0s autopkgtest [18:49:20]: starting date and time: 2025-12-03 18:49:20+0000 0s autopkgtest [18:49:20]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:49:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4bfjhxr_/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-3.secgroup --name adt-resolute-amd64-bedtools-20251203-184920-juju-7f2275-prod-proposed-migration-environment-15-a93863be-2b02-4289-8025-0d84d6abf7a9 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-bedtools-20251203-184920-juju-7f2275-prod-proposed-migration-environment-15-a93863be-2b02-4289-8025-0d84d6abf7a9 from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID 32968f47-375b-4278-ba47-0724b7286e54)... 53s autopkgtest [18:50:13]: testbed dpkg architecture: amd64 53s autopkgtest [18:50:13]: testbed apt version: 3.1.12 53s autopkgtest [18:50:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [18:50:14]: testbed release detected to be: None 54s autopkgtest [18:50:14]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 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 55s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [954 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [157 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [161 kB] 56s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [220 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6252 B] 56s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 56s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [764 kB] 56s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [349 kB] 56s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.0 kB] 56s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 56s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 56s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [764 B] 60s Fetched 2796 kB in 2s (1355 kB/s) 61s Reading package lists... 62s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 62s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 62s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Reading package lists... 63s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Calculating upgrade... 64s The following packages will be upgraded: 64s libpython3-stdlib python3 python3-gdbm python3-minimal 64s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 72.9 kB of archives. 64s After this operation, 2048 B of additional disk space will be used. 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 64s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 65s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 65s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 65s dpkg-preconfigure: unable to re-open stdin: No such file or directory 65s Fetched 72.9 kB in 0s (201 kB/s) 65s (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 ... 123179 files and directories currently installed.) 65s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 65s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 65s Setting up python3-minimal (3.13.9-2) ... 66s (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 ... 123179 files and directories currently installed.) 66s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 66s running python pre-rtupdate hooks for python3.13... 66s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 66s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 66s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 66s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 66s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 66s Setting up python3-gdbm (3.13.9-2) ... 