0s autopkgtest [17:10:31]: starting date and time: 2024-03-16 17:10:31+0000
  0s autopkgtest [17:10:31]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [17:10:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zjvzicxu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-20.secgroup --name adt-noble-arm64-bedtools-20240316-171030-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
101s autopkgtest [17:12:12]: testbed dpkg architecture: arm64
101s autopkgtest [17:12:12]: testbed apt version: 2.7.12
101s autopkgtest [17:12:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
102s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB]
102s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB]
102s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
102s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
102s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
102s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
102s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
102s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
102s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB]
103s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
103s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB]
103s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
105s Fetched 9063 kB in 2s (5081 kB/s)
105s Reading package lists...
109s Reading package lists...
109s Building dependency tree...
109s Reading state information...
110s Calculating upgrade...
111s The following packages will be REMOVED:
111s   libssl3
111s The following NEW packages will be installed:
111s   libssl3t64
111s The following packages have been kept back:
111s   curl
111s The following packages will be upgraded:
111s   openssl ubuntu-minimal ubuntu-standard
111s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
111s Need to get 2775 kB of archives.
111s After this operation, 72.7 kB of additional disk space will be used.
111s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
112s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
112s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
114s Fetched 2775 kB in 2s (1607 kB/s)
115s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
115s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
115s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
116s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
116s  wget depends on libssl3 (>= 3.0.0).
116s  u-boot-tools depends on libssl3 (>= 3.0.0).
116s  tnftp depends on libssl3 (>= 3.0.0).
116s  tcpdump depends on libssl3 (>= 3.0.0).
116s  systemd-resolved depends on libssl3 (>= 3.0.0).
116s  systemd depends on libssl3 (>= 3.0.0).
116s  sudo depends on libssl3 (>= 3.0.0).
116s  sbsigntool depends on libssl3 (>= 3.0.0).
116s  rsync depends on libssl3 (>= 3.0.0).
116s  python3-cryptography depends on libssl3 (>= 3.0.0).
116s  openssh-server depends on libssl3 (>= 3.0.10).
116s  openssh-client depends on libssl3 (>= 3.0.10).
116s  mtd-utils depends on libssl3 (>= 3.0.0).
116s  mokutil depends on libssl3 (>= 3.0.0).
116s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
116s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
116s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
116s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
116s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
116s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
116s  libnvme1 depends on libssl3 (>= 3.0.0).
116s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
116s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
116s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
116s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
116s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
116s  kmod depends on libssl3 (>= 3.0.0).
116s  dhcpcd-base depends on libssl3 (>= 3.0.0).
116s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
116s 
116s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74758 files and directories currently installed.)
116s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
116s Selecting previously unselected package libssl3t64:arm64.
116s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74747 files and directories currently installed.)
116s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
116s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
117s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ...
117s Unpacking ubuntu-minimal (1.536) over (1.535) ...
118s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ...
118s Unpacking ubuntu-standard (1.536) over (1.535) ...
119s Setting up ubuntu-minimal (1.536) ...
119s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
119s Setting up ubuntu-standard (1.536) ...
119s Setting up openssl (3.0.13-0ubuntu1) ...
119s Processing triggers for man-db (2.12.0-3) ...
120s Processing triggers for libc-bin (2.39-0ubuntu2) ...
121s Reading package lists...
121s Building dependency tree...
121s Reading state information...
124s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
127s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
127s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
127s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
128s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
130s Reading package lists...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
131s Calculating upgrade...
132s The following packages have been kept back:
132s   curl
132s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
132s Reading package lists...
133s Building dependency tree...
133s Reading state information...
133s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
137s autopkgtest [17:12:48]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
138s autopkgtest [17:12:49]: @@@@@@@@@@@@@@@@@@@@ apt-source bedtools
148s Get:1 http://ftpmaster.internal/ubuntu noble/universe bedtools 2.31.1+dfsg-2 (dsc) [2230 B]
148s Get:2 http://ftpmaster.internal/ubuntu noble/universe bedtools 2.31.1+dfsg-2 (tar) [14.5 MB]
148s Get:3 http://ftpmaster.internal/ubuntu noble/universe bedtools 2.31.1+dfsg-2 (diff) [14.5 kB]
148s gpgv: Signature made Mon Dec  4 19:20:23 2023 UTC
148s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
148s gpgv:                issuer "emollier@debian.org"
148s gpgv: Can't check signature: No public key
148s dpkg-source: warning: cannot verify inline signature for ./bedtools_2.31.1+dfsg-2.dsc: no acceptable signature found
150s autopkgtest [17:13:01]: testing package bedtools version 2.31.1+dfsg-2
150s autopkgtest [17:13:01]: build not needed
153s autopkgtest [17:13:04]: test run-unit-test: preparing testbed
154s Reading package lists...
