0s autopkgtest [07:58:02]: starting date and time: 2025-12-03 07:58:02+0000
  0s autopkgtest [07:58:02]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message
  0s autopkgtest [07:58:02]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hmhqv7p4/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.115 lxd-armhf-10.145.243.115:autopkgtest/ubuntu/resolute/armhf
 31s autopkgtest [07:58:33]: testbed dpkg architecture: armhf
 33s autopkgtest [07:58:35]: testbed apt version: 3.1.12
 38s autopkgtest [07:58:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 40s autopkgtest [07:58:42]: testbed release detected to be: None
 48s autopkgtest [07:58:50]: updating testbed package index (apt update)
 53s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 54s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB]
 55s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB]
 55s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB]
 55s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1051 kB]
 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [146 kB]
 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [28.2 kB]
 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [183 kB]
 56s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [709 kB]
 56s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [10.2 kB]
 56s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1414 kB]
 57s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1366 kB]
 58s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.9 MB]
 66s Fetched 20.3 MB in 15s (1309 kB/s)
 67s Reading package lists...
 78s autopkgtest [07:59:20]: upgrading testbed (apt dist-upgrade and autopurge)
 80s Reading package lists...
 81s Building dependency tree...
 81s Reading state information...
 81s Calculating upgrade...
 82s The following packages will be upgraded:
 82s   libpython3-stdlib python3 python3-gdbm python3-minimal
 82s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 82s Need to get 72.9 kB of archives.
 82s After this operation, 2048 B of additional disk space will be used.
 82s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.13.9-2 [28.1 kB]
 83s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.13.9-2 [23.0 kB]
 83s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.13.9-2 [10.8 kB]
 83s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-gdbm armhf 3.13.9-2 [11.0 kB]
 83s Fetched 72.9 kB in 0s (156 kB/s)
 83s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 65928 files and directories currently installed.)
 83s Preparing to unpack .../python3-minimal_3.13.9-2_armhf.deb ...
 83s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ...
 83s Setting up python3-minimal (3.13.9-2) ...
 84s (Reading database ... 
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(Reading database ... 55%
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(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 ... 65928 files and directories currently installed.)
 84s Preparing to unpack .../python3_3.13.9-2_armhf.deb ...
 84s Unpacking python3 (3.13.9-2) over (3.13.7-1) ...
 84s Preparing to unpack .../libpython3-stdlib_3.13.9-2_armhf.deb ...
 84s Unpacking libpython3-stdlib:armhf (3.13.9-2) over (3.13.7-1) ...
 84s Preparing to unpack .../python3-gdbm_3.13.9-2_armhf.deb ...
 84s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ...
 84s Setting up python3-gdbm (3.13.9-2) ...
 84s Setting up libpython3-stdlib:armhf (3.13.9-2) ...
 84s Setting up python3 (3.13.9-2) ...
 84s Processing triggers for man-db (2.13.1-1) ...
 87s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 88s Solving dependencies...
 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 92s autopkgtest [07:59:34]: rebooting testbed after setup commands that affected boot
137s autopkgtest [08:00:19]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2
168s autopkgtest [08:00:50]: @@@@@@@@@@@@@@@@@@@@ apt-source bedtools
188s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (dsc) [2230 B]
188s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (tar) [14.5 MB]
188s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedtools 2.31.1+dfsg-2 (diff) [14.5 kB]
188s gpgv: Signature made Mon Dec  4 19:20:23 2023 UTC
188s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
188s gpgv:                issuer "emollier@debian.org"
188s gpgv: Can't check signature: No public key
188s dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found
189s autopkgtest [08:01:11]: testing package bedtools version 2.31.1+dfsg-2
192s autopkgtest [08:01:14]: build not needed
206s autopkgtest [08:01:28]: test run-unit-test: preparing testbed
208s Reading package lists...
208s Building dependency tree...
208s Reading state information...
210s Solving dependencies...
210s The following NEW packages will be installed:
210s   bedtools bedtools-test libdeflate0 libhtscodecs2 tabix
216s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded.
216s Need to get 19.5 MB of archives.
216s After this operation, 51.2 MB of additional disk space will be used.
216s Get:1 http://ftpmaster.internal/ubuntu resolute/universe armhf bedtools armhf 2.31.1+dfsg-2 [739 kB]
216s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf bedtools-test all 2.31.1+dfsg-2 [18.2 MB]
218s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB]
218s Get:4 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB]
218s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf tabix armhf 1.22.1+ds2-1 [444 kB]
219s Fetched 19.5 MB in 9s (2107 kB/s)
219s Selecting previously unselected package bedtools.
