0s autopkgtest [14:29:08]: starting date and time: 2025-12-04 14:29:08+0000 0s autopkgtest [14:29:08]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:29:08]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.syv6u_h8/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-13.secgroup --name adt-resolute-arm64-bedtools-20251204-142049-juju-7f2275-prod-proposed-migration-environment-15-a4e9ab92-5021-4c38-bdb5-a85a4228443b --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-bedtools-20251204-142049-juju-7f2275-prod-proposed-migration-environment-15-a4e9ab92-5021-4c38-bdb5-a85a4228443b from image adt/ubuntu-resolute-arm64-server-20251204.img (UUID d10d485b-270b-4b77-bdc2-f40c1cd474cf)... 60s autopkgtest [14:30:08]: testbed dpkg architecture: arm64 61s autopkgtest [14:30:09]: testbed apt version: 3.1.12 61s autopkgtest [14:30:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [14:30:09]: testbed release detected to be: None 62s autopkgtest [14:30:10]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [158 kB] 64s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [952 kB] 64s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 64s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [228 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6632 B] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [120 B] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [758 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [20.6 kB] 64s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [8716 B] 64s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [644 B] 67s Fetched 2280 kB in 2s (1277 kB/s) 68s Reading package lists... 68s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 71s The following packages will be upgraded: 71s libpython3-stdlib python3 python3-gdbm python3-minimal 71s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 72.9 kB of archives. 71s After this operation, 2048 B of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.9-2 [28.1 kB] 71s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.9-2 [23.0 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.9-2 [10.8 kB] 71s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.13.9-2 [11.0 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 72.9 kB in 0s (208 kB/s) 72s (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 ... 88300 files and directories currently installed.) 72s Preparing to unpack .../python3-minimal_3.13.9-2_arm64.deb ... 72s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 72s Setting up python3-minimal (3.13.9-2) ... 72s (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 ... 88300 files and directories currently installed.) 72s Preparing to unpack .../python3_3.13.9-2_arm64.deb ... 72s running python pre-rtupdate hooks for python3.13... 72s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 72s Preparing to unpack .../libpython3-stdlib_3.13.9-2_arm64.deb ... 72s Unpacking libpython3-stdlib:arm64 (3.13.9-2) over (3.13.7-1) ... 72s Preparing to unpack .../python3-gdbm_3.13.9-2_arm64.deb ... 72s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 72s Setting up python3-gdbm (3.13.9-2) ... 72s Setting up libpython3-stdlib:arm64 (3.13.9-2) ... 72s Setting up python3 (3.13.9-2) ... 72s running python rtupdate hooks for python3.13... 72s running python post-rtupdate hooks for python3.13... 72s Processing triggers for man-db (2.13.1-1) ... 