0s autopkgtest [22:41:21]: starting date: 2024-03-17 0s autopkgtest [22:41:21]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [22:41:21]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2bipyisd/out --timeout-copy=6000 --setup-commands 'ls /etc/apt/sources.list.d/*.list 2>/dev/null || true; 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,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade bedtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- lxd -r lxd-armhf-10.44.124.162 lxd-armhf-10.44.124.162:autopkgtest/ubuntu/noble/armhf 82s autopkgtest [22:42:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 85s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 85s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3691 kB] 87s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 87s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 87s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [574 kB] 87s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 87s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 87s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 87s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3500 kB] 88s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 88s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [33.8 kB] 88s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 100s Fetched 8470 kB in 5s (1693 kB/s) 101s Reading package lists... 115s /etc/apt/sources.list.d/proposed.list 117s tee: /proc/self/fd/2: Permission denied 152s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 152s Get:2 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 152s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 152s Hit:4 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 152s Hit:5 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 152s Hit:6 http://ftpmaster.internal/ubuntu noble-updates InRelease 152s Hit:7 http://ftpmaster.internal/ubuntu noble-security InRelease 153s Get:8 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 155s Get:9 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 159s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.4 MB] 159s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3726 kB] 160s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3500 kB] 167s Fetched 41.8 MB in 15s (2729 kB/s) 171s Reading package lists... 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 174s Calculating upgrade... 175s The following packages have been kept back: 175s curl openssl 175s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 179s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 181s autopkgtest [22:44:22]: rebooting testbed after setup commands that affected boot 219s autopkgtest [22:45:00]: testbed running kernel: Linux 5.4.0-170-generic #188-Ubuntu SMP Wed Jan 10 09:51:10 UTC 2024 224s autopkgtest [22:45:05]: testbed dpkg architecture: armhf 240s autopkgtest [22:45:21]: @@@@@@@@@@@@@@@@@@@@ apt-source bedtools 253s Get:1 http://ftpmaster.internal/ubuntu noble/universe bedtools 2.31.1+dfsg-2 (dsc) [2230 B] 253s Get:2 http://ftpmaster.internal/ubuntu noble/universe bedtools 2.31.1+dfsg-2 (tar) [14.5 MB] 253s Get:3 http://ftpmaster.internal/ubuntu noble/universe bedtools 2.31.1+dfsg-2 (diff) [14.5 kB] 255s gpgv: Signature made Mon Dec 4 19:20:23 2023 UTC 255s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 255s gpgv: issuer "emollier@debian.org" 255s gpgv: Can't check signature: No public key 255s dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found 258s autopkgtest [22:45:39]: testing package bedtools version 2.31.1+dfsg-2 258s autopkgtest [22:45:39]: build not needed 264s autopkgtest [22:45:45]: test run-unit-test: preparing testbed 280s Reading package lists... 