66s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 66s Setting up python3 (3.13.9-2) ... 66s running python rtupdate hooks for python3.13... 66s running python post-rtupdate hooks for python3.13... 66s Processing triggers for man-db (2.13.1-1) ... 67s autopkgtest [18:50:27]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Solving dependencies... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [18:50:31]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 71s autopkgtest [18:50:31]: @@@@@@@@@@@@@@@@@@@@ apt-source bedtools 77s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (dsc) [2230 B] 77s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (tar) [14.5 MB] 77s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (diff) [14.5 kB] 77s gpgv: Signature made Mon Dec 4 19:20:23 2023 UTC 77s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 77s gpgv: issuer "emollier@debian.org" 77s gpgv: Can't check signature: No public key 77s dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found 78s autopkgtest [18:50:38]: testing package bedtools version 2.31.1+dfsg-2 78s autopkgtest [18:50:38]: build not needed 84s autopkgtest [18:50:44]: test run-unit-test: preparing testbed 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Solving dependencies... 86s The following NEW packages will be installed: 86s bedtools bedtools-test libdeflate0 libhtscodecs2 tabix 86s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 19.6 MB of archives. 86s After this operation, 52.4 MB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu resolute/universe amd64 bedtools amd64 2.31.1+dfsg-2 [674 kB] 86s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 bedtools-test all 2.31.1+dfsg-2 [18.2 MB] 88s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 88s Get:4 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 88s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 tabix amd64 1.22.1+ds2-1 [535 kB] 88s Fetched 19.6 MB in 2s (7877 kB/s) 89s Selecting previously unselected package bedtools. 89s (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 ... 123179 files and directories currently installed.) 89s Preparing to unpack .../bedtools_2.31.1+dfsg-2_amd64.deb ... 89s Unpacking bedtools (2.31.1+dfsg-2) ... 89s Selecting previously unselected package bedtools-test. 89s Preparing to unpack .../bedtools-test_2.31.1+dfsg-2_all.deb ... 89s Unpacking bedtools-test (2.31.1+dfsg-2) ... 89s Selecting previously unselected package libdeflate0:amd64. 89s Preparing to unpack .../libdeflate0_1.23-2_amd64.deb ... 89s Unpacking libdeflate0:amd64 (1.23-2) ... 89s Selecting previously unselected package libhtscodecs2:amd64. 89s Preparing to unpack .../libhtscodecs2_1.6.1-2_amd64.deb ... 89s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 89s Selecting previously unselected package tabix. 89s Preparing to unpack .../tabix_1.22.1+ds2-1_amd64.deb ... 89s Unpacking tabix (1.22.1+ds2-1) ... 89s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 89s Setting up libdeflate0:amd64 (1.23-2) ... 89s Setting up bedtools-test (2.31.1+dfsg-2) ... 89s Setting up tabix (1.22.1+ds2-1) ... 89s Setting up bedtools (2.31.1+dfsg-2) ... 89s Processing triggers for man-db (2.13.1-1) ... 89s Processing triggers for libc-bin (2.42-2ubuntu2) ... 