73s autopkgtest [14:30:21]: upgrading testbed (apt dist-upgrade and autopurge) 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Solving dependencies... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [14:30:27]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 14:22:06 UTC 2025 80s autopkgtest [14:30:28]: @@@@@@@@@@@@@@@@@@@@ apt-source bedtools 83s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (dsc) [2230 B] 83s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (tar) [14.5 MB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (diff) [14.5 kB] 84s gpgv: Signature made Mon Dec 4 19:20:23 2023 UTC 84s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 84s gpgv: issuer "emollier@debian.org" 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found 84s autopkgtest [14:30:32]: testing package bedtools version 2.31.1+dfsg-2 85s autopkgtest [14:30:33]: build not needed 90s autopkgtest [14:30:38]: test run-unit-test: preparing testbed 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Solving dependencies... 91s The following NEW packages will be installed: 91s bedtools bedtools-test libdeflate0 libhtscodecs2 tabix 91s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 19.5 MB of archives. 91s After this operation, 52.3 MB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 92s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 bedtools-test all 2.31.1+dfsg-2 [18.2 MB] 93s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 93s Get:4 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 93s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 tabix arm64 1.22.1+ds2-1 [525 kB] 93s Fetched 19.5 MB in 2s (8720 kB/s) 94s Selecting previously unselected package bedtools. 94s (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 ... 88300 files and directories currently installed.) 94s Preparing to unpack .../bedtools_2.31.1+dfsg-2_arm64.deb ... 94s Unpacking bedtools (2.31.1+dfsg-2) ... 94s Selecting previously unselected package bedtools-test. 94s Preparing to unpack .../bedtools-test_2.31.1+dfsg-2_all.deb ... 94s Unpacking bedtools-test (2.31.1+dfsg-2) ... 94s Selecting previously unselected package libdeflate0:arm64. 94s Preparing to unpack .../libdeflate0_1.23-2_arm64.deb ... 94s Unpacking libdeflate0:arm64 (1.23-2) ... 94s Selecting previously unselected package libhtscodecs2:arm64. 94s Preparing to unpack .../libhtscodecs2_1.6.1-2_arm64.deb ... 94s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 94s Selecting previously unselected package tabix. 94s Preparing to unpack .../tabix_1.22.1+ds2-1_arm64.deb ... 94s Unpacking tabix (1.22.1+ds2-1) ... 94s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 94s Setting up libdeflate0:arm64 (1.23-2) ... 94s Setting up bedtools-test (2.31.1+dfsg-2) ... 94s Setting up tabix (1.22.1+ds2-1) ... 94s Setting up bedtools (2.31.1+dfsg-2) ... 94s Processing triggers for man-db (2.13.1-1) ... 94s Processing triggers for libc-bin (2.42-2ubuntu2) ... 