282s Building dependency tree... 282s Reading state information... 283s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 283s Starting 2 pkgProblemResolver with broken count: 0 283s Done 284s Done 286s Starting pkgProblemResolver with broken count: 0 286s Starting 2 pkgProblemResolver with broken count: 0 286s Done 288s The following additional packages will be installed: 288s bedtools bedtools-test libdeflate0 libhtscodecs2 tabix 288s The following NEW packages will be installed: 288s bedtools bedtools-test libdeflate0 libhtscodecs2 tabix 288s 0 upgraded, 5 newly installed, 0 to remove and 2 not upgraded. 288s 1 not fully installed or removed. 288s Need to get 19.5 MB of archives. 288s After this operation, 50.9 MB of additional disk space will be used. 288s Get:1 http://ftpmaster.internal/ubuntu noble/universe armhf bedtools armhf 2.31.1+dfsg-2 [739 kB] 289s Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf bedtools-test all 2.31.1+dfsg-2 [18.2 MB] 291s Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 291s Get:4 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB] 291s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tabix armhf 1.19+ds-1.1build2 [428 kB] 293s Fetched 19.5 MB in 3s (7097 kB/s) 293s Selecting previously unselected package bedtools. 293s (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 ... 58620 files and directories currently installed.) 293s Preparing to unpack .../bedtools_2.31.1+dfsg-2_armhf.deb ... 293s Unpacking bedtools (2.31.1+dfsg-2) ... 293s Selecting previously unselected package bedtools-test. 293s Preparing to unpack .../bedtools-test_2.31.1+dfsg-2_all.deb ... 293s Unpacking bedtools-test (2.31.1+dfsg-2) ... 297s Selecting previously unselected package libdeflate0:armhf. 297s Preparing to unpack .../libdeflate0_1.19-1_armhf.deb ... 297s Unpacking libdeflate0:armhf (1.19-1) ... 297s Selecting previously unselected package libhtscodecs2:armhf. 297s Preparing to unpack .../libhtscodecs2_1.6.0-1_armhf.deb ... 297s Unpacking libhtscodecs2:armhf (1.6.0-1) ... 297s Selecting previously unselected package tabix. 297s Preparing to unpack .../tabix_1.19+ds-1.1build2_armhf.deb ... 297s Unpacking tabix (1.19+ds-1.1build2) ... 297s Setting up libhtscodecs2:armhf (1.6.0-1) ... 297s Setting up libdeflate0:armhf (1.19-1) ... 297s Setting up bedtools-test (2.31.1+dfsg-2) ... 297s Setting up tabix (1.19+ds-1.1build2) ... 297s Setting up bedtools (2.31.1+dfsg-2) ... 297s Setting up autopkgtest-satdep (0) ... 297s Processing triggers for man-db (2.12.0-3) ... 299s Processing triggers for libc-bin (2.39-0ubuntu2) ... 322s (Reading database ... 59192 files and directories currently installed.) 323s Removing autopkgtest-satdep (0) ... 333s autopkgtest [22:46:54]: test run-unit-test: [----------------------- 336s Testing bedtools bamtobed: 337s bamtobed.t1...ok 337s bamtobed.t2...ok 337s bamtobed.t3...ok 337s bamtobed.t4...ok 337s bamtobed.t5...ok 337s bamtobed.t6...ok 337s bamtobed.t7...ok 337s bamtobed.t8...ok 337s bamtobed.t9...ok 337s bamtobed.t10...ok 337s bamtobed.t9...ok 337s bamtobed.t11...ok 337s bamtobed.t12..ok 337s bamtobed.t13..ok 337s Testing bedtools bamtofastq: 337s ok 337s ok 337s Testing bedtools bed12tobed6: 337s bed12tobed6.t1...ok 337s bed12tobed6.t2...ok 337s bed12tobed6.t3...ok 337s bed12tobed6.t4...ok 