155s Building dependency tree...
155s Reading state information...
155s Starting pkgProblemResolver with broken count: 0
155s Starting 2 pkgProblemResolver with broken count: 0
155s Done
156s The following additional packages will be installed:
156s   bedtools bedtools-test libdeflate0 libhtscodecs2 tabix
157s The following NEW packages will be installed:
157s   autopkgtest-satdep bedtools bedtools-test libdeflate0 libhtscodecs2 tabix
158s 0 upgraded, 6 newly installed, 0 to remove and 1 not upgraded.
158s Need to get 19.5 MB/19.5 MB of archives.
158s After this operation, 52.0 MB of additional disk space will be used.
158s Get:1 /tmp/autopkgtest.MKviUE/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B]
158s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB]
158s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 bedtools-test all 2.31.1+dfsg-2 [18.2 MB]
160s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
160s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
160s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 tabix arm64 1.19+ds-1.1build2 [515 kB]
163s Fetched 19.5 MB in 3s (6150 kB/s)
164s Selecting previously unselected package bedtools.
164s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74760 files and directories currently installed.)
164s Preparing to unpack .../0-bedtools_2.31.1+dfsg-2_arm64.deb ...
164s Unpacking bedtools (2.31.1+dfsg-2) ...
164s Selecting previously unselected package bedtools-test.
164s Preparing to unpack .../1-bedtools-test_2.31.1+dfsg-2_all.deb ...
164s Unpacking bedtools-test (2.31.1+dfsg-2) ...
164s Selecting previously unselected package libdeflate0:arm64.
165s Preparing to unpack .../2-libdeflate0_1.19-1_arm64.deb ...
165s Unpacking libdeflate0:arm64 (1.19-1) ...
165s Selecting previously unselected package libhtscodecs2:arm64.
165s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_arm64.deb ...
165s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
165s Selecting previously unselected package tabix.
165s Preparing to unpack .../4-tabix_1.19+ds-1.1build2_arm64.deb ...
165s Unpacking tabix (1.19+ds-1.1build2) ...
165s Selecting previously unselected package autopkgtest-satdep.
165s Preparing to unpack .../5-1-autopkgtest-satdep.deb ...
165s Unpacking autopkgtest-satdep (0) ...
165s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
165s Setting up libdeflate0:arm64 (1.19-1) ...
165s Setting up bedtools-test (2.31.1+dfsg-2) ...
165s Setting up tabix (1.19+ds-1.1build2) ...
165s Setting up bedtools (2.31.1+dfsg-2) ...
165s Setting up autopkgtest-satdep (0) ...
165s Processing triggers for man-db (2.12.0-3) ...
166s Processing triggers for libc-bin (2.39-0ubuntu2) ...
171s (Reading database ... 75332 files and directories currently installed.)
171s Removing autopkgtest-satdep (0) ...