219s (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 ... 65928 files and directories currently installed.)
219s Preparing to unpack .../bedtools_2.31.1+dfsg-2_armhf.deb ...
219s Unpacking bedtools (2.31.1+dfsg-2) ...
219s Selecting previously unselected package bedtools-test.
219s Preparing to unpack .../bedtools-test_2.31.1+dfsg-2_all.deb ...
219s Unpacking bedtools-test (2.31.1+dfsg-2) ...
220s Selecting previously unselected package libdeflate0:armhf.
220s Preparing to unpack .../libdeflate0_1.23-2_armhf.deb ...
220s Unpacking libdeflate0:armhf (1.23-2) ...
220s Selecting previously unselected package libhtscodecs2:armhf.
220s Preparing to unpack .../libhtscodecs2_1.6.1-2_armhf.deb ...
220s Unpacking libhtscodecs2:armhf (1.6.1-2) ...
220s Selecting previously unselected package tabix.
220s Preparing to unpack .../tabix_1.22.1+ds2-1_armhf.deb ...
220s Unpacking tabix (1.22.1+ds2-1) ...
220s Setting up libhtscodecs2:armhf (1.6.1-2) ...
220s Setting up libdeflate0:armhf (1.23-2) ...
220s Setting up bedtools-test (2.31.1+dfsg-2) ...
220s Setting up tabix (1.22.1+ds2-1) ...
220s Setting up bedtools (2.31.1+dfsg-2) ...
220s Processing triggers for man-db (2.13.1-1) ...
220s Processing triggers for libc-bin (2.42-2ubuntu2) ...
233s autopkgtest [08:01:55]: test run-unit-test: [-----------------------
237s Testing bedtools bamtobed:
237s     bamtobed.t1...ok
237s     bamtobed.t2...ok
237s     bamtobed.t3...ok
237s     bamtobed.t4...ok
237s     bamtobed.t5...ok
237s     bamtobed.t6...ok
237s     bamtobed.t7...ok
237s     bamtobed.t8...ok
237s     bamtobed.t9...ok
237s     bamtobed.t10...ok
237s     bamtobed.t9...ok
237s     bamtobed.t11...ok
237s     bamtobed.t12..ok
237s     bamtobed.t13..ok
237s Testing bedtools bamtofastq:
237s ok
237s ok
237s Testing bedtools bed12tobed6:
237s     bed12tobed6.t1...ok
237s     bed12tobed6.t2...ok
237s     bed12tobed6.t3...ok
237s     bed12tobed6.t4...ok
237s     bed12tobed6.t5...ok
237s Testing bedtools bedtobam:
237s     bedtobam.t1...ok
237s Testing bedtools bigchroms:
237s     bigchroms.t01...ok
237s     bigchroms.t02...ok
237s     bigchroms.t03... skip  set env var 'BT_NO_BIG_FILES' to run this test
237s     bigchroms.t04... merge ok
237s     bigchroms.t05... closest ok
237s Testing bedtools closest:
237s     closest.t1...ok
237s     closest.t2...ok
237s     closest.t3...ok
237s     closest.t4...ok
237s     closest.t5...ok
237s     closest.t6...ok
237s     closest.t7...ok
237s     closest.t8...ok
237s     closest.t9...ok
237s     closest.t10...ok
237s     closest.t11...ok
237s     closest.t13...ok
237s     closest.t14...ok
237s     closest.t15...ok
237s     closest.t16...ok
237s     closest.t17...ok
237s     closest.t18...ok
237s     closest.t19...ok
237s     closest.t20...ok
237s     closest.t21...ok
237s     closest.t22...ok
237s     closest.t23...ok
237s     closest.t24...ok
237s     closest.t25...ok
237s     closest.t26...ok
237s     closest.t27...ok
237s     closest.t28...ok
237s     closest.t29...ok
237s     closest.t30...ok
237s     closest.t31...ok
237s     closest.t32...ok
237s     closest.t33...ok
237s     closest.t34...ok
237s     closest.t35...ok
237s     closest.t36...ok
237s     closest.t37...ok
237s     closest.t38...ok
237s     closest.t39...ok
237s     closest.t40...ok
237s     closest.t41...ok
237s     closest.t42...ok
237s     closest.t43...ok
237s     closest.t44...ok
237s     closest.t45...ok
237s     closest.t46...ok
237s     closest.t47...ok
237s     closest.t48...ok
237s     closest.t49...ok
237s     closest.t50...ok
237s     closest.t51...ok
237s     closest.t52...ok
237s     closest.t53...ok
237s     closest.t54...ok
237s     closest.t55...ok
237s     closest.t56...ok
237s     closest.t57...ok
238s     closest.t58...ok
238s     closest.t59...ok
238s     closest.t60...ok
238s     closest.t61...ok