96s autopkgtest [14:30:44]: test run-unit-test: [----------------------- 96s Testing bedtools bamtobed: 96s bamtobed.t1...ok 96s bamtobed.t2...ok 96s bamtobed.t3...ok 96s bamtobed.t4...ok 96s bamtobed.t5...ok 96s bamtobed.t6...ok 96s bamtobed.t7...ok 96s bamtobed.t8...ok 96s bamtobed.t9...ok 96s bamtobed.t10...ok 96s bamtobed.t9...ok 96s bamtobed.t11...ok 96s bamtobed.t12..ok 96s bamtobed.t13..ok 96s Testing bedtools bamtofastq: 96s ok 96s ok 96s Testing bedtools bed12tobed6: 96s bed12tobed6.t1...ok 96s bed12tobed6.t2...ok 96s bed12tobed6.t3...ok 96s bed12tobed6.t4...ok 96s bed12tobed6.t5...ok 96s Testing bedtools bedtobam: 96s bedtobam.t1...ok 96s Testing bedtools bigchroms: 96s bigchroms.t01...ok 96s bigchroms.t02...ok 96s bigchroms.t03... skip set env var 'BT_NO_BIG_FILES' to run this test 96s bigchroms.t04... merge ok 96s bigchroms.t05... closest ok 96s Testing bedtools closest: 96s closest.t1...ok 96s closest.t2...ok 96s closest.t3...ok 96s closest.t4...ok 96s closest.t5...ok 96s closest.t6...ok 96s closest.t7...ok 96s closest.t8...ok 96s closest.t9...ok 96s closest.t10...ok 96s closest.t11...ok 96s closest.t13...ok 96s closest.t14...ok 96s closest.t15...ok 96s closest.t16...ok 96s closest.t17...ok 96s closest.t18...ok 96s closest.t19...ok 96s closest.t20...ok 96s closest.t21...ok 96s closest.t22...ok 96s closest.t23...ok 96s closest.t24...ok 96s closest.t25...ok 96s closest.t26...ok 96s closest.t27...ok 96s closest.t28...ok 96s closest.t29...ok 96s closest.t30...ok 96s closest.t31...ok 96s closest.t32...ok 96s closest.t33...ok 96s closest.t34...ok 96s closest.t35...ok 96s closest.t36...ok 96s closest.t37...ok 96s closest.t38...ok 96s closest.t39...ok 96s closest.t40...ok 96s closest.t41...ok 96s closest.t42...ok 97s closest.t43...ok 97s closest.t44...ok 97s closest.t45...ok 97s closest.t46...ok 97s closest.t47...ok 97s closest.t48...ok 97s closest.t49...ok 97s closest.t50...ok 97s closest.t51...ok 97s closest.t52...ok 97s closest.t53...ok 97s closest.t54...ok 97s closest.t55...ok 97s closest.t56...ok 97s closest.t57...ok 97s closest.t58...ok 97s closest.t59...ok 97s closest.t60...ok 97s closest.t61...ok 97s closest.t62...ok 97s closest.t63...ok 97s closest.t64...ok 97s closest.t65...ok 97s closest.t66...ok 97s closest.t67...ok 97s closest.t68...ok 97s closest.t69...ok 97s closest.t70...ok 97s closest.t71...ok 97s 97s ########################################################### 97s # 97s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 97s # 97s ########################################################### 97s 97s closest.t01...ok 97s closest.t02...ok 97s closest.t03...ok 97s closest.t04...ok 97s closest.t05...ok 97s closest.t06...ok 97s closest.t07...ok 97s closest.t08...ok 97s closest.t09...ok 97s closest.t10...ok 97s closest.t11...ok 97s closest.t12...ok 97s closest.t13...ok 97s closest.t14...ok 97s closest.t15...ok 97s closest.t16...ok 97s closest.t17...ok 97s closest.t18...ok 97s closest.t19...ok 97s closest.20...ok 97s closest.21...ok 97s closest.22...ok 97s closest.23...ok 97s 97s ########################################################### 97s # 97s # K CLOSEST HITS TESTS 97s # 97s ########################################################### 97s 97s kclosest.t1...ok 97s kclosest.t2...ok 97s kclosest.t3...ok 97s kclosest.t4...ok 97s kclosest.t5...ok 97s kclosest.t6...ok 97s kclosest.t7...ok 97s kclosest.t8...ok 97s kclosest.t9...ok 97s kclosest.t10...ok 97s 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. 97s ok 97s 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. 97s ok 97s 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. 97s ok 97s 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. 97s ok 97s 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. 97s ok 97s kclosest.t16...ok 97s 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. 97s ok 97s 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. 