok 119s getfasta.t16..ok 119s getfasta.t17..ok 119s getfasta.t18...ok 119s Testing bedtools groupby: 119s groupby.t1...ok 119s groupby.t2...ok 119s groupby.t3...ok 119s groupby.t4...ok 119s groupby.t5...ok 119s groupby.t6...ok 119s groupby.t7...ok 119s groupby.t8...ok 119s groupby.t9...ok 119s groupby.t10...ok 119s groupby.t11...ok 119s groupby.t12...ok 119s groupby.t13...ok 119s groupby.t14...ok 119s groupby.t16...ok 119s groupby.t17...ok 119s groupby.t18...ok 119s groupby.t19...\c 119s ok 119s groupby.t20...\c 119s ok 119s Testing bedtools intersect: 119s intersect.t01...ok 119s intersect.t02...ok 119s intersect.t03...ok 119s intersect.t04...ok 119s intersect.t05...ok 119s intersect.t06...ok 119s intersect.t07...ok 119s intersect.t08...ok 119s intersect.t09...ok 119s intersect.t10...ok 119s intersect.t11...ok 119s intersect.t12...ok 119s intersect.t13...ok 119s intersect.t14...ok 119s intersect.t15...ok 119s intersect.t16...ok 119s intersect.t17...ok 119s intersect.t18...ok 119s intersect.t19...ok 119s intersect.t20...ok 119s intersect.t21...ok 119s intersect.t22...ok 119s intersect.t22.a...ok 119s intersect.t22.b...ok 119s intersect.t22.c...ok 119s intersect.t22.d...ok 119s intersect.t22.e...ok 119s intersect.t22.f...ok 119s intersect.t22.g...ok 119s intersect.t22.h...ok 119s intersect.t22.i...ok 119s intersect.t22.j...ok 119s intersect.t22.j...ok 119s intersect.t22.k...ok 119s intersect.t22.l...ok 119s intersect.t22.m...ok 119s intersect.t22.n...ok 119s intersect.t22.o...ok 119s intersect.t22.p...ok 119s intersect.t22.q...ok 119s intersect.t22.r...ok 119s intersect.t22.s...ok 119s intersect.t22.t...ok 119s intersect.t22.u...ok 119s intersect.t22.v...ok 119s intersect.t22.w...ok 119s intersect.t23...ok 119s intersect.t24...ok 119s intersect.t25...ok 119s intersect.t26...ok 119s intersect.t27...ok 119s intersect.t28...ok 119s intersect.t29...ok 119s intersect.t30...ok 119s intersect.t31...ok 119s intersect.t32...ok 119s intersect.t33...ok 119s intersect.t34...ok 119s intersect.t35...ok 119s intersect.t36...ok 119s intersect.t37...ok 119s intersect.t38...ok 119s intersect.t39...ok 119s intersect.t40...ok 119s intersect.t41...ok 119s intersect.t42...ok 119s intersect.t43...ok 119s intersect.t44...ok 119s intersect.t45...ok 119s intersect.t46...ok 119s intersect.t47...ok 119s intersect.t48...ok 119s intersect.t49...ok 119s intersect.t50...ok 119s intersect.t51...ok 119s intersect.t52...ok 119s intersect.t53...ok 119s intersect.t54...ok 119s intersect.t55...ok 119s intersect.t56...ok 119s intersect.t57...ok 119s intersect.t58...ok 119s intersect.t59...ok 119s intersect.t60...ok 119s intersect.t61...ok 119s intersect.t62...ok 119s intersect.t63...ok 119s intersect.t64...ok 119s intersect.t65...ok 119s intersect.t66...ok 119s intersect.t67...ok 119s intersect.t68...ok 119s intersect.t69...ok 119s intersect.t70...ok 119s intersect.t71...ok 119s intersect.t72...ok 119s intersect.t73...ok 119s intersect.t74...ok 119s intersect.t75...ok 119s intersect.t76...ok 119s intersect.t77...ok 119s intersect.t78...ok 119s intersect.t79...ok 119s intersect.t80...ok 119s intersect.t81...ok 119s intersect.t82...ok 119s intersect.t83...ok 119s intersect.new.t01...ok 119s intersect.new.t02...ok 119s intersect.new.t03...ok 119s