337s bed12tobed6.t5...ok 337s Testing bedtools bedtobam: 337s bedtobam.t1...ok 337s Testing bedtools bigchroms: 337s bigchroms.t01...ok 337s bigchroms.t02...ok 337s bigchroms.t03... skip set env var 'BT_NO_BIG_FILES' to run this test 337s bigchroms.t04... merge ok 337s bigchroms.t05... closest ok 337s Testing bedtools closest: 337s closest.t1...ok 338s closest.t2...ok 338s closest.t3...ok 338s closest.t4...ok 338s closest.t5...ok 338s closest.t6...ok 338s closest.t7...ok 338s closest.t8...ok 338s closest.t9...ok 338s closest.t10...ok 338s closest.t11...ok 338s closest.t13...ok 338s closest.t14...ok 338s closest.t15...ok 338s closest.t16...ok 338s closest.t17...ok 338s closest.t18...ok 338s closest.t19...ok 338s closest.t20...ok 338s closest.t21...ok 338s closest.t22...ok 338s closest.t23...ok 338s closest.t24...ok 338s closest.t25...ok 338s closest.t26...ok 338s closest.t27...ok 338s closest.t28...ok 338s closest.t29...ok 338s closest.t30...ok 338s closest.t31...ok 338s closest.t32...ok 338s closest.t33...ok 338s closest.t34...ok 338s closest.t35...ok 338s closest.t36...ok 338s closest.t37...ok 339s closest.t38...ok 339s closest.t39...ok 339s closest.t40...ok 339s closest.t41...ok 339s closest.t42...ok 339s closest.t43...ok 339s closest.t44...ok 339s closest.t45...ok 339s closest.t46...ok 339s closest.t47...ok 339s closest.t48...ok 339s closest.t49...ok 339s closest.t50...ok 339s closest.t51...ok 339s closest.t52...ok 339s closest.t53...ok 339s closest.t54...ok 339s closest.t55...ok 339s closest.t56...ok 339s closest.t57...ok 339s closest.t58...ok 339s closest.t59...ok 339s closest.t60...ok 339s closest.t61...ok 339s closest.t62...ok 339s closest.t63...ok 339s closest.t64...ok 339s closest.t65...ok 339s closest.t66...ok 340s closest.t67...ok 340s closest.t68...ok 340s closest.t69...ok 340s closest.t70...ok 340s closest.t71...ok 340s 340s ########################################################### 340s # 340s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 340s # 340s ########################################################### 340s 340s closest.t01...ok 340s closest.t02...ok 340s closest.t03...ok 340s closest.t04...ok 340s closest.t05...ok 340s closest.t06...ok 340s closest.t07...ok 340s closest.t08...ok 340s closest.t09...ok 340s closest.t10...ok 340s closest.t11...ok 340s closest.t12...ok 340s closest.t13...ok 340s closest.t14...ok 340s closest.t15...ok 340s closest.t16...ok 340s closest.t17...ok 340s closest.t18...ok 340s closest.t19...ok 340s closest.20...ok 340s closest.21...ok 340s closest.22...ok 341s closest.23...ok 341s 341s ########################################################### 341s # 341s # K CLOSEST HITS TESTS 341s # 341s ########################################################### 341s 341s kclosest.t1...ok 341s kclosest.t2...ok 341s kclosest.t3...ok 341s kclosest.t4...ok 341s kclosest.t5...ok 341s kclosest.t6...ok 341s kclosest.t7...ok 341s kclosest.t8...ok 341s kclosest.t9...ok 341s kclosest.t10...ok 341s 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. 341s ok 341s 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. 341s ok 341s kclosest.t13...ok 341s Warning: Fewer hits (3) found on chr1 than requested (7). It is likely that there are fewer total records on that chromosome than requested. 341s 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. 341s ok 341s 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. 341s ok 341s kclosest.t16...ok 341s 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. 