238s     closest.t62...ok
238s     closest.t63...ok
238s     closest.t64...ok
238s     closest.t65...ok
238s     closest.t66...ok
238s     closest.t67...ok
238s     closest.t68...ok
238s     closest.t69...ok
238s     closest.t70...ok
238s     closest.t71...ok
238s 
238s ###########################################################
238s #  
238s #  CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 
238s #
238s ###########################################################
238s 
238s     closest.t01...ok
238s     closest.t02...ok
238s     closest.t03...ok
238s     closest.t04...ok
238s     closest.t05...ok
238s     closest.t06...ok
238s     closest.t07...ok
238s     closest.t08...ok
238s     closest.t09...ok
238s     closest.t10...ok
238s     closest.t11...ok
238s     closest.t12...ok
238s     closest.t13...ok
238s     closest.t14...ok
238s     closest.t15...ok
238s     closest.t16...ok
238s     closest.t17...ok
238s     closest.t18...ok
238s     closest.t19...ok
238s     closest.20...ok
238s     closest.21...ok
238s     closest.22...ok
238s     closest.23...ok
238s 
238s ###########################################################
238s #  
238s #  K CLOSEST HITS TESTS
238s #
238s ###########################################################
238s 
238s     kclosest.t1...ok
238s     kclosest.t2...ok
238s     kclosest.t3...ok
238s     kclosest.t4...ok
238s     kclosest.t5...ok
238s     kclosest.t6...ok
238s     kclosest.t7...ok
238s     kclosest.t8...ok
238s     kclosest.t9...ok
238s     kclosest.t10...ok
238s     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.
238s ok
238s     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.
238s ok
238s     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.
238s ok
238s     kclosest.t14...ok
238s Warning: Fewer hits (1) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested.
238s     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.
238s ok
238s     kclosest.t16...ok
238s     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.
238s ok
238s     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.
238s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s     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.
238s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s     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.
238s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s     kclosest.t21...ok
238s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s     kclosest.t22...ok
238s     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.
238s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s     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.
238s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s     kclosest.t25...ok
238s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s     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.
238s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s     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.
238s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s     kclosest.t28...ok
238s     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.
238s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
238s ok
238s     kclosest.t30...ok
238s Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested.
238s     kclosest.t31...ok
238s     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.
238s ok
238s     kclosest.t33...ok
238s     kclosest.t34...ok
238s     kclosest.t35...ok
238s     kclosest.t36...ok
238s     kclosest.t37...ok
238s     kclosest.t38...ok
238s     kclosest.t39...ok
238s     kclosest.t40...ok
238s     kclosest.t41...ok
238s     kclosest.t42...ok
238s     kclosest.t43...ok
238s     kclosest.t44...ok
238s     kclosest.t45...ok
238s Testing bedtools cluster:
238s     cluster.t1...ok
238s     cluster.t2...ok