intersect.new.t04...ok 119s intersect.new.t05...ok 119s intersect.new.t06...ok 119s intersect.new.t07...ok 119s intersect.new.t08...ok 119s intersect.new.t09...ok 119s intersect.new.t10...ok 119s intersect.new.t11...ok 120s intersect.new.t12...ok 120s intersect.new.t13...ok 120s intersect.new.t14...ok 120s intersect.new.t15...ok 120s intersect.new.t16...ok 120s intersect.new.t17...ok 120s intersect.new.t18...ok 120s intersect.new.t19...ok 120s intersect.new.t20...ok 120s intersect.new.t20.b...ok 120s intersect.new.t20.c...ok 120s intersect.new.t21...ok 120s intersect.new.t22...ok 120s intersect.new.t23...ok 120s intersect.new.t24...ok 120s intersect.new.t25...ok 120s intersect.new.t26...ok 120s intersect.new.t27...ok 120s intersect.new.t28...ok 120s intersect.new.t29...ok 120s intersect.new.t30...ok 120s intersect.new.t31...ok 120s intersect.new.t32...ok 120s intersect.new.t33...ok 120s intersect.new.t34...ok 120s intersect.new.t35...ok 121s intersect.new.t36...ok 121s intersect.new.t37...ok 121s intersect.new.t38...ok 121s intersect.new.t39...ok 121s intersect.new.t40...ok 121s intersect.new.t41...ok 121s intersect.new.t42...ok 121s intersect.new.t43...ok 121s intersect.new.t44...ok 121s intersect.new.t45...ok 121s intersect.new.t46...ok 121s intersect.new.t47...ok 121s intersect.new.t48...ok 121s intersect.new.t49...ok 121s intersect.new.t50...ok 121s intersect.new.t51...ok 121s intersect.new.t52...ok 121s intersect.new.t53...ok 121s intersect.new.t54...ok 121s intersect.new.t55...ok 121s intersect.new.t56...ok 121s intersect.new.t57...ok 121s intersect.new.t58...ok 121s intersect.new.t59...ok 121s intersect.new.t60...ok 121s intersect.new.t61...ok 121s intersect.new.t62...ok 121s intersect.new.t63...ok 121s intersect.new.t64...ok 121s intersect.new.t65...ok 121s intersect.new.t66...ok 121s intersect.new.t67a...ok 121s intersect.new.t67b...ok 121s intersect.new.t68a...ok 121s intersect.new.t68b...ok 121s intersect.new.t69...ok 121s intersect.new.t70...ok 121s intersect.new.t71...ok 121s intersect.new.t72...ok 121s intersect.new.t73...ok 121s intersect.new.t74...ok 121s intersect.new.t75...ok 121s intersect.new.t76...ok 121s intersect.new.t77...ok 121s intersect.new.t78...ok 121s intersect.new.t79...ok 121s intersect.new.t80...ok 121s intersect.new.t81...ok 121s 121s ########################################################### 121s # 121s # MULTIPLE DATABASE INTERSECTION 121s # 121s ########################################################### 121s 121s intersect.t01...ok 121s intersect.t02...ok 121s intersect.t03...ok 121s intersect.t04...ok 121s intersect.t05...ok 121s intersect.t06...ok 121s intersect.t07...ok 121s intersect.t08...ok 121s intersect.t09...ok 121s intersect.t10...ok 121s intersect.t11...ok 121s intersect.t12...ok 121s intersect.t13...ok 121s intersect.t14...ok 121s intersect.t15...ok 121s intersect.t16...ok 121s intersect.t17...ok 121s intersect.t18...ok 121s intersect.t13...ok 121s intersect.t19...ok 121s intersect.t20...ok 121s intersect.t21...ok 121s intersect.t22...ok 121s intersect.t23...ok 121s intersect.t24...ok 121s 121s ########################################################### 121s # 121s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 121s # 121s ########################################################### 121s 121s intersect.t01...ok 121s intersect.t02...ok 121s intersect.t03...ok 121s intersect.t04...ok 121s intersect.t05...ok 121s intersect.t06...ok 121s intersect.t07...ok 121s intersect.t08...ok 121s intersect.t09...ok 121s intersect.t10...ok 121s intersect.t11...ok 121s intersect.t12...ok 121s intersect.t13...ok 122s intersect.t14...ok 122s intersect.t15...ok 122s intersect.t16...ok 122s intersect.t17...ok 122s intersect.t18...ok 122s intersect.t19...ok 122s intersect.20...ok 122s intersect.21...ok 122s intersect.22...ok 122s intersect.23...ok 122s Testing bedtools jaccard: 122s jaccard.t01...ok 122s jaccard.t02...ok 122s jaccard.t03...ok 122s jaccard.t05...ok 122s jaccard.t06...ok 122s jaccard.t07...ok 122s jaccard.t08...ok 122s jaccard.t09...ok 122s jaccard.t10...ok 122s jaccard.t11...ok 122s jaccard.t12...ok 122s jaccard.t13...ok 122s jaccard.t14...ok 122s jaccard.t15...ok 122s jaccard.t16...ok 122s Testing bedtools makewindows: 122s makewindows.t01...ok 122s makewindows.t02...ok 122s makewindows.t03...ok 122s makewindows.t04...ok 122s makewindows.t05...ok 122s makewindows.t06...ok 122s makewindows.t07...ok 122s makewindows.t08...ok 122s makewindows.t09...ok 122s Testing bedtools map: 122s map.t01...ok 122s map.t02...ok 122s map.t03...ok 122s map.t04...ok 122s map.t05...ok 122s map.t06...ok 122s map.t07...ok 122s map.t08...ok 122s map.t09...ok 122s map.t10...ok 122s map.t11...ok 122s map.t12...ok 122s map.t13...ok 122s map.t14...ok 122s map.t15...ok 122s map.t16...ok 122s map.t17...ok 122s map.t18...ok 122s map.t19...ok 122s map.t20...ok 122s map.t21...ok 122s map.t22..ok 122s map.t23..ok 122s map.t24..ok 122s map.t25..ok 122s map.t26..ok 122s map.t27..ok 122s map.t28..ok 122s map.t29..ok 122s map.t30..ok 122s map.t31..ok 122s map.t32..ok 122s map.t33..ok 122s map.t33..ok 122s map.t33..ok 122s map.t34..ok 122s map.t35..ok 122s map.t36..ok 122s map.t37..ok 122s map.t38..ok 122s map.t39..ok 122s map.t40..ok 122s map.t41..ok 122s map.t42..ok 122s map.t43..ok 122s map.t44...ok 122s map.t45...ok 122s map.t46...ok 122s map.t47...ok 122s map.t48...ok 122s map.t49...ok 122s map.t50...ok 122s map.t51...ok 122s map.t52...ok 122s map.t53...ok 122s map.t54...ok 122s map.t55...ok 122s Testing bedtools merge: 122s merge.t1...ok 122s merge.t2...ok 122s merge.t3...ok 122s merge.t4...ok 122s merge.t5...ok 122s merge.t6...ok 122s merge.t7...ok 122s merge.t8...ok 122s merge.t9a...ok 122s merge.t9b...ok 122s merge.t10...ok 122s merge.t11...ok 122s merge.t12...ok 122s merge.t13...ok 122s merge.t14...ok 122s merge.t15...ok 122s merge.t16...ok 122s merge.t17...ok 122s merge.t18...ok 122s merge.t19...ok 122s merge.t20...ok 122s merge.t21...ok 122s merge.t22...ok 122s merge.t23a...ok 122s merge.t23b...ok 122s merge.t24...ok 122s merge.t25...ok 122s merge.t26...ok 122s merge.t27...ok 122s merge.t28...ok 122s merge.t29...ok 122s merge.t30...ok 122s merge.t31...ok 122s merge.t32...ok 122s merge.t33...ok 122s merge.t34...ok 122s merge.t35...ok 122s merge.t36...ok 122s merge.t37...ok 122s merge.t38...ok 122s merge.t39...ok 122s merge.t40...ok 122s merge.t41...ok 122s merge.t42...ok 122s merge.t43...ok 122s merge.t44a...ok 122s merge.t44b...skipped - could not find vcfSVtest.2.vcf 122s merge.t45...ok 