91s autopkgtest [18:50:51]: test run-unit-test: [----------------------- 91s Testing bedtools bamtobed: 91s bamtobed.t1...ok 91s bamtobed.t2...ok 91s bamtobed.t3...ok 91s bamtobed.t4...ok 91s bamtobed.t5...ok 91s bamtobed.t6...ok 91s bamtobed.t7...ok 91s bamtobed.t8...ok 91s bamtobed.t9...ok 91s bamtobed.t10...ok 91s bamtobed.t9...ok 91s bamtobed.t11...ok 91s bamtobed.t12..ok 91s bamtobed.t13..ok 91s Testing bedtools bamtofastq: 91s ok 91s ok 91s Testing bedtools bed12tobed6: 91s bed12tobed6.t1...ok 91s bed12tobed6.t2...ok 91s bed12tobed6.t3...ok 91s bed12tobed6.t4...ok 91s bed12tobed6.t5...ok 91s Testing bedtools bedtobam: 91s bedtobam.t1...ok 91s Testing bedtools bigchroms: 91s bigchroms.t01...ok 91s bigchroms.t02...ok 91s bigchroms.t03... skip set env var 'BT_NO_BIG_FILES' to run this test 91s bigchroms.t04... merge ok 91s bigchroms.t05... closest ok 91s Testing bedtools closest: 91s closest.t1...ok 91s closest.t2...ok 91s closest.t3...ok 91s closest.t4...ok 91s closest.t5...ok 91s closest.t6...ok 91s closest.t7...ok 91s closest.t8...ok 91s closest.t9...ok 91s closest.t10...ok 91s closest.t11...ok 91s closest.t13...ok 91s closest.t14...ok 91s closest.t15...ok 91s closest.t16...ok 91s closest.t17...ok 91s closest.t18...ok 91s closest.t19...ok 91s closest.t20...ok 91s closest.t21...ok 91s closest.t22...ok 91s closest.t23...ok 91s closest.t24...ok 91s closest.t25...ok 91s closest.t26...ok 91s closest.t27...ok 91s closest.t28...ok 91s closest.t29...ok 91s closest.t30...ok 91s closest.t31...ok 91s closest.t32...ok 91s closest.t33...ok 91s closest.t34...ok 91s closest.t35...ok 91s closest.t36...ok 91s closest.t37...ok 91s closest.t38...ok 91s closest.t39...ok 91s closest.t40...ok 91s closest.t41...ok 91s closest.t42...ok 91s closest.t43...ok 91s closest.t44...ok 91s closest.t45...ok 91s closest.t46...ok 91s closest.t47...ok 91s closest.t48...ok 91s closest.t49...ok 91s closest.t50...ok 91s closest.t51...ok 91s closest.t52...ok 91s closest.t53...ok 91s closest.t54...ok 91s closest.t55...ok 91s closest.t56...ok 91s closest.t57...ok 91s closest.t58...ok 91s closest.t59...ok 91s closest.t60...ok 91s closest.t61...ok 92s closest.t62...ok 92s closest.t63...ok 92s closest.t64...ok 92s closest.t65...ok 92s closest.t66...ok 92s closest.t67...ok 92s closest.t68...ok 92s closest.t69...ok 92s closest.t70...ok 92s closest.t71...ok 92s 92s ########################################################### 92s # 92s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 92s # 92s ########################################################### 92s 92s closest.t01...ok 92s closest.t02...ok 92s closest.t03...ok 92s closest.t04...ok 92s closest.t05...ok 92s closest.t06...ok 92s closest.t07...ok 92s closest.t08...ok 92s closest.t09...ok 92s closest.t10...ok 92s closest.t11...ok 92s closest.t12...ok 92s closest.t13...ok 92s closest.t14...ok 92s closest.t15...ok 92s closest.t16...ok 92s closest.t17...ok 92s closest.t18...ok 92s closest.t19...ok 92s closest.20...ok 92s closest.21...ok 92s closest.22...ok 92s closest.23...ok 92s 92s ########################################################### 92s # 92s # K CLOSEST HITS TESTS 92s # 92s ########################################################### 92s 92s kclosest.t1...ok 92s kclosest.t2...ok 92s kclosest.t3...ok 92s kclosest.t4...ok 92s kclosest.t5...ok 92s kclosest.t6...ok 92s kclosest.t7...ok 92s kclosest.t8...ok 92s kclosest.t9...ok 92s kclosest.t10...ok 92s 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. 