238s Testing bedtools complement:
238s     complement.t1...ok
238s     complement.t2...ok
238s     complement.t3...ok
238s     complement.t4...ok
238s     complement.t5...ok
238s     complement.t6...ok
238s     complement.t7...ok
238s     complement.t8...ok
238s     complement.t9...ok
238s     complement.t9...ok
238s     complement.t10...ok
238s Testing bedtools coverage:
238s     coverage.t1...ok
238s     coverage.t1b...ok
238s     coverage.t2...ok
238s     coverage.t2b...ok
238s     coverage.t3...ok
238s     coverage.t3b...ok
238s     coverage.t4...ok
238s     coverage.t4b...ok
238s     coverage.t5...ok
238s     coverage.t5b...ok
238s     coverage.t6...ok
238s     coverage.t6b...ok
238s     coverage.t7...ok
238s     coverage.t7b...ok
238s     coverage.t8...ok
238s     coverage.t8b...ok
238s     coverage.t9...ok
238s     coverage.t9b...ok
238s     coverage.t10...ok
238s     coverage.t10b...ok
238s     coverage.t11...ok
238s     coverage.t11b...ok
238s     coverage.t12...ok
238s     coverage.t12b...ok
238s     coverage.t13...ok
238s     coverage.t13b...ok
238s     coverage.t14...ok
238s     coverage.t14b...ok
239s     coverage.t15...ok
239s     coverage.t15b...ok
239s     coverage.t16...ok
239s     coverage.t16b...ok
239s     coverage.t17...ok
239s     coverage.t17b...ok
239s     coverage.t18...ok
239s     coverage.t18b...ok
239s     coverage.t19...ok
239s     coverage.t19b...ok
239s     coverage.t20...ok
239s Testing bedtools expand:
239s     expand.t1...ok
239s     expand.t2...ok
239s     expand.t3...ok
239s Testing bedtools fisher:
239s     fisher.t1...ok
239s     fisher.t2...ok
239s     fisher.t3...ok
239s     fisher.t4...ok
239s     fisher.t5...ok
239s     fisher.t6...ok
239s Testing bedtools flank:
239s     flank.t1...ok
239s     flank.t2...ok
239s     flank.t3...ok
239s     flank.t4...ok
239s     flank.t5...ok
239s     flank.t6...ok
239s     flank.t7...ok
239s     flank.t8...ok
239s     flank.t9...ok
239s     flank.t10...ok
239s     flank.t11...ok
239s Testing bedtools general:
239s     general.t01...ok
239s     general.t02...ok
239s     general.t03...ok
239s     general.t05...ok
239s     general.t06...ok
239s     general.t07...ok
239s     general.t08...ok
239s     general.t09...ok
239s     general.t10...ok
239s     general.t11...ok
239s     general.t12...ok
239s     general.t13...ok
239s     general.t14...ok
239s     general.15...ok
239s     general.t16...ok
239s     general.t17...ok
239s     general.t18...ok
239s     general.t19...ok
239s     general.t20...ok
239s     general.t21...ok
239s     general.22...ok
239s     general.t23...ok
239s     general.t24...ok
239s     general.t25...ok
239s     general.t26...ok
239s     general.t27...ok
239s     general.t28...ok
239s     general.29...ok
239s     general.t30...ok
239s     general.t31...ok
239s     general.t32...ok
239s     general.t33...ok
239s     general.t34...ok
239s     general.t35...ok
239s     general.36...ok
239s     general.t37...ok
239s     general.t38...ok
239s     general.t39...ok
239s     general.t40...ok
239s     general.t41...ok
239s     general.t42...ok
239s     general.t43...ok
239s     general.t44...ok
239s     general.t45...ok
239s     general.t46...ok
239s Testing bedtools genomecov:
239s     genomecov.t1...ok
239s     genomecov.t2...ok
239s     genomecov.t3...ok
239s     genomecov.t4...ok
239s     genomecov.t5...ok
239s     genomecov.t6...ok
239s     genomecov.t7...ok
239s     genomecov.t8...ok
239s     genomecov.t9...ok
239s     genomecov.t10...ok
239s     genomecov.t11...ok
239s     genomecov.t12...ok
239s     genomecov.t13...ok
239s     genomecov.t14...ok
239s     genomecov.t15...ok
239s     genomecov.t16...ok
239s     genomecov.t17...ok
241s     genomecov.t18...ok
241s Testing bedtools getfasta:
241s     getfasta.t01...ok
241s     getfasta.t02...ok
241s     getfasta.t03...ok
241s     getfasta.t04...ok