97s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s 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. 97s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 97s ok 97s kclosest.t30...ok 97s 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. 97s ok 97s 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. 97s ok 97s kclosest.t33...ok 97s kclosest.t34...ok 97s kclosest.t35...ok 97s kclosest.t36...ok 97s kclosest.t37...ok 97s kclosest.t38...ok 97s kclosest.t39...ok 97s kclosest.t40...ok 97s kclosest.t41...ok 97s kclosest.t42...ok 97s kclosest.t43...ok 97s kclosest.t44...ok 97s kclosest.t45...ok 97s Testing bedtools cluster: 97s cluster.t1...ok 97s cluster.t2...ok 97s Testing bedtools complement: 97s complement.t1...ok 97s complement.t2...ok 97s complement.t3...ok 97s complement.t4...ok 97s complement.t5...ok 97s complement.t6...ok 97s complement.t7...ok 97s complement.t8...ok 97s complement.t9...ok 97s complement.t9...ok 97s complement.t10...ok 97s Testing bedtools coverage: 97s coverage.t1...ok 97s coverage.t1b...ok 97s coverage.t2...ok 97s coverage.t2b...ok 97s coverage.t3...ok 97s coverage.t3b...ok 97s coverage.t4...ok 97s coverage.t4b...ok 97s coverage.t5...ok 97s coverage.t5b...ok 97s coverage.t6...ok 97s coverage.t6b...ok 97s coverage.t7...ok 97s coverage.t7b...ok 98s coverage.t8...ok 98s coverage.t8b...ok 98s coverage.t9...ok 98s coverage.t9b...ok 98s coverage.t10...ok 98s coverage.t10b...ok 98s coverage.t11...ok 98s coverage.t11b...ok 98s coverage.t12...ok 98s coverage.t12b...ok 98s coverage.t13...ok 98s coverage.t13b...ok 98s coverage.t14...ok 98s coverage.t14b...ok 98s coverage.t15...ok 98s coverage.t15b...ok 98s coverage.t16...ok 98s coverage.t16b...ok 98s coverage.t17...ok 98s coverage.t17b...ok 98s coverage.t18...ok 98s coverage.t18b...ok 98s coverage.t19...ok 98s coverage.t19b...ok 98s coverage.t20...ok 98s Testing bedtools expand: 98s expand.t1...ok 98s expand.t2...ok 98s expand.t3...ok 98s Testing bedtools fisher: 98s fisher.t1...ok 98s fisher.t2...ok 98s fisher.t3...ok 98s fisher.t4...ok 98s fisher.t5...ok 98s fisher.t6...ok 98s Testing bedtools flank: 98s flank.t1...ok 98s flank.t2...ok 98s flank.t3...ok 98s flank.t4...ok 98s flank.t5...ok 98s flank.t6...ok 98s flank.t7...ok 98s flank.t8...ok 98s flank.t9...ok 98s flank.t10...ok 98s flank.t11...ok 98s Testing bedtools general: 98s general.t01...ok 98s general.t02...ok 98s general.t03...ok 98s general.t05...ok 98s general.t06...ok 98s general.t07...ok 98s general.t08...ok 98s general.t09...ok 98s general.t10...ok 98s general.t11...ok 98s general.t12...ok 98s general.t13...ok 98s general.t14...ok 98s general.15...ok 98s general.t16...ok 98s general.t17...ok 98s general.t18...ok 98s general.t19...ok 98s general.t20...ok 98s general.t21...ok 98s general.22...ok 98s general.t23...ok 98s general.t24...ok 98s general.t25...ok 98s general.t26...ok 98s general.t27...ok 98s general.t28...ok 98s general.29...ok 98s general.t30...ok 98s general.t31...ok 98s general.t32...ok 98s general.t33...ok 98s general.t34...ok 98s general.t35...ok 98s general.36...ok 98s general.t37...ok 98s general.t38...ok 98s general.t39...ok 98s general.t40...ok 98s general.t41...ok 98s general.t42...ok 98s general.t43...ok 98s general.t44...ok 98s general.t45...ok 98s general.t46...ok 98s Testing bedtools genomecov: 98s genomecov.t1...ok 98s genomecov.t2...ok 98s genomecov.t3...ok 98s genomecov.t4...ok 