92s ok 92s 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. 92s ok 92s kclosest.t13...Warning: Fewer hits (3) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s ok 92s 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. 92s ok 92s kclosest.t16...ok 92s 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. 92s ok 92s 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. 92s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s kclosest.t24...Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s kclosest.t25...Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s 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. 92s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s kclosest.t30...ok 92s kclosest.t31...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s kclosest.t32...Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. 92s ok 92s kclosest.t33...ok 92s kclosest.t34...ok 92s kclosest.t35...ok 92s kclosest.t36...ok 92s kclosest.t37...ok 92s kclosest.t38...ok 92s kclosest.t39...ok 92s kclosest.t40...ok 92s kclosest.t41...ok 92s kclosest.t42...ok 92s kclosest.t43...ok 92s kclosest.t44...ok 92s kclosest.t45...ok 92s Testing bedtools cluster: 92s cluster.t1...ok 92s cluster.t2...ok 92s Testing bedtools complement: 92s complement.t1...ok 92s complement.t2...ok 92s complement.t3...ok 92s complement.t4...ok 92s complement.t5...ok 92s complement.t6...ok 92s complement.t7...ok 92s complement.t8...ok 92s complement.t9...ok 92s complement.t9...ok 92s complement.t10...ok 92s Testing bedtools coverage: 92s coverage.t1...ok 92s coverage.t1b...ok 92s coverage.t2...ok 92s coverage.t2b...ok 92s coverage.t3...ok 92s coverage.t3b...ok 92s coverage.t4...ok 92s coverage.t4b...ok 92s coverage.t5...ok 92s coverage.t5b...ok 92s coverage.t6...ok 92s coverage.t6b...ok 92s coverage.t7...ok 92s coverage.t7b...ok 92s coverage.t8...ok 92s coverage.t8b...ok 92s coverage.t9...ok 92s coverage.t9b...ok 92s coverage.t10...ok 92s coverage.t10b...ok 92s coverage.t11...ok 92s coverage.t11b...ok 92s coverage.t12...ok 92s coverage.t12b...ok 92s coverage.t13...ok 92s coverage.t13b...ok 92s coverage.t14...ok 92s coverage.t14b...ok 92s coverage.t15...ok 92s coverage.t15b...ok 92s coverage.t16...ok 92s coverage.t16b...ok 92s coverage.t17...ok 92s coverage.t17b...ok 92s coverage.t18...ok 92s coverage.t18b...ok 92s coverage.t19...ok 92s coverage.t19b...ok 92s coverage.t20...ok 92s Testing bedtools expand: 92s expand.t1...ok 92s expand.t2...ok 92s expand.t3...ok 92s Testing bedtools fisher: 92s fisher.t1...ok 92s fisher.t2...ok 92s fisher.t3...ok 92s fisher.t4...ok 92s fisher.t5...ok 92s fisher.t6...ok 92s Testing bedtools flank: 92s flank.t1...ok 92s flank.t2...ok 92s flank.t3...ok 92s flank.t4...ok 92s flank.t5...ok 92s flank.t6...ok 92s flank.t7...ok 92s flank.t8...ok 92s flank.t9...ok 92s flank.t10...ok 92s flank.t11...ok 92s Testing bedtools general: 92s general.t01...ok 92s general.t02...ok 92s general.t03...ok 92s general.t05...ok 92s general.t06...ok 92s general.t07...ok 92s general.t08...ok 92s general.t09...ok 93s general.t10...ok 93s general.t11...ok 93s general.t12...ok 93s general.t13...ok 93s general.t14...ok 93s general.15...ok 93s general.t16...ok 93s general.t17...ok 93s general.t18...ok 93s general.t19...ok 93s general.t20...ok 93s general.t21...ok 93s general.22...ok 93s general.t23...ok 93s general.t24...ok 93s general.t25...ok 93s general.t26...ok 