241s     getfasta.t05...ok
241s     getfasta.t06...ok
241s     getfasta.t07...ok
241s     getfasta.t08...ok
241s     getfasta.t09...ok
242s     getfasta.t10...ok
242s     getfasta.t11...ok
242s     getfasta.t12a...ok
242s     getfasta.t12a...ok
242s     getfasta.t12b...ok
242s     getfasta.t13a...ok
242s     getfasta.t13b...ok
242s     getfasta.t13c...ok
242s     getfasta.t14...ok
242s     getfasta.t15...ok
242s     getfasta.t134..ok
242s     getfasta.t16..ok
242s     getfasta.t17..ok
242s     getfasta.t18...ok
242s Testing bedtools groupby:
242s     groupby.t1...ok
242s     groupby.t2...ok
242s     groupby.t3...ok
242s     groupby.t4...ok
242s     groupby.t5...ok
242s     groupby.t6...ok
242s     groupby.t7...ok
242s     groupby.t8...ok
242s     groupby.t9...ok
242s     groupby.t10...ok
242s     groupby.t11...ok
242s     groupby.t12...ok
242s     groupby.t13...ok
242s     groupby.t14...ok
242s     groupby.t16...ok
242s     groupby.t17...ok
242s     groupby.t18...ok
242s     groupby.t19...\c
242s ok
242s     groupby.t20...\c
242s ok
242s Testing bedtools intersect:
242s     intersect.t01...ok
242s     intersect.t02...ok
242s     intersect.t03...ok
242s     intersect.t04...ok
242s     intersect.t05...ok
242s     intersect.t06...ok
242s     intersect.t07...ok
242s     intersect.t08...ok
242s     intersect.t09...ok
242s     intersect.t10...ok
242s     intersect.t11...ok
242s     intersect.t12...ok
242s     intersect.t13...ok
242s     intersect.t14...ok
242s     intersect.t15...ok
242s     intersect.t16...ok
242s     intersect.t17...ok
242s     intersect.t18...ok
242s     intersect.t19...ok
242s     intersect.t20...ok
242s     intersect.t21...ok
242s     intersect.t22...ok
242s     intersect.t22.a...ok
242s     intersect.t22.b...ok
242s     intersect.t22.c...ok
242s     intersect.t22.d...ok
242s     intersect.t22.e...ok
242s     intersect.t22.f...ok
242s     intersect.t22.g...ok
242s     intersect.t22.h...ok
242s     intersect.t22.i...ok
242s     intersect.t22.j...ok
242s     intersect.t22.j...ok
242s     intersect.t22.k...ok
242s     intersect.t22.l...ok
242s     intersect.t22.m...ok
242s     intersect.t22.n...ok
242s     intersect.t22.o...ok
242s     intersect.t22.p...ok
242s     intersect.t22.q...ok
242s     intersect.t22.r...ok
242s     intersect.t22.s...ok
242s     intersect.t22.t...ok
242s     intersect.t22.u...ok
243s     intersect.t22.v...ok
243s     intersect.t22.w...ok
243s     intersect.t23...ok
243s     intersect.t24...ok
243s     intersect.t25...ok
243s     intersect.t26...ok
243s     intersect.t27...ok
243s     intersect.t28...ok
243s     intersect.t29...ok
243s     intersect.t30...ok
243s     intersect.t31...ok
243s     intersect.t32...ok
243s     intersect.t33...ok
243s     intersect.t34...ok
243s     intersect.t35...ok
243s     intersect.t36...ok
243s     intersect.t37...ok
243s     intersect.t38...ok
243s     intersect.t39...ok
243s     intersect.t40...ok
243s     intersect.t41...ok
243s     intersect.t42...ok
243s     intersect.t43...ok
243s     intersect.t44...ok
243s     intersect.t45...ok
243s     intersect.t46...ok
243s     intersect.t47...ok
243s     intersect.t48...ok
243s     intersect.t49...ok
243s     intersect.t50...ok
243s     intersect.t51...ok
243s     intersect.t52...ok
243s     intersect.t53...ok
243s     intersect.t54...ok
243s     intersect.t55...ok
243s     intersect.t56...ok
243s     intersect.t57...ok
243s     intersect.t58...ok
243s     intersect.t59...ok
243s     intersect.t60...ok
243s     intersect.t61...ok
243s     intersect.t62...ok
243s     intersect.t63...ok
243s     intersect.t64...ok
243s     intersect.t65...ok
243s     intersect.t66...ok
243s     intersect.t67...ok
243s     intersect.t68...ok
243s     intersect.t69...ok
243s     intersect.t70...ok
243s     intersect.t71...ok
243s     intersect.t72...ok