172s autopkgtest [17:13:23]: test run-unit-test: [-----------------------
172s Testing bedtools bamtobed:
172s     bamtobed.t1...ok
172s     bamtobed.t2...ok
173s     bamtobed.t3...ok
173s     bamtobed.t4...ok
173s     bamtobed.t5...ok
173s     bamtobed.t6...ok
173s     bamtobed.t7...ok
173s     bamtobed.t8...ok
173s     bamtobed.t9...ok
173s     bamtobed.t10...ok
173s     bamtobed.t9...ok
173s     bamtobed.t11...ok
173s     bamtobed.t12..ok
173s     bamtobed.t13..ok
173s Testing bedtools bamtofastq:
173s ok
173s ok
173s Testing bedtools bed12tobed6:
173s     bed12tobed6.t1...ok
173s     bed12tobed6.t2...ok
173s     bed12tobed6.t3...ok
173s     bed12tobed6.t4...ok
173s     bed12tobed6.t5...ok
173s Testing bedtools bedtobam:
173s     bedtobam.t1...ok
173s Testing bedtools bigchroms:
173s     bigchroms.t01...ok
173s     bigchroms.t02...ok
173s     bigchroms.t03... skip  set env var 'BT_NO_BIG_FILES' to run this test
173s     bigchroms.t04... merge ok
173s     bigchroms.t05... closest ok
173s Testing bedtools closest:
173s     closest.t1...ok
173s     closest.t2...ok
173s     closest.t3...ok
173s     closest.t4...ok
173s     closest.t5...ok
173s     closest.t6...ok
173s     closest.t7...ok
173s     closest.t8...ok
173s     closest.t9...ok
173s     closest.t10...ok
173s     closest.t11...ok
173s     closest.t13...ok
173s     closest.t14...ok
173s     closest.t15...ok
173s     closest.t16...ok
173s     closest.t17...ok
173s     closest.t18...ok
173s     closest.t19...ok
173s     closest.t20...ok
173s     closest.t21...ok
173s     closest.t22...ok
173s     closest.t23...ok
173s     closest.t24...ok
173s     closest.t25...ok
173s     closest.t26...ok
173s     closest.t27...ok
173s     closest.t28...ok
173s     closest.t29...ok
173s     closest.t30...ok
173s     closest.t31...ok
173s     closest.t32...ok
174s     closest.t33...ok
174s     closest.t34...ok
174s     closest.t35...ok
174s     closest.t36...ok
174s     closest.t37...ok
174s     closest.t38...ok
174s     closest.t39...ok
174s     closest.t40...ok
174s     closest.t41...ok
174s     closest.t42...ok
174s     closest.t43...ok
174s     closest.t44...ok
174s     closest.t45...ok
174s     closest.t46...ok
174s     closest.t47...ok
174s     closest.t48...ok
174s     closest.t49...ok
174s     closest.t50...ok
174s     closest.t51...ok
174s     closest.t52...ok
174s     closest.t53...ok
174s     closest.t54...ok
174s     closest.t55...ok
174s     closest.t56...ok
174s     closest.t57...ok
174s     closest.t58...ok
174s     closest.t59...ok
174s     closest.t60...ok
174s     closest.t61...ok
174s     closest.t62...ok
174s     closest.t63...ok
174s     closest.t64...ok
174s     closest.t65...ok
174s     closest.t66...ok
174s     closest.t67...ok
174s     closest.t68...ok
174s     closest.t69...ok
174s     closest.t70...ok
174s     closest.t71...ok
174s 
174s ###########################################################
174s #  
174s #  CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 
174s #
174s ###########################################################
174s 
174s     closest.t01...ok
174s     closest.t02...ok
174s     closest.t03...ok
174s     closest.t04...ok
174s     closest.t05...ok
174s     closest.t06...ok
174s     closest.t07...ok
175s     closest.t08...ok
175s     closest.t09...ok
175s     closest.t10...ok
175s     closest.t11...ok
175s     closest.t12...ok
175s     closest.t13...ok
175s     closest.t14...ok
175s     closest.t15...ok
175s     closest.t16...ok
175s     closest.t17...ok
175s     closest.t18...ok
175s     closest.t19...ok
175s     closest.20...ok
175s     closest.21...ok
175s     closest.22...ok
175s     closest.23...ok
175s 
175s ###########################################################
175s #  
175s #  K CLOSEST HITS TESTS
175s #
175s ###########################################################
175s 
175s     kclosest.t1...ok
175s     kclosest.t2...ok
175s     kclosest.t3...ok
175s     kclosest.t4...ok
175s     kclosest.t5...ok
175s     kclosest.t6...ok
175s     kclosest.t7...ok
175s     kclosest.t8...ok
175s     kclosest.t9...ok
175s     kclosest.t10...ok
175s     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.
175s ok
175s     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.
175s ok
175s     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.
175s ok
175s     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.
175s ok
175s     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.
175s ok
175s     kclosest.t16...ok
175s     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.
175s ok
175s     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.
175s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (10) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (9) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (6) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (5) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     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.
175s Warning: Fewer hits (4) found on chr1 than requested (15). It is likely that there are fewer total records on that chromosome than requested.