93s general.t27...ok 93s general.t28...ok 93s general.29...ok 93s general.t30...ok 93s general.t31...ok 93s general.t32...ok 93s general.t33...ok 93s general.t34...ok 93s general.t35...ok 93s general.36...ok 93s general.t37...ok 93s general.t38...ok 93s general.t39...ok 93s general.t40...ok 93s general.t41...ok 93s general.t42...ok 93s general.t43...ok 93s general.t44...ok 93s general.t45...ok 93s general.t46...ok 93s Testing bedtools genomecov: 93s genomecov.t1...ok 93s genomecov.t2...ok 93s genomecov.t3...ok 93s genomecov.t4...ok 93s genomecov.t5...ok 93s genomecov.t6...ok 93s genomecov.t7...ok 93s genomecov.t8...ok 93s genomecov.t9...ok 93s genomecov.t10...ok 93s genomecov.t11...ok 93s genomecov.t12...ok 93s genomecov.t13...ok 93s genomecov.t14...ok 93s genomecov.t15...ok 93s genomecov.t16...ok 93s genomecov.t17...ok 94s genomecov.t18...ok 94s Testing bedtools getfasta: 94s getfasta.t01...ok 94s getfasta.t02...ok 94s getfasta.t03...ok 94s getfasta.t04...ok 94s getfasta.t05...ok 94s getfasta.t06...ok 94s getfasta.t07...ok 94s getfasta.t08...ok 94s getfasta.t09...ok 95s getfasta.t10...ok 95s getfasta.t11...ok 95s getfasta.t12a...ok 95s getfasta.t12a...ok 95s getfasta.t12b...ok 95s getfasta.t13a...ok 95s getfasta.t13b...ok 95s getfasta.t13c...ok 95s getfasta.t14...ok 95s getfasta.t15...ok 95s getfasta.t134..ok 95s getfasta.t16..ok 95s getfasta.t17..ok 95s getfasta.t18...ok 95s Testing bedtools groupby: 95s groupby.t1...ok 95s groupby.t2...ok 95s groupby.t3...ok 95s groupby.t4...ok 95s groupby.t5...ok 95s groupby.t6...ok 95s groupby.t7...ok 95s groupby.t8...ok 95s groupby.t9...ok 95s groupby.t10...ok 95s groupby.t11...ok 95s groupby.t12...ok 95s groupby.t13...ok 95s groupby.t14...ok 95s groupby.t16...ok 95s groupby.t17...ok 95s groupby.t18...ok 95s groupby.t19...\c 95s ok 95s groupby.t20...\c 95s ok 95s Testing bedtools intersect: 95s intersect.t01...ok 95s intersect.t02...ok 95s intersect.t03...ok 95s intersect.t04...ok 95s intersect.t05...ok 95s intersect.t06...ok 95s intersect.t07...ok 95s intersect.t08...ok 96s intersect.t09...ok 96s intersect.t10...ok 96s intersect.t11...ok 96s intersect.t12...ok 96s intersect.t13...ok 96s intersect.t14...ok 96s intersect.t15...ok 96s intersect.t16...ok 96s intersect.t17...ok 96s intersect.t18...ok 96s intersect.t19...ok 96s intersect.t20...ok 96s intersect.t21...ok 96s intersect.t22...ok 96s intersect.t22.a...ok 96s intersect.t22.b...ok 96s intersect.t22.c...ok 96s intersect.t22.d...ok 96s intersect.t22.e...ok 96s intersect.t22.f...ok 96s intersect.t22.g...ok 96s intersect.t22.h...ok 96s intersect.t22.i...ok 96s intersect.t22.j...ok 96s intersect.t22.j...ok 96s intersect.t22.k...ok 96s intersect.t22.l...ok 96s intersect.t22.m...ok 96s intersect.t22.n...ok 96s intersect.t22.o...ok 96s intersect.t22.p...ok 96s intersect.t22.q...ok 96s intersect.t22.r...ok 96s intersect.t22.s...ok 96s intersect.t22.t...ok 96s intersect.t22.u...ok 96s intersect.t22.v...ok 96s intersect.t22.w...ok 96s intersect.t23...ok 96s intersect.t24...ok 96s intersect.t25...ok 96s intersect.t26...ok 96s intersect.t27...ok 96s intersect.t28...ok 96s intersect.t29...ok 96s intersect.t30...ok 96s intersect.t31...ok 96s intersect.t32...ok 96s intersect.t33...ok 96s intersect.t34...ok 96s intersect.t35...ok 96s intersect.t36...ok 96s intersect.t37...ok 96s intersect.t38...ok 96s intersect.t39...ok 96s intersect.t40...ok 96s intersect.t41...ok 96s intersect.t42...ok 