243s     intersect.t73...ok
243s     intersect.t74...ok
243s     intersect.t75...ok
243s     intersect.t76...ok
243s     intersect.t77...ok
243s     intersect.t78...ok
243s     intersect.t79...ok
243s     intersect.t80...ok
243s     intersect.t81...ok
243s     intersect.t82...ok
243s     intersect.t83...ok
243s     intersect.new.t01...ok
243s     intersect.new.t02...ok
243s     intersect.new.t03...ok
243s     intersect.new.t04...ok
243s     intersect.new.t05...ok
243s     intersect.new.t06...ok
243s     intersect.new.t07...ok
243s     intersect.new.t08...ok
243s     intersect.new.t09...ok
243s     intersect.new.t10...ok
243s     intersect.new.t11...ok
243s     intersect.new.t12...ok
243s     intersect.new.t13...ok
243s     intersect.new.t14...ok
243s     intersect.new.t15...ok
243s     intersect.new.t16...ok
243s     intersect.new.t17...ok
243s     intersect.new.t18...ok
243s     intersect.new.t19...ok
243s     intersect.new.t20...ok
243s     intersect.new.t20.b...ok
243s     intersect.new.t20.c...ok
243s     intersect.new.t21...ok
243s     intersect.new.t22...ok
243s     intersect.new.t23...ok
243s     intersect.new.t24...ok
244s     intersect.new.t25...ok
244s     intersect.new.t26...ok
244s     intersect.new.t27...ok
244s     intersect.new.t28...ok
244s     intersect.new.t29...ok
244s     intersect.new.t30...ok
244s     intersect.new.t31...ok
244s     intersect.new.t32...ok
245s     intersect.new.t33...ok
245s     intersect.new.t34...ok
245s     intersect.new.t35...ok
245s     intersect.new.t36...ok
245s     intersect.new.t37...ok
245s     intersect.new.t38...ok
245s     intersect.new.t39...ok
245s     intersect.new.t40...ok
245s     intersect.new.t41...ok
245s     intersect.new.t42...ok
245s     intersect.new.t43...ok
245s     intersect.new.t44...ok
245s     intersect.new.t45...ok
245s     intersect.new.t46...ok
245s     intersect.new.t47...ok
245s     intersect.new.t48...ok
245s     intersect.new.t49...ok
245s     intersect.new.t50...ok
245s     intersect.new.t51...ok
245s     intersect.new.t52...ok
245s     intersect.new.t53...ok
245s     intersect.new.t54...ok
245s     intersect.new.t55...ok
245s     intersect.new.t56...ok
245s     intersect.new.t57...ok
245s     intersect.new.t58...ok
245s     intersect.new.t59...ok
245s     intersect.new.t60...ok
245s     intersect.new.t61...ok
245s     intersect.new.t62...ok
245s     intersect.new.t63...ok
245s     intersect.new.t64...ok
245s     intersect.new.t65...ok
245s     intersect.new.t66...ok
245s     intersect.new.t67a...ok
245s     intersect.new.t67b...ok
245s     intersect.new.t68a...ok
245s     intersect.new.t68b...ok
245s     intersect.new.t69...ok
245s     intersect.new.t70...ok
245s     intersect.new.t71...ok
245s     intersect.new.t72...ok
245s     intersect.new.t73...ok
245s     intersect.new.t74...ok
245s     intersect.new.t75...ok
245s     intersect.new.t76...ok
245s     intersect.new.t77...ok
245s     intersect.new.t78...ok
245s     intersect.new.t79...ok
245s     intersect.new.t80...ok
245s     intersect.new.t81...ok
245s 
245s ###########################################################
245s #  
245s #  MULTIPLE DATABASE INTERSECTION
245s #
245s ###########################################################
245s 
246s     intersect.t01...ok
246s     intersect.t02...ok
246s     intersect.t03...ok
246s     intersect.t04...ok
246s     intersect.t05...ok
246s     intersect.t06...ok
246s     intersect.t07...ok
246s     intersect.t08...ok
246s     intersect.t09...ok
246s     intersect.t10...ok
246s     intersect.t11...ok
246s     intersect.t12...ok
246s     intersect.t13...ok
246s     intersect.t14...ok
246s     intersect.t15...ok
246s     intersect.t16...ok
246s     intersect.t17...ok
246s     intersect.t18...ok
246s     intersect.t13...ok
246s     intersect.t19...ok
246s     intersect.t20...ok