98s genomecov.t5...ok 98s genomecov.t6...ok 98s genomecov.t7...ok 98s genomecov.t8...ok 98s genomecov.t9...ok 98s genomecov.t10...ok 98s genomecov.t11...ok 98s genomecov.t12...ok 98s genomecov.t13...ok 98s genomecov.t14...ok 98s genomecov.t15...ok 98s genomecov.t16...ok 98s genomecov.t17...ok 100s genomecov.t18...ok 100s Testing bedtools getfasta: 100s getfasta.t01...ok 100s getfasta.t02...ok 100s getfasta.t03...ok 100s getfasta.t04...ok 100s getfasta.t05...ok 100s getfasta.t06...ok 100s getfasta.t07...ok 100s getfasta.t08...ok 100s getfasta.t09...ok 101s getfasta.t10...ok 101s getfasta.t11...ok 101s getfasta.t12a...ok 101s getfasta.t12a...ok 101s getfasta.t12b...ok 101s getfasta.t13a...ok 101s getfasta.t13b...ok 101s getfasta.t13c...ok 101s getfasta.t14...ok 101s getfasta.t15...ok 101s getfasta.t134..ok 101s getfasta.t16..ok 101s getfasta.t17..ok 101s getfasta.t18...ok 101s Testing bedtools groupby: 101s groupby.t1...ok 101s groupby.t2...ok 101s groupby.t3...ok 101s groupby.t4...ok 101s groupby.t5...ok 101s groupby.t6...ok 101s groupby.t7...ok 101s groupby.t8...ok 101s groupby.t9...ok 101s groupby.t10...ok 101s groupby.t11...ok 101s groupby.t12...ok 101s groupby.t13...ok 101s groupby.t14...ok 101s groupby.t16...ok 101s groupby.t17...ok 101s groupby.t18...ok 101s groupby.t19...\c 101s ok 101s groupby.t20...\c 101s ok 101s Testing bedtools intersect: 101s intersect.t01...ok 101s intersect.t02...ok 101s intersect.t03...ok 101s intersect.t04...ok 101s intersect.t05...ok 101s intersect.t06...ok 101s intersect.t07...ok 101s intersect.t08...ok 101s intersect.t09...ok 101s intersect.t10...ok 101s intersect.t11...ok 101s intersect.t12...ok 101s intersect.t13...ok 101s intersect.t14...ok 101s intersect.t15...ok 101s intersect.t16...ok 101s intersect.t17...ok 101s intersect.t18...ok 101s intersect.t19...ok 101s intersect.t20...ok 101s intersect.t21...ok 101s intersect.t22...ok 101s intersect.t22.a...ok 101s intersect.t22.b...ok 101s intersect.t22.c...ok 101s intersect.t22.d...ok 101s intersect.t22.e...ok 101s intersect.t22.f...ok 101s intersect.t22.g...ok 101s intersect.t22.h...ok 101s intersect.t22.i...ok 101s intersect.t22.j...ok 101s intersect.t22.j...ok 101s intersect.t22.k...ok 101s intersect.t22.l...ok 101s intersect.t22.m...ok 101s intersect.t22.n...ok 101s intersect.t22.o...ok 101s intersect.t22.p...ok 101s intersect.t22.q...ok 101s intersect.t22.r...ok 101s intersect.t22.s...ok 101s intersect.t22.t...ok 101s intersect.t22.u...ok 101s intersect.t22.v...ok 101s intersect.t22.w...ok 101s intersect.t23...ok 101s intersect.t24...ok 101s intersect.t25...ok 101s intersect.t26...ok 101s intersect.t27...ok 101s intersect.t28...ok 101s intersect.t29...ok 101s intersect.t30...ok 101s intersect.t31...ok 101s intersect.t32...ok 101s intersect.t33...ok 101s intersect.t34...ok 101s intersect.t35...ok 101s intersect.t36...ok 101s intersect.t37...ok 101s intersect.t38...ok 101s intersect.t39...ok 101s intersect.t40...ok 101s intersect.t41...ok 101s intersect.t42...ok 101s intersect.t43...ok 101s intersect.t44...ok 101s intersect.t45...ok 101s intersect.t46...ok 101s intersect.t47...ok 101s intersect.t48...ok 101s intersect.t49...ok 101s intersect.t50...ok 101s intersect.t51...ok 101s intersect.t52...ok 101s intersect.t53...ok 101s intersect.t54...ok 101s intersect.t55...ok 101s intersect.t56...ok 101s intersect.t57...ok 101s intersect.t58...ok 101s intersect.t59...ok 