96s intersect.t43...ok 96s intersect.t44...ok 96s intersect.t45...ok 96s intersect.t46...ok 96s intersect.t47...ok 96s intersect.t48...ok 96s intersect.t49...ok 96s intersect.t50...ok 96s intersect.t51...ok 96s intersect.t52...ok 96s intersect.t53...ok 96s intersect.t54...ok 96s intersect.t55...ok 96s intersect.t56...ok 96s intersect.t57...ok 96s intersect.t58...ok 96s intersect.t59...ok 96s intersect.t60...ok 96s intersect.t61...ok 96s intersect.t62...ok 96s intersect.t63...ok 96s intersect.t64...ok 96s intersect.t65...ok 96s intersect.t66...ok 96s intersect.t67...ok 96s intersect.t68...ok 96s intersect.t69...ok 96s intersect.t70...ok 96s intersect.t71...ok 96s intersect.t72...ok 96s intersect.t73...ok 96s intersect.t74...ok 96s intersect.t75...ok 96s intersect.t76...ok 96s intersect.t77...ok 96s intersect.t78...ok 96s intersect.t79...ok 96s intersect.t80...ok 96s intersect.t81...ok 96s intersect.t82...ok 96s intersect.t83...ok 96s intersect.new.t01...ok 96s intersect.new.t02...ok 96s intersect.new.t03...ok 96s intersect.new.t04...ok 96s intersect.new.t05...ok 96s intersect.new.t06...ok 96s intersect.new.t07...ok 96s intersect.new.t08...ok 96s intersect.new.t09...ok 96s intersect.new.t10...ok 96s intersect.new.t11...ok 96s intersect.new.t12...ok 96s intersect.new.t13...ok 96s intersect.new.t14...ok 96s intersect.new.t15...ok 96s intersect.new.t16...ok 96s intersect.new.t17...ok 96s intersect.new.t18...ok 96s intersect.new.t19...ok 96s intersect.new.t20...ok 96s intersect.new.t20.b...ok 96s intersect.new.t20.c...ok 96s intersect.new.t21...ok 96s intersect.new.t22...ok 96s intersect.new.t23...ok 96s intersect.new.t24...ok 96s intersect.new.t25...ok 97s intersect.new.t26...ok 97s intersect.new.t27...ok 97s intersect.new.t28...ok 97s intersect.new.t29...ok 97s intersect.new.t30...ok 97s intersect.new.t31...ok 97s intersect.new.t32...ok 97s intersect.new.t33...ok 97s intersect.new.t34...ok 97s intersect.new.t35...ok 97s intersect.new.t36...ok 97s intersect.new.t37...ok 97s intersect.new.t38...ok 97s intersect.new.t39...ok 97s intersect.new.t40...ok 97s intersect.new.t41...ok 97s intersect.new.t42...ok 98s intersect.new.t43...ok 98s intersect.new.t44...ok 98s intersect.new.t45...ok 98s intersect.new.t46...ok 98s intersect.new.t47...ok 98s intersect.new.t48...ok 98s intersect.new.t49...ok 98s intersect.new.t50...ok 98s intersect.new.t51...ok 98s intersect.new.t52...ok 98s intersect.new.t53...ok 98s intersect.new.t54...ok 98s intersect.new.t55...ok 98s intersect.new.t56...ok 98s intersect.new.t57...ok 98s intersect.new.t58...ok 98s intersect.new.t59...ok 98s intersect.new.t60...ok 98s intersect.new.t61...ok 98s intersect.new.t62...ok 98s intersect.new.t63...ok 98s intersect.new.t64...ok 98s intersect.new.t65...ok 98s intersect.new.t66...ok 98s intersect.new.t67a...ok 98s intersect.new.t67b...ok 98s intersect.new.t68a...ok 98s intersect.new.t68b...ok 98s intersect.new.t69...ok 98s intersect.new.t70...ok 98s intersect.new.t71...ok 98s intersect.new.t72...ok 98s intersect.new.t73...ok 98s intersect.new.t74...ok 98s intersect.new.t75...ok 98s intersect.new.t76...ok 98s intersect.new.t77...ok 98s intersect.new.t78...ok 98s intersect.new.t79...ok 98s intersect.new.t80...ok 98s intersect.new.t81...ok 98s 98s ########################################################### 98s # 98s # MULTIPLE DATABASE INTERSECTION 98s # 98s ########################################################### 