341s ok 341s 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. 341s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s kclosest.t25...ok 341s 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. 341s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s 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. 341s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s ok 341s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested. 341s kclosest.t29...ok 341s kclosest.t30...ok 341s 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. 341s ok 341s Warning: Fewer hits (9) found on chr1 than requested (10). It is likely that there are fewer total records on that chromosome than requested. 341s kclosest.t32...ok 341s kclosest.t33...ok 341s kclosest.t34...ok 342s kclosest.t35...ok 342s kclosest.t36...ok 342s kclosest.t37...ok 342s kclosest.t38...ok 342s kclosest.t39...ok 342s kclosest.t40...ok 342s kclosest.t41...ok 342s kclosest.t42...ok 342s kclosest.t43...ok 342s kclosest.t44...ok 342s kclosest.t45...ok 342s Testing bedtools cluster: 342s cluster.t1...ok 342s cluster.t2...ok 342s Testing bedtools complement: 342s complement.t1...ok 342s complement.t2...ok 342s complement.t3...ok 342s complement.t4...ok 342s complement.t5...ok 342s complement.t6...ok 342s complement.t7...ok 342s complement.t8...ok 342s complement.t9...ok 342s complement.t9...ok 342s complement.t10...ok 342s Testing bedtools coverage: 342s coverage.t1...ok 342s coverage.t1b...ok 342s coverage.t2...ok 342s coverage.t2b...ok 342s coverage.t3...ok 342s coverage.t3b...ok 342s coverage.t4...ok 342s coverage.t4b...ok 342s coverage.t5...ok 342s coverage.t5b...ok 342s coverage.t6...ok 342s coverage.t6b...ok 342s coverage.t7...ok 343s coverage.t7b...ok 343s coverage.t8...ok 343s coverage.t8b...ok 343s coverage.t9...ok 343s coverage.t9b...ok 343s coverage.t10...ok 343s coverage.t10b...ok 343s coverage.t11...ok 343s coverage.t11b...ok 343s coverage.t12...ok 343s coverage.t12b...ok 343s coverage.t13...ok 343s coverage.t13b...ok 343s coverage.t14...ok 343s coverage.t14b...ok 343s coverage.t15...ok 343s coverage.t15b...ok 343s coverage.t16...ok 343s coverage.t16b...ok 343s coverage.t17...ok 343s coverage.t17b...ok 343s coverage.t18...ok 343s coverage.t18b...ok 343s coverage.t19...ok 343s coverage.t19b...ok 343s coverage.t20...ok 343s Testing bedtools expand: 343s expand.t1...ok 343s expand.t2...ok 343s expand.t3...ok 343s Testing bedtools fisher: 343s fisher.t1...ok 343s fisher.t2...ok 343s fisher.t3...ok 343s fisher.t4...ok 343s fisher.t5...ok 343s fisher.t6...ok 343s Testing bedtools flank: 343s flank.t1...ok 343s flank.t2...ok 343s flank.t3...ok 343s flank.t4...ok 343s flank.t5...ok 343s flank.t6...ok 344s flank.t7...ok 344s flank.t8...ok 344s flank.t9...ok 344s flank.t10...ok 344s flank.t11...ok 344s Testing bedtools general: 344s general.t01...ok 344s general.t02...ok 344s general.t03...ok 344s general.t05...ok 344s general.t06...ok 344s general.t07...ok 344s general.t08...ok 344s general.t09...ok 344s general.t10...ok 344s general.t11...ok 344s general.t12...ok 344s general.t13...ok 344s general.t14...ok 344s general.15...ok 344s general.t16...ok 344s general.t17...ok 344s general.t18...ok 344s general.t19...ok 344s general.t20...ok 344s general.t21...ok 344s general.22...ok 344s general.t23...ok 344s general.t24...ok 344s general.t25...ok 344s general.t26...ok 344s general.t27...ok 344s general.t28...ok 344s general.29...ok 345s general.t30...ok 345s general.t31...ok 345s general.t32...ok 345s general.t33...ok 