101s intersect.t60...ok 101s intersect.t61...ok 101s intersect.t62...ok 101s intersect.t63...ok 101s intersect.t64...ok 101s intersect.t65...ok 101s intersect.t66...ok 101s intersect.t67...ok 101s intersect.t68...ok 101s intersect.t69...ok 101s intersect.t70...ok 101s intersect.t71...ok 101s intersect.t72...ok 101s intersect.t73...ok 101s intersect.t74...ok 101s intersect.t75...ok 101s intersect.t76...ok 102s intersect.t77...ok 102s intersect.t78...ok 102s intersect.t79...ok 102s intersect.t80...ok 102s intersect.t81...ok 102s intersect.t82...ok 102s intersect.t83...ok 102s intersect.new.t01...ok 102s intersect.new.t02...ok 102s intersect.new.t03...ok 102s intersect.new.t04...ok 102s intersect.new.t05...ok 102s intersect.new.t06...ok 102s intersect.new.t07...ok 102s intersect.new.t08...ok 102s intersect.new.t09...ok 102s intersect.new.t10...ok 102s intersect.new.t11...ok 102s intersect.new.t12...ok 102s intersect.new.t13...ok 102s intersect.new.t14...ok 102s intersect.new.t15...ok 102s intersect.new.t16...ok 102s intersect.new.t17...ok 102s intersect.new.t18...ok 102s intersect.new.t19...ok 102s intersect.new.t20...ok 102s intersect.new.t20.b...ok 102s intersect.new.t20.c...ok 102s intersect.new.t21...ok 102s intersect.new.t22...ok 102s intersect.new.t23...ok 102s intersect.new.t24...ok 102s intersect.new.t25...ok 102s intersect.new.t26...ok 102s intersect.new.t27...ok 102s intersect.new.t28...ok 102s intersect.new.t29...ok 102s intersect.new.t30...ok 103s intersect.new.t31...ok 103s intersect.new.t32...ok 103s intersect.new.t33...ok 103s intersect.new.t34...ok 103s intersect.new.t35...ok 103s intersect.new.t36...ok 103s intersect.new.t37...ok 103s intersect.new.t38...ok 103s intersect.new.t39...ok 103s intersect.new.t40...ok 103s intersect.new.t41...ok 103s intersect.new.t42...ok 104s intersect.new.t43...ok 104s intersect.new.t44...ok 104s intersect.new.t45...ok 104s intersect.new.t46...ok 104s intersect.new.t47...ok 104s intersect.new.t48...ok 104s intersect.new.t49...ok 104s intersect.new.t50...ok 104s intersect.new.t51...ok 104s intersect.new.t52...ok 104s intersect.new.t53...ok 104s intersect.new.t54...ok 104s intersect.new.t55...ok 104s intersect.new.t56...ok 104s intersect.new.t57...ok 104s intersect.new.t58...ok 104s intersect.new.t59...ok 104s intersect.new.t60...ok 104s intersect.new.t61...ok 104s intersect.new.t62...ok 104s intersect.new.t63...ok 104s intersect.new.t64...ok 104s intersect.new.t65...ok 104s intersect.new.t66...ok 104s intersect.new.t67a...ok 104s intersect.new.t67b...ok 104s intersect.new.t68a...ok 104s intersect.new.t68b...ok 104s intersect.new.t69...ok 104s intersect.new.t70...ok 104s intersect.new.t71...ok 104s intersect.new.t72...ok 104s intersect.new.t73...ok 104s intersect.new.t74...ok 104s intersect.new.t75...ok 104s intersect.new.t76...ok 104s intersect.new.t77...ok 104s intersect.new.t78...ok 104s intersect.new.t79...ok 104s intersect.new.t80...ok 104s intersect.new.t81...ok 104s 104s ########################################################### 104s # 104s # MULTIPLE DATABASE INTERSECTION 104s # 104s ########################################################### 104s 104s intersect.t01...ok 104s intersect.t02...ok 104s intersect.t03...ok 104s intersect.t04...ok 104s intersect.t05...ok 104s intersect.t06...ok 104s intersect.t07...ok 104s intersect.t08...ok 104s intersect.t09...ok 104s intersect.t10...ok 104s intersect.t11...ok 