98s 98s intersect.t01...ok 98s intersect.t02...ok 98s intersect.t03...ok 98s intersect.t04...ok 98s intersect.t05...ok 98s intersect.t06...ok 98s intersect.t07...ok 98s intersect.t08...ok 98s intersect.t09...ok 98s intersect.t10...ok 98s intersect.t11...ok 98s intersect.t12...ok 98s intersect.t13...ok 98s intersect.t14...ok 98s intersect.t15...ok 98s intersect.t16...ok 98s intersect.t17...ok 98s intersect.t18...ok 98s intersect.t13...ok 98s intersect.t19...ok 98s intersect.t20...ok 98s intersect.t21...ok 98s intersect.t22...ok 98s intersect.t23...ok 98s intersect.t24...ok 98s 98s ########################################################### 98s # 98s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 98s # 98s ########################################################### 98s 98s intersect.t01...ok 98s intersect.t02...ok 98s intersect.t03...ok 98s intersect.t04...ok 98s intersect.t05...ok 98s intersect.t06...ok 98s intersect.t07...ok 98s intersect.t08...ok 98s intersect.t09...ok 98s intersect.t10...ok 98s intersect.t11...ok 98s intersect.t12...ok 98s intersect.t13...ok 98s intersect.t14...ok 98s intersect.t15...ok 98s intersect.t16...ok 98s intersect.t17...ok 98s intersect.t18...ok 98s intersect.t19...ok 98s intersect.20...ok 98s intersect.21...ok 98s intersect.22...ok 98s intersect.23...ok 98s Testing bedtools jaccard: 98s jaccard.t01...ok 98s jaccard.t02...ok 98s jaccard.t03...ok 98s jaccard.t05...ok 98s jaccard.t06...ok 98s jaccard.t07...ok 98s jaccard.t08...ok 98s jaccard.t09...ok 98s jaccard.t10...ok 98s jaccard.t11...ok 98s jaccard.t12...ok 98s jaccard.t13...ok 98s jaccard.t14...ok 98s jaccard.t15...ok 98s jaccard.t16...ok 98s Testing bedtools makewindows: 98s makewindows.t01...ok 98s makewindows.t02...ok 98s makewindows.t03...ok 98s makewindows.t04...ok 98s makewindows.t05...ok 98s makewindows.t06...ok 98s makewindows.t07...ok 98s makewindows.t08...ok 98s makewindows.t09...ok 98s Testing bedtools map: 98s map.t01...ok 98s map.t02...ok 98s map.t03...ok 98s map.t04...ok 98s map.t05...ok 98s map.t06...ok 98s map.t07...ok 98s map.t08...ok 98s map.t09...ok 98s map.t10...ok 98s map.t11...ok 98s map.t12...ok 98s map.t13...ok 98s map.t14...ok 98s map.t15...ok 98s map.t16...ok 98s map.t17...ok 98s map.t18...ok 98s map.t19...ok 98s map.t20...ok 98s map.t21...ok 98s map.t22..ok 98s map.t23..ok 98s map.t24..ok 98s map.t25..ok 98s map.t26..ok 98s map.t27..ok 98s map.t28..ok 98s map.t29..ok 98s map.t30..ok 98s map.t31..ok 98s map.t32..ok 98s map.t33..ok 98s map.t33..ok 98s map.t33..ok 98s map.t34..ok 98s map.t35..ok 98s map.t36..ok 99s map.t37..ok 99s map.t38..ok 99s map.t39..ok 99s map.t40..ok 99s map.t41..ok 99s map.t42..ok 99s map.t43..ok 99s map.t44...ok 99s map.t45...ok 99s map.t46...ok 99s map.t47...ok 99s map.t48...ok 99s map.t49...ok 99s map.t50...ok 99s map.t51...ok 99s map.t52...ok 99s map.t53...ok 99s map.t54...ok 99s map.t55...ok 99s Testing bedtools merge: 99s merge.t1...ok 99s merge.t2...ok 99s merge.t3...ok 99s merge.t4...ok 99s merge.t5...ok 99s merge.t6...ok 99s merge.t7...ok 99s merge.t8...ok 99s merge.t9a...ok 99s merge.t9b...ok 99s merge.t10...ok 99s merge.t11...ok 99s merge.t12...ok 99s merge.t13...ok 99s merge.t14...ok 99s merge.t15...ok 99s merge.t16...ok 99s merge.t17...ok 99s merge.t18...ok 99s merge.t19...ok 99s merge.t20...ok 99s merge.t21...ok 99s merge.t22...ok 99s merge.t23a...ok 99s merge.t23b...ok 99s merge.t24...ok 99s merge.t25...ok 99s