345s general.t34...ok 345s general.t35...ok 345s general.36...ok 345s general.t37...ok 345s general.t38...ok 345s general.t39...ok 345s general.t40...ok 345s general.t41...ok 345s general.t42...ok 345s general.t43...ok 345s general.t44...ok 345s general.t45...ok 345s general.t46...ok 345s Testing bedtools genomecov: 345s genomecov.t1...ok 345s genomecov.t2...ok 345s genomecov.t3...ok 345s genomecov.t4...ok 345s genomecov.t5...ok 345s genomecov.t6...ok 345s genomecov.t7...ok 345s genomecov.t8...ok 345s genomecov.t9...ok 345s genomecov.t10...ok 345s genomecov.t11...ok 345s genomecov.t12...ok 345s genomecov.t13...ok 345s genomecov.t14...ok 345s genomecov.t15...ok 345s genomecov.t16...ok 346s genomecov.t17...ok 350s genomecov.t18...ok 350s Testing bedtools getfasta: 350s getfasta.t01...ok 350s getfasta.t02...ok 350s getfasta.t03...ok 350s getfasta.t04...ok 350s getfasta.t05...ok 350s getfasta.t06...ok 350s getfasta.t07...ok 350s getfasta.t08...ok 350s getfasta.t09...ok 351s getfasta.t10...ok 351s getfasta.t11...ok 351s getfasta.t12a...ok 351s getfasta.t12a...ok 351s getfasta.t12b...ok 351s getfasta.t13a...ok 351s getfasta.t13b...ok 351s getfasta.t13c...ok 351s getfasta.t14...ok 351s getfasta.t15...ok 351s getfasta.t134..ok 351s getfasta.t16..ok 351s getfasta.t17..ok 351s getfasta.t18...ok 351s Testing bedtools groupby: 351s groupby.t1...ok 351s groupby.t2...ok 351s groupby.t3...ok 351s groupby.t4...ok 351s groupby.t5...ok 351s groupby.t6...ok 351s groupby.t7...ok 351s groupby.t8...ok 351s groupby.t9...ok 351s groupby.t10...ok 351s groupby.t11...ok 351s groupby.t12...ok 351s groupby.t13...ok 351s groupby.t14...ok 351s groupby.t16...ok 351s groupby.t17...ok 351s groupby.t18...ok 351s groupby.t19...\c 351s ok 351s groupby.t20...\c 352s ok 352s Testing bedtools intersect: 352s intersect.t01...ok 352s intersect.t02...ok 352s intersect.t03...ok 352s intersect.t04...ok 352s intersect.t05...ok 352s intersect.t06...ok 352s intersect.t07...ok 352s intersect.t08...ok 352s intersect.t09...ok 352s intersect.t10...ok 352s intersect.t11...ok 352s intersect.t12...ok 352s intersect.t13...ok 352s intersect.t14...ok 352s intersect.t15...ok 352s intersect.t16...ok 352s intersect.t17...ok 352s intersect.t18...ok 352s intersect.t19...ok 352s intersect.t20...ok 352s intersect.t21...ok 352s intersect.t22...ok 352s intersect.t22.a...ok 352s intersect.t22.b...ok 352s intersect.t22.c...ok 352s intersect.t22.d...ok 352s intersect.t22.e...ok 352s intersect.t22.f...ok 352s intersect.t22.g...ok 352s intersect.t22.h...ok 352s intersect.t22.i...ok 352s intersect.t22.j...ok 352s intersect.t22.j...ok 353s intersect.t22.k...ok 353s intersect.t22.l...ok 353s intersect.t22.m...ok 353s intersect.t22.n...ok 353s intersect.t22.o...ok 353s intersect.t22.p...ok 353s intersect.t22.q...ok 353s intersect.t22.r...ok 353s intersect.t22.s...ok 353s intersect.t22.t...ok 353s intersect.t22.u...ok 353s intersect.t22.v...ok 353s intersect.t22.w...ok 353s intersect.t23...ok 353s intersect.t24...ok 353s intersect.t25...ok 353s intersect.t26...ok 353s intersect.t27...ok 353s intersect.t28...ok 353s intersect.t29...ok 353s intersect.t30...ok 353s intersect.t31...ok 353s intersect.t32...ok 353s intersect.t33...ok 353s intersect.t34...ok 353s intersect.t35...ok 353s intersect.t36...ok 353s intersect.t37...ok 353s intersect.t38...ok 353s intersect.t39...ok 353s intersect.t40...ok 353s intersect.t41...ok 354s intersect.t42...ok 354s intersect.t43...ok 354s intersect.t44...ok 354s intersect.t45...ok 354s intersect.t46...ok 