104s intersect.t12...ok 104s intersect.t13...ok 104s intersect.t14...ok 104s intersect.t15...ok 104s intersect.t16...ok 104s intersect.t17...ok 104s intersect.t18...ok 104s intersect.t13...ok 104s intersect.t19...ok 104s intersect.t20...ok 104s intersect.t21...ok 104s intersect.t22...ok 104s intersect.t23...ok 104s intersect.t24...ok 104s 104s ########################################################### 104s # 104s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 104s # 104s ########################################################### 104s 104s intersect.t01...ok 104s intersect.t02...ok 104s intersect.t03...ok 105s intersect.t04...ok 105s intersect.t05...ok 105s intersect.t06...ok 105s intersect.t07...ok 105s intersect.t08...ok 105s intersect.t09...ok 105s intersect.t10...ok 105s intersect.t11...ok 105s intersect.t12...ok 105s intersect.t13...ok 105s intersect.t14...ok 105s intersect.t15...ok 105s intersect.t16...ok 105s intersect.t17...ok 105s intersect.t18...ok 105s intersect.t19...ok 105s intersect.20...ok 105s intersect.21...ok 105s intersect.22...ok 105s intersect.23...ok 105s Testing bedtools jaccard: 105s jaccard.t01...ok 105s jaccard.t02...ok 105s jaccard.t03...ok 105s jaccard.t05...ok 105s jaccard.t06...ok 105s jaccard.t07...ok 105s jaccard.t08...ok 105s jaccard.t09...ok 105s jaccard.t10...ok 105s jaccard.t11...ok 105s jaccard.t12...ok 105s jaccard.t13...ok 105s jaccard.t14...ok 105s jaccard.t15...ok 105s jaccard.t16...ok 105s Testing bedtools makewindows: 105s makewindows.t01...ok 105s makewindows.t02...ok 105s makewindows.t03...ok 105s makewindows.t04...ok 105s makewindows.t05...ok 105s makewindows.t06...ok 105s makewindows.t07...ok 105s makewindows.t08...ok 105s makewindows.t09...ok 105s Testing bedtools map: 105s map.t01...ok 105s map.t02...ok 105s map.t03...ok 105s map.t04...ok 105s map.t05...ok 105s map.t06...ok 105s map.t07...ok 105s map.t08...ok 105s map.t09...ok 105s map.t10...ok 105s map.t11...ok 105s map.t12...ok 105s map.t13...ok 105s map.t14...ok 105s map.t15...ok 105s map.t16...ok 105s map.t17...ok 105s map.t18...ok 105s map.t19...ok 105s map.t20...ok 105s map.t21...ok 105s map.t22..ok 105s map.t23..ok 105s map.t24..ok 105s map.t25..ok 105s map.t26..ok 105s map.t27..ok 105s map.t28..ok 105s map.t29..ok 105s map.t30..ok 105s map.t31..ok 105s map.t32..ok 105s map.t33..ok 105s map.t33..ok 105s map.t33..ok 105s map.t34..ok 105s map.t35..ok 105s map.t36..ok 105s map.t37..ok 105s map.t38..ok 105s map.t39..ok 105s map.t40..ok 105s map.t41..ok 105s map.t42..ok 105s map.t43..ok 105s map.t44...ok 105s map.t45...ok 105s map.t46...ok 105s map.t47...ok 105s map.t48...ok 105s map.t49...ok 105s map.t50...ok 105s map.t51...ok 105s map.t52...ok 105s map.t53...ok 105s map.t54...ok 105s map.t55...ok 105s Testing bedtools merge: 105s merge.t1...ok 105s merge.t2...ok 105s merge.t3...ok 105s merge.t4...ok 105s merge.t5...ok 105s merge.t6...ok 105s merge.t7...ok 105s merge.t8...ok 105s merge.t9a...ok 105s merge.t9b...ok 105s merge.t10...ok 105s merge.t11...ok 105s merge.t12...ok 105s merge.t13...ok 105s merge.t14...ok 105s merge.t15...ok 105s merge.t16...ok 105s merge.t17...ok 105s merge.t18...ok 105s merge.t19...ok 105s merge.t20...ok 105s merge.t21...ok 105s merge.t22...ok 105s merge.t23a...ok 105s merge.t23b...ok 105s merge.t24...ok 105s merge.t25...ok 105s merge.t26...ok 105s merge.t27...ok 105s merge.t28...ok 105s merge.t29...ok 105s merge.t30...ok 