246s     intersect.t21...ok
246s     intersect.t22...ok
246s     intersect.t23...ok
246s     intersect.t24...ok
246s 
246s ###########################################################
246s #  
246s #  CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 
246s #
246s ###########################################################
246s 
246s     intersect.t01...ok
246s     intersect.t02...ok
246s     intersect.t03...ok
246s     intersect.t04...ok
246s     intersect.t05...ok
246s     intersect.t06...ok
246s     intersect.t07...ok
246s     intersect.t08...ok
246s     intersect.t09...ok
246s     intersect.t10...ok
246s     intersect.t11...ok
246s     intersect.t12...ok
246s     intersect.t13...ok
246s     intersect.t14...ok
246s     intersect.t15...ok
246s     intersect.t16...ok
246s     intersect.t17...ok
246s     intersect.t18...ok
246s     intersect.t19...ok
246s     intersect.20...ok
246s     intersect.21...ok
246s     intersect.22...ok
246s     intersect.23...ok
246s Testing bedtools jaccard:
246s     jaccard.t01...ok
246s     jaccard.t02...ok
246s     jaccard.t03...ok
246s     jaccard.t05...ok
246s     jaccard.t06...ok
246s     jaccard.t07...ok
246s     jaccard.t08...ok
246s     jaccard.t09...ok
246s     jaccard.t10...ok
246s     jaccard.t11...ok
246s     jaccard.t12...ok
246s     jaccard.t13...ok
246s     jaccard.t14...ok
246s     jaccard.t15...ok
246s     jaccard.t16...ok
246s Testing bedtools makewindows:
246s     makewindows.t01...ok
246s     makewindows.t02...ok
246s     makewindows.t03...ok
246s     makewindows.t04...ok
246s     makewindows.t05...ok
246s     makewindows.t06...ok
246s     makewindows.t07...ok
246s     makewindows.t08...ok
246s     makewindows.t09...ok
246s Testing bedtools map:
246s     map.t01...ok
246s     map.t02...ok
246s     map.t03...ok
246s     map.t04...ok
246s     map.t05...ok
246s     map.t06...ok
246s     map.t07...ok
246s     map.t08...ok
246s     map.t09...ok
246s     map.t10...ok
246s     map.t11...ok
246s     map.t12...ok
246s     map.t13...ok
246s     map.t14...ok
246s     map.t15...ok
246s     map.t16...ok
246s     map.t17...ok
246s     map.t18...ok
246s     map.t19...ok
246s     map.t20...ok
246s     map.t21...ok
246s     map.t22..ok
246s     map.t23..ok
246s     map.t24..ok
246s     map.t25..ok
246s     map.t26..ok
246s     map.t27..ok
246s     map.t28..ok
246s     map.t29..ok
246s     map.t30..ok
246s     map.t31..ok
246s     map.t32..ok
246s     map.t33..ok
246s     map.t33..ok
246s     map.t33..ok
246s     map.t34..ok
246s     map.t35..ok
246s     map.t36..ok
246s     map.t37..ok
246s     map.t38..ok
246s     map.t39..ok
246s     map.t40..ok
246s     map.t41..ok
246s     map.t42..ok
246s     map.t43..ok
246s     map.t44...ok
246s     map.t45...ok
246s     map.t46...ok
246s     map.t47...ok
246s     map.t48...ok
246s     map.t49...ok
246s     map.t50...ok
246s     map.t51...ok
246s     map.t52...ok
246s     map.t53...ok
246s     map.t54...ok
246s     map.t55...ok
246s Testing bedtools merge:
246s     merge.t1...ok
246s     merge.t2...ok
246s     merge.t3...ok
246s     merge.t4...ok
246s     merge.t5...ok
246s     merge.t6...ok
246s     merge.t7...ok
246s     merge.t8...ok
247s     merge.t9a...ok
247s     merge.t9b...ok
247s     merge.t10...ok
247s     merge.t11...ok
247s     merge.t12...ok
247s     merge.t13...ok
247s     merge.t14...ok
247s     merge.t15...ok
247s     merge.t16...ok
247s     merge.t17...ok
247s     merge.t18...ok
247s     merge.t19...ok
247s     merge.t20...ok
247s     merge.t21...ok
247s     merge.t22...ok
247s     merge.t23a...ok
247s     merge.t23b...ok
247s     merge.t24...ok
247s     merge.t25...ok
247s     merge.t26...ok
247s     merge.t27...ok
247s     merge.t28...ok
247s     merge.t29...ok
247s     merge.t30...ok
247s     merge.t31...ok
247s     merge.t32...ok
247s     merge.t33...ok
247s     merge.t34...ok