merge.t26...ok 99s merge.t27...ok 99s merge.t28...ok 99s merge.t29...ok 99s merge.t30...ok 99s merge.t31...ok 99s merge.t32...ok 99s merge.t33...ok 99s merge.t34...ok 99s merge.t35...ok 99s merge.t36...ok 99s merge.t37...ok 99s merge.t38...ok 99s merge.t39...ok 99s merge.t40...ok 99s merge.t41...ok 99s merge.t42...ok 99s merge.t43...ok 99s merge.t44a...ok 99s merge.t44b...skipped - could not find vcfSVtest.2.vcf 99s merge.t45...ok 99s merge.t46...ok 99s merge.t47...ok 99s merge.t48...ok 99s merge.t49...ok 99s merge.t50...ok 99s Testing bedtools multicov: 99s multicov.t1...ok 99s multicov.t2...ok 99s multicov.t3...ok 99s multicov.t4...ok 99s multicov.t5...ok 99s multicov.t6...ok 99s multicov.t7...ok 99s multicov.t8...ok 99s multicov.t9...ok 99s multicov.t10...ok 99s Testing bedtools negativecontrol: 99s Testing bedtools reldist: 99s reldist.t01...ok 99s reldist.t02...ok 99s reldist.t03...ok 99s reldist.t02...ok 99s Testing bedtools sample: 99s sample.t01...ok 99s sample.new.t02...ok 99s sample.new.t03...ok 99s sample.new.t04...ok 99s sample.new.t05...ok 99s sample.new.t06...ok 99s sample.new.t07...ok 99s sample.new.t08...ok 99s sample.new.t09...ok 99s Testing bedtools shift: 99s shift.t1...ok 99s shift.t2...ok 99s shift.t3...ok 99s shift.t3...ok 99s shift.t4...ok 99s shift.t5...ok 99s shift.t6...ok 99s shift.t7...ok 99s shift.t8...ok 99s shift.t9...ok 99s shift.t10...ok 99s shift.t11...ok 99s Testing bedtools shuffle: 99s shuffle.t1...ok 99s shuffle.t2...ok 99s shuffle.t3...ok 99s shuffle.t4...ok 99s shuffle.t5...ok 99s shuffle.t6...ok 99s Testing bedtools slop: 99s slop.t1...ok 99s slop.t2...ok 100s slop.t3...ok 100s slop.t4...ok 100s slop.t5...ok 100s slop.t6...ok 100s slop.t7...ok 100s slop.t8...ok 100s slop.t9...ok 100s slop.t10...ok 100s slop.t11...ok 100s slop.t12...ok 100s slop.t13...ok 100s slop.t14...ok 100s slop.t15...ok 100s slop.t16...ok 100s slop.t17...ok 100s slop.t18...ok 100s slop.t19...ok 100s slop.t20...ok 100s slop.t21...ok 100s slop.t22...ok 100s Testing bedtools sort: 100s sort.t01...ok 100s sort.t02...ok 100s sort.t03...ok 100s sort.t04...ok 100s sort.t05...ok 100s sort.t06...ok 100s sort.t07...ok 100s sort.t08...ok 100s sort.t09...ok 100s sort.t10...ok 100s Testing bedtools spacing: 100s spacing.t01...ok 100s Testing bedtools split: 100s split.01.size...ok 100s split.02.simple...ok 100s spliit.03.simple...ok 100s Testing bedtools subtract: 100s subtract.t1...ok 100s subtract.t2...ok 100s subtract.t3...ok 100s subtract.t4...ok 100s subtract.t5...ok 100s subtract.t6...ok 100s subtract.t7...ok 100s subtract.t8...ok 100s subtract.t9...ok 100s subtract.t10...ok 100s subtract.t11...ok 100s subtract.t12...ok 100s subtract.t13...ok 100s subtract.t14...ok 100s subtract.t15...ok 100s subtract.t16...ok 100s subtract.t17...ok 100s subtract.t18...ok 100s subtract.t19...ok 100s subtract.t20...ok 100s subtract.t21...ok 100s 100s 100s -------------------------- 100s Test Results 100s -------------------------- 100s 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 100s Tools failing: negativecontrol 100s NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, 100s something went wrong with this test script. 100s autopkgtest [18:51:00]: test run-unit-test: -----------------------] 101s run-unit-test PASS 101s autopkgtest [18:51:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 101s autopkgtest [18:51:01]: @@@@@@@@@@@@@@@@@@@@ summary 101s run-unit-test PASS