105s merge.t31...ok 105s merge.t32...ok 105s merge.t33...ok 105s merge.t34...ok 105s merge.t35...ok 105s merge.t36...ok 105s merge.t37...ok 106s merge.t38...ok 106s merge.t39...ok 106s merge.t40...ok 106s merge.t41...ok 106s merge.t42...ok 106s merge.t43...ok 106s merge.t44a...ok 106s merge.t44b...skipped - could not find vcfSVtest.2.vcf 106s merge.t45...ok 106s merge.t46...ok 106s merge.t47...ok 106s merge.t48...ok 106s merge.t49...ok 106s merge.t50...ok 106s Testing bedtools multicov: 106s multicov.t1...ok 106s multicov.t2...ok 106s multicov.t3...ok 106s multicov.t4...ok 106s multicov.t5...ok 106s multicov.t6...ok 106s multicov.t7...ok 106s multicov.t8...ok 106s multicov.t9...ok 106s multicov.t10...ok 106s Testing bedtools negativecontrol: 106s Testing bedtools reldist: 106s reldist.t01...ok 106s reldist.t02...ok 106s reldist.t03...ok 106s reldist.t02...ok 106s Testing bedtools sample: 106s sample.t01...ok 106s sample.new.t02...ok 106s sample.new.t03...ok 106s sample.new.t04...ok 106s sample.new.t05...ok 106s sample.new.t06...ok 106s sample.new.t07...ok 106s sample.new.t08...ok 106s sample.new.t09...ok 106s Testing bedtools shift: 106s shift.t1...ok 106s shift.t2...ok 106s shift.t3...ok 106s shift.t3...ok 106s shift.t4...ok 106s shift.t5...ok 106s shift.t6...ok 106s shift.t7...ok 106s shift.t8...ok 106s shift.t9...ok 106s shift.t10...ok 106s shift.t11...ok 106s Testing bedtools shuffle: 106s shuffle.t1...ok 106s shuffle.t2...ok 106s shuffle.t3...ok 106s shuffle.t4...ok 106s shuffle.t5...ok 106s shuffle.t6...ok 106s Testing bedtools slop: 106s slop.t1...ok 106s slop.t2...ok 106s slop.t3...ok 106s slop.t4...ok 106s slop.t5...ok 106s slop.t6...ok 106s slop.t7...ok 106s slop.t8...ok 106s slop.t9...ok 106s slop.t10...ok 106s slop.t11...ok 106s slop.t12...ok 106s slop.t13...ok 106s slop.t14...ok 106s slop.t15...ok 106s slop.t16...ok 106s slop.t17...ok 106s slop.t18...ok 106s slop.t19...ok 106s slop.t20...ok 106s slop.t21...ok 106s slop.t22...ok 106s Testing bedtools sort: 106s sort.t01...ok 106s sort.t02...ok 106s sort.t03...ok 106s sort.t04...ok 106s sort.t05...ok 106s sort.t06...ok 106s sort.t07...ok 106s sort.t08...ok 106s sort.t09...ok 106s sort.t10...ok 106s Testing bedtools spacing: 106s spacing.t01...ok 106s Testing bedtools split: 106s split.01.size...ok 106s split.02.simple...ok 106s spliit.03.simple...ok 106s Testing bedtools subtract: 106s subtract.t1...ok 107s subtract.t2...ok 107s subtract.t3...ok 107s subtract.t4...ok 107s subtract.t5...ok 107s subtract.t6...ok 107s subtract.t7...ok 107s subtract.t8...ok 107s subtract.t9...ok 107s subtract.t10...ok 107s subtract.t11...ok 107s subtract.t12...ok 107s subtract.t13...ok 107s subtract.t14...ok 107s subtract.t15...ok 107s subtract.t16...ok 107s subtract.t17...ok 107s subtract.t18...ok 107s subtract.t19...ok 107s subtract.t20...ok 107s subtract.t21...ok 107s 107s 107s -------------------------- 107s Test Results 107s -------------------------- 107s 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 107s Tools failing: negativecontrol 107s NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, 107s something went wrong with this test script. 107s autopkgtest [14:30:55]: test run-unit-test: -----------------------] 108s run-unit-test PASS 108s autopkgtest [14:30:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 109s autopkgtest [14:30:57]: @@@@@@@@@@@@@@@@@@@@ summary 109s run-unit-test PASS