354s intersect.t47...ok 354s intersect.t48...ok 354s intersect.t49...ok 354s intersect.t50...ok 354s intersect.t51...ok 354s intersect.t52...ok 354s intersect.t53...ok 354s intersect.t54...ok 354s intersect.t55...ok 354s intersect.t56...ok 354s intersect.t57...ok 354s intersect.t58...ok 354s intersect.t59...ok 354s intersect.t60...ok 354s intersect.t61...ok 354s intersect.t62...ok 354s intersect.t63...ok 354s intersect.t64...ok 354s intersect.t65...ok 354s intersect.t66...ok 354s intersect.t67...ok 354s intersect.t68...ok 354s intersect.t69...ok 354s intersect.t70...ok 354s intersect.t71...ok 354s intersect.t72...ok 354s intersect.t73...ok 354s intersect.t74...ok 355s intersect.t75...ok 355s intersect.t76...ok 355s intersect.t77...ok 355s intersect.t78...ok 355s intersect.t79...ok 355s intersect.t80...ok 355s intersect.t81...ok 355s intersect.t82...ok 355s intersect.t83...ok 355s intersect.new.t01...ok 355s intersect.new.t02...ok 355s intersect.new.t03...ok 355s intersect.new.t04...ok 355s intersect.new.t05...ok 355s intersect.new.t06...ok 355s intersect.new.t07...ok 355s intersect.new.t08...ok 355s intersect.new.t09...ok 355s intersect.new.t10...ok 355s intersect.new.t11...ok 355s intersect.new.t12...ok 355s intersect.new.t13...ok 355s intersect.new.t14...ok 355s intersect.new.t15...ok 355s intersect.new.t16...ok 355s intersect.new.t17...ok 356s intersect.new.t18...ok 356s intersect.new.t19...ok 356s intersect.new.t20...ok 356s intersect.new.t20.b...ok 356s intersect.new.t20.c...ok 356s intersect.new.t21...ok 356s intersect.new.t22...ok 356s intersect.new.t23...ok 356s intersect.new.t24...ok 356s intersect.new.t25...ok 357s intersect.new.t26...ok 358s intersect.new.t27...ok 358s intersect.new.t28...ok 358s intersect.new.t29...ok 358s intersect.new.t30...ok 358s intersect.new.t31...ok 359s intersect.new.t32...ok 359s intersect.new.t33...ok 359s intersect.new.t34...ok 359s intersect.new.t35...ok 360s intersect.new.t36...ok 360s intersect.new.t37...ok 361s intersect.new.t38...ok 361s intersect.new.t39...ok 361s intersect.new.t40...ok 361s intersect.new.t41...ok 362s intersect.new.t42...ok 362s intersect.new.t43...ok 362s intersect.new.t44...ok 362s intersect.new.t45...ok 363s intersect.new.t46...ok 363s intersect.new.t47...ok 363s intersect.new.t48...ok 363s intersect.new.t49...ok 363s intersect.new.t50...ok 363s intersect.new.t51...ok 363s intersect.new.t52...ok 363s intersect.new.t53...ok 363s intersect.new.t54...ok 363s intersect.new.t55...ok 363s intersect.new.t56...ok 363s intersect.new.t57...ok 363s intersect.new.t58...ok 363s intersect.new.t59...ok 363s intersect.new.t60...ok 363s intersect.new.t61...ok 363s intersect.new.t62...ok 363s intersect.new.t63...ok 363s intersect.new.t64...ok 363s intersect.new.t65...ok 363s intersect.new.t66...ok 363s intersect.new.t67a...ok 363s intersect.new.t67b...ok 363s intersect.new.t68a...ok 364s intersect.new.t68b...ok 364s intersect.new.t69...ok 364s intersect.new.t70...ok 364s intersect.new.t71...ok 364s intersect.new.t72...ok 364s intersect.new.t73...ok 364s intersect.new.t74...ok 364s intersect.new.t75...ok 364s intersect.new.t76...ok 364s intersect.new.t77...ok 364s intersect.new.t78...ok 364s intersect.new.t79...ok 364s intersect.new.t80...ok 364s intersect.new.t81...ok 364s 364s ########################################################### 364s # 364s # MULTIPLE DATABASE INTERSECTION 364s # 364s ########################################################### 364s 364s intersect.t01...ok 364s intersect.t02...ok 364s