247s     merge.t35...ok
247s     merge.t36...ok
247s     merge.t37...ok
247s     merge.t38...ok
247s     merge.t39...ok
247s     merge.t40...ok
247s     merge.t41...ok
247s     merge.t42...ok
247s     merge.t43...ok
247s     merge.t44a...ok
247s     merge.t44b...skipped - could not find vcfSVtest.2.vcf
247s     merge.t45...ok
247s     merge.t46...ok
247s     merge.t47...ok
247s     merge.t48...ok
247s     merge.t49...ok
247s     merge.t50...ok
247s Testing bedtools multicov:
247s     multicov.t1...ok
247s     multicov.t2...ok
247s     multicov.t3...ok
247s     multicov.t4...ok
247s     multicov.t5...ok
247s     multicov.t6...ok
247s     multicov.t7...ok
247s     multicov.t8...ok
247s     multicov.t9...ok
247s     multicov.t10...ok
247s Testing bedtools negativecontrol:
247s Testing bedtools reldist:
247s     reldist.t01...ok
247s     reldist.t02...ok
247s     reldist.t03...ok
247s     reldist.t02...ok
247s Testing bedtools sample:
247s     sample.t01...ok
247s     sample.new.t02...ok
247s     sample.new.t03...ok
248s     sample.new.t04...ok
248s     sample.new.t05...ok
248s     sample.new.t06...ok
248s     sample.new.t07...ok
248s     sample.new.t08...ok
248s     sample.new.t09...ok
248s Testing bedtools shift:
248s     shift.t1...ok
248s     shift.t2...ok
248s     shift.t3...ok
248s     shift.t3...ok
248s     shift.t4...ok
248s     shift.t5...ok
248s     shift.t6...ok
248s     shift.t7...ok
248s     shift.t8...ok
248s     shift.t9...ok
248s     shift.t10...ok
248s     shift.t11...ok
248s Testing bedtools shuffle:
248s     shuffle.t1...ok
248s     shuffle.t2...ok
248s     shuffle.t3...ok
248s     shuffle.t4...ok
248s     shuffle.t5...ok
248s     shuffle.t6...ok
248s Testing bedtools slop:
248s     slop.t1...ok
248s     slop.t2...ok
248s     slop.t3...ok
248s     slop.t4...ok
248s     slop.t5...ok
248s     slop.t6...ok
248s     slop.t7...ok
248s     slop.t8...ok
248s     slop.t9...ok
248s     slop.t10...ok
248s     slop.t11...ok
248s     slop.t12...ok
248s     slop.t13...ok
248s     slop.t14...ok
248s     slop.t15...ok
248s     slop.t16...ok
248s     slop.t17...ok
248s     slop.t18...ok
248s     slop.t19...ok
248s     slop.t20...ok
248s     slop.t21...ok
248s     slop.t22...ok
248s Testing bedtools sort:
248s     sort.t01...ok
248s     sort.t02...ok
248s     sort.t03...ok
248s     sort.t04...ok
248s     sort.t05...ok
248s     sort.t06...ok
248s     sort.t07...ok
248s     sort.t08...ok
248s     sort.t09...ok
248s     sort.t10...ok
248s Testing bedtools spacing:
248s     spacing.t01...ok
248s Testing bedtools split:
248s     split.01.size...ok
248s     split.02.simple...ok
248s     spliit.03.simple...ok
248s Testing bedtools subtract:
248s     subtract.t1...ok
248s     subtract.t2...ok
248s     subtract.t3...ok
248s     subtract.t4...ok
248s     subtract.t5...ok
248s     subtract.t6...ok
248s     subtract.t7...ok
248s     subtract.t8...ok
248s     subtract.t9...ok
248s     subtract.t10...ok
248s     subtract.t11...ok
248s     subtract.t12...ok
248s     subtract.t13...ok
248s     subtract.t14...ok
248s     subtract.t15...ok
248s     subtract.t16...ok
248s     subtract.t17...ok
248s     subtract.t18...ok
248s     subtract.t19...ok
248s     subtract.t20...ok
248s     subtract.t21...ok
248s 
248s 
248s --------------------------
248s  Test Results             
248s --------------------------
248s 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
248s Tools failing:  negativecontrol
248s NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, 
248s something went wrong with this test script.
249s autopkgtest [08:02:11]: test run-unit-test: -----------------------]
253s autopkgtest [08:02:15]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
253s run-unit-test        PASS
256s autopkgtest [08:02:18]: @@@@@@@@@@@@@@@@@@@@ summary
256s run-unit-test        PASS