122s merge.t46...ok 122s merge.t47...ok 122s merge.t48...ok 122s merge.t49...ok 122s merge.t50...ok 122s Testing bedtools multicov: 122s multicov.t1...ok 122s multicov.t2...ok 122s multicov.t3...ok 122s multicov.t4...ok 122s multicov.t5...ok 122s multicov.t6...ok 122s multicov.t7...ok 122s multicov.t8...ok 122s multicov.t9...ok 122s multicov.t10...ok 122s Testing bedtools negativecontrol: 122s Testing bedtools reldist: 122s reldist.t01...ok 122s reldist.t02...ok 125s reldist.t03...ok 125s autopkgtest [02:02:31]: test run-unit-test: -----------------------] 125s reldist.t02...ok 125s Testing bedtools sample: 125s sample.t01...ok 125s sample.new.t02...ok 125s sample.new.t03...ok 125s sample.new.t04...ok 125s sample.new.t05...ok 125s sample.new.t06...ok 125s sample.new.t07...ok 125s sample.new.t08...ok 125s sample.new.t09...ok 125s Testing bedtools shift: 125s shift.t1...ok 125s shift.t2...ok 125s shift.t3...ok 125s shift.t3...ok 125s shift.t4...ok 125s shift.t5...ok 125s shift.t6...ok 125s shift.t7...ok 125s shift.t8...ok 125s shift.t9...ok 125s shift.t10...ok 125s shift.t11...ok 125s Testing bedtools shuffle: 125s shuffle.t1...ok 125s shuffle.t2...ok 125s shuffle.t3...ok 125s shuffle.t4...ok 125s shuffle.t5...ok 125s shuffle.t6...ok 125s Testing bedtools slop: 125s slop.t1...ok 125s slop.t2...ok 125s slop.t3...ok 125s slop.t4...ok 125s slop.t5...ok 125s slop.t6...ok 125s slop.t7...ok 125s slop.t8...ok 125s slop.t9...ok 125s slop.t10...ok 125s slop.t11...ok 125s slop.t12...ok 125s slop.t13...ok 125s slop.t14...ok 125s slop.t15...ok 125s slop.t16...ok 125s slop.t17...ok 125s slop.t18...ok 125s slop.t19...ok 125s slop.t20...ok 125s slop.t21...ok 125s slop.t22...ok 125s Testing bedtools sort: 125s sort.t01...ok 125s sort.t02...ok 125s sort.t03...ok 125s sort.t04...ok 125s sort.t05...ok 125s sort.t06...ok 125s sort.t07...ok 125s sort.t08...ok 125s sort.t09...ok 125s sort.t10...ok 125s Testing bedtools spacing: 125s spacing.t01...ok 125s Testing bedtools split: 125s split.01.size...ok 125s split.02.simple...ok 125s spliit.03.simple...ok 125s Testing bedtools subtract: 125s subtract.t1...ok 125s subtract.t2...ok 125s subtract.t3...ok 125s subtract.t4...ok 125s subtract.t5...ok 125s subtract.t6...ok 125s subtract.t7...ok 125s subtract.t8...ok 125s subtract.t9...ok 125s subtract.t10...ok 125s subtract.t11...ok 125s subtract.t12...ok 125s subtract.t13...ok 125s subtract.t14...ok 125s subtract.t15...ok 125s subtract.t16...ok 125s subtract.t17...ok 125s subtract.t18...ok 125s subtract.t19...ok 125s subtract.t20...ok 125s subtract.t21...ok 125s 125s 125s -------------------------- 125s Test Results 125s -------------------------- 125s Tools passing: bamtobed bamtofastq bed12tobed6 bedtobam bigchroms closest cluster complement coverage expand fisher flank general genomecov getfasta groupby intersect jaccard makewindows map merge multicov reldist sample shift shuffle slop sort spacing split subtract 125s Tools failing: negativecontrol 125s NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, 125s something went wrong with this test script. 126s run-unit-test PASS 126s autopkgtest [02:02:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 126s autopkgtest [02:02:34]: @@@@@@@@@@@@@@@@@@@@ summary 126s run-unit-test PASS