intersect.t03...ok 364s intersect.t04...ok 364s intersect.t05...ok 364s intersect.t06...ok 364s intersect.t07...ok 364s intersect.t08...ok 364s intersect.t09...ok 364s intersect.t10...ok 365s intersect.t11...ok 365s intersect.t12...ok 365s intersect.t13...ok 365s intersect.t14...ok 365s intersect.t15...ok 365s intersect.t16...ok 365s intersect.t17...ok 365s intersect.t18...ok 365s intersect.t13...ok 365s intersect.t19...ok 365s intersect.t20...ok 365s intersect.t21...ok 365s intersect.t22...ok 365s intersect.t23...ok 365s intersect.t24...ok 365s 365s ########################################################### 365s # 365s # CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 365s # 365s ########################################################### 365s 365s intersect.t01...ok 365s intersect.t02...ok 365s intersect.t03...ok 365s intersect.t04...ok 365s intersect.t05...ok 365s intersect.t06...ok 365s intersect.t07...ok 365s intersect.t08...ok 365s intersect.t09...ok 365s intersect.t10...ok 365s intersect.t11...ok 365s intersect.t12...ok 365s intersect.t13...ok 365s intersect.t14...ok 366s intersect.t15...ok 366s intersect.t16...ok 366s intersect.t17...ok 366s intersect.t18...ok 366s intersect.t19...ok 366s intersect.20...ok 366s intersect.21...ok 366s intersect.22...ok 366s intersect.23...ok 366s Testing bedtools jaccard: 366s jaccard.t01...ok 366s jaccard.t02...ok 366s jaccard.t03...ok 366s jaccard.t05...ok 366s jaccard.t06...ok 366s jaccard.t07...ok 366s jaccard.t08...ok 366s jaccard.t09...ok 366s jaccard.t10...ok 366s jaccard.t11...ok 366s jaccard.t12...ok 366s jaccard.t13...ok 366s jaccard.t14...ok 366s jaccard.t15...ok 366s jaccard.t16...ok 366s Testing bedtools makewindows: 366s makewindows.t01...ok 366s makewindows.t02...ok 366s makewindows.t03...ok 366s makewindows.t04...ok 366s makewindows.t05...ok 366s makewindows.t06...ok 366s makewindows.t07...ok 366s makewindows.t08...ok 366s makewindows.t09...ok 366s Testing bedtools map: 367s map.t01...ok 367s map.t02...ok 367s map.t03...ok 367s map.t04...ok 367s map.t05...ok 367s map.t06...ok 367s map.t07...ok 367s map.t08...ok 367s map.t09...ok 367s map.t10...ok 367s map.t11...ok 367s map.t12...ok 367s map.t13...ok 367s map.t14...ok 367s map.t15...ok 367s map.t16...ok 367s map.t17...ok 367s map.t18...ok 367s map.t19...ok 367s map.t20...ok 367s map.t21...ok 367s map.t22..ok 367s map.t23..ok 367s map.t24..ok 367s map.t25..ok 367s map.t26..ok 367s map.t27..ok 367s map.t28..ok 367s map.t29..ok 367s map.t30..ok 367s map.t31..ok 367s map.t32..ok 367s map.t33..ok 367s map.t33..ok 367s map.t33..ok 367s map.t34..ok 367s map.t35..ok 367s map.t36..ok 367s map.t37..ok 367s map.t38..ok 368s map.t39..ok 368s map.t40..ok 368s map.t41..ok 368s map.t42..ok 368s map.t43..ok 368s map.t44...ok 368s map.t45...ok 368s map.t46...ok 368s map.t47...ok 368s map.t48...ok 368s map.t49...ok 368s map.t50...ok 368s map.t51...ok 368s map.t52...ok 368s map.t53...ok 368s map.t54...ok 368s map.t55...ok 368s Testing bedtools merge: 368s merge.t1...ok 368s merge.t2...ok 368s merge.t3...ok 368s merge.t4...ok 368s merge.t5...ok 368s merge.t6...ok 368s merge.t7...ok 368s merge.t8...ok 368s merge.t9a...ok 368s merge.t9b...ok 368s merge.t10...ok 368s merge.t11...ok 368s merge.t12...ok 369s merge.t13...ok 369s merge.t14...ok 369s merge.t15...ok 369s merge.t16...ok 369s merge.t17...ok 369s merge.t18...ok 369s merge.t19...ok 369s merge.t20...ok 369s merge.t21...ok 369s merge.t22...ok 369s merge.t23a...ok 369s merge.t23b...ok 369s merge.t24...ok 369s merge.t25...ok 369s merge.t26...ok 369s merge.t27...ok 369s merge.t28...ok 369s merge.t29...ok 369s merge.t30...ok 369s merge.t31...ok 369s merge.t32...ok 369s merge.t33...ok 369s merge.t34...ok 369s merge.t35...ok 369s merge.t36...ok 369s merge.t37...ok 370s merge.t38...ok 370s merge.t39...ok 370s merge.t40...ok 370s merge.t41...ok 370s merge.t42...ok 370s merge.t43...ok 370s merge.t44a...ok 370s merge.t44b...skipped - could not find vcfSVtest.2.vcf 370s merge.t45...ok 370s merge.t46...ok 370s merge.t47...ok 370s merge.t48...ok 370s merge.t49...ok 371s merge.t50...ok 371s Testing bedtools multicov: 371s multicov.t1...ok 371s multicov.t2...ok 371s multicov.t3...ok 371s multicov.t4...ok 371s multicov.t5...ok 371s multicov.t6...ok 371s multicov.t7...ok 371s multicov.t8...ok 371s multicov.t9...ok 371s multicov.t10...ok 371s Testing bedtools negativecontrol: 371s Testing bedtools reldist: 371s reldist.t01...ok 372s reldist.t02...ok 372s reldist.t03...ok 372s reldist.t02...ok 372s Testing bedtools sample: 373s sample.t01...ok 373s sample.new.t02...ok 373s sample.new.t03...ok 373s sample.new.t04...ok 373s sample.new.t05...ok 373s sample.new.t06...ok 373s sample.new.t07...ok 373s sample.new.t08...ok 373s sample.new.t09...ok 373s Testing bedtools shift: 373s shift.t1...ok 373s shift.t2...ok 373s shift.t3...ok 373s shift.t3...ok 373s shift.t4...ok 373s shift.t5...ok 373s shift.t6...ok 373s shift.t7...ok 373s shift.t8...ok 373s shift.t9...ok 373s shift.t10...ok 373s shift.t11...ok 373s Testing bedtools shuffle: 373s shuffle.t1...ok 373s shuffle.t2...ok 373s shuffle.t3...ok 373s shuffle.t4...ok 373s shuffle.t5...ok 373s shuffle.t6...ok 373s Testing bedtools slop: 373s slop.t1...ok 373s slop.t2...ok 373s slop.t3...ok 373s slop.t4...ok 373s slop.t5...ok 373s slop.t6...ok 373s slop.t7...ok 373s slop.t8...ok 373s slop.t9...ok 374s slop.t10...ok 374s slop.t11...ok 374s slop.t12...ok 374s slop.t13...ok 374s slop.t14...ok 374s slop.t15...ok 374s slop.t16...ok 374s slop.t17...ok 374s slop.t18...ok 374s slop.t19...ok 374s slop.t20...ok 374s slop.t21...ok 374s slop.t22...ok 374s Testing bedtools sort: 374s sort.t01...ok 374s sort.t02...ok 374s sort.t03...ok 374s sort.t04...ok 374s sort.t05...ok 374s sort.t06...ok 374s sort.t07...ok 374s sort.t08...ok 374s sort.t09...ok 374s sort.t10...ok 374s Testing bedtools spacing: 374s spacing.t01...ok 374s Testing bedtools split: 374s split.01.size...ok 374s split.02.simple...ok 375s spliit.03.simple...ok 375s Testing bedtools subtract: 375s subtract.t1...ok 375s subtract.t2...ok 375s subtract.t3...ok 375s subtract.t4...ok 375s subtract.t5...ok 375s subtract.t6...ok 375s subtract.t7...ok 375s subtract.t8...ok 375s subtract.t9...ok 375s subtract.t10...ok 375s subtract.t11...ok 375s subtract.t12...ok 375s subtract.t13...ok 375s subtract.t14...ok 375s subtract.t15...ok 375s subtract.t16...ok 375s subtract.t17...ok 375s subtract.t18...ok 375s subtract.t19...ok 375s subtract.t20...ok 375s subtract.t21...ok 375s 375s 375s -------------------------- 375s Test Results 375s -------------------------- 375s 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 375s Tools failing: negativecontrol 375s NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, 375s something went wrong with this test script. 376s autopkgtest [22:47:37]: test run-unit-test: -----------------------] 380s autopkgtest [22:47:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 380s run-unit-test PASS 384s autopkgtest [22:47:45]: @@@@@@@@@@@@@@@@@@@@ summary 384s run-unit-test PASS