175s ok
175s     kclosest.t30...ok
175s     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.
175s ok
175s     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.
175s ok
175s     kclosest.t33...ok
175s     kclosest.t34...ok
175s     kclosest.t35...ok
175s     kclosest.t36...ok
175s     kclosest.t37...ok
175s     kclosest.t38...ok
175s     kclosest.t39...ok
175s     kclosest.t40...ok
175s     kclosest.t41...ok
175s     kclosest.t42...ok
175s     kclosest.t43...ok
175s     kclosest.t44...ok
175s     kclosest.t45...ok
175s Testing bedtools cluster:
175s     cluster.t1...ok
175s     cluster.t2...ok
175s Testing bedtools complement:
175s     complement.t1...ok
175s     complement.t2...ok
175s     complement.t3...ok
175s     complement.t4...ok
175s     complement.t5...ok
175s     complement.t6...ok
175s     complement.t7...ok
175s     complement.t8...ok
175s     complement.t9...ok
176s     complement.t9...ok
176s     complement.t10...ok
176s Testing bedtools coverage:
176s     coverage.t1...ok
176s     coverage.t1b...ok
176s     coverage.t2...ok
176s     coverage.t2b...ok
176s     coverage.t3...ok
176s     coverage.t3b...ok
176s     coverage.t4...ok
176s     coverage.t4b...ok
176s     coverage.t5...ok
176s     coverage.t5b...ok
176s     coverage.t6...ok
176s     coverage.t6b...ok
176s     coverage.t7...ok
176s     coverage.t7b...ok
176s     coverage.t8...ok
176s     coverage.t8b...ok
176s     coverage.t9...ok
176s     coverage.t9b...ok
176s     coverage.t10...ok
176s     coverage.t10b...ok
176s     coverage.t11...ok
176s     coverage.t11b...ok
176s     coverage.t12...ok
176s     coverage.t12b...ok
176s     coverage.t13...ok
176s     coverage.t13b...ok
176s     coverage.t14...ok
176s     coverage.t14b...ok
176s     coverage.t15...ok
176s     coverage.t15b...ok
176s     coverage.t16...ok
176s     coverage.t16b...ok
176s     coverage.t17...ok
176s     coverage.t17b...ok
176s     coverage.t18...ok
176s     coverage.t18b...ok
176s     coverage.t19...ok
176s     coverage.t19b...ok
176s     coverage.t20...ok
176s Testing bedtools expand:
176s     expand.t1...ok
176s     expand.t2...ok
176s     expand.t3...ok
176s Testing bedtools fisher:
176s     fisher.t1...ok
176s     fisher.t2...ok
176s     fisher.t3...ok
176s     fisher.t4...ok
176s     fisher.t5...ok
176s     fisher.t6...ok
176s Testing bedtools flank:
176s     flank.t1...ok
176s     flank.t2...ok
176s     flank.t3...ok
176s     flank.t4...ok
176s     flank.t5...ok
176s     flank.t6...ok
176s     flank.t7...ok
176s     flank.t8...ok
176s     flank.t9...ok
176s     flank.t10...ok
176s     flank.t11...ok
176s Testing bedtools general:
176s     general.t01...ok
176s     general.t02...ok
176s     general.t03...ok
176s     general.t05...ok
176s     general.t06...ok
176s     general.t07...ok
176s     general.t08...ok
176s     general.t09...ok
176s     general.t10...ok
176s     general.t11...ok
176s     general.t12...ok
176s     general.t13...ok
176s     general.t14...ok
176s     general.15...ok
176s     general.t16...ok
176s     general.t17...ok
176s     general.t18...ok
176s     general.t19...ok
176s     general.t20...ok
176s     general.t21...ok
176s     general.22...ok
176s     general.t23...ok
176s     general.t24...ok
177s     general.t25...ok
177s     general.t26...ok
177s     general.t27...ok
177s     general.t28...ok
177s     general.29...ok
177s     general.t30...ok
177s     general.t31...ok
177s     general.t32...ok
177s     general.t33...ok
177s     general.t34...ok
177s     general.t35...ok
177s     general.36...ok
177s     general.t37...ok
177s     general.t38...ok
177s     general.t39...ok
177s     general.t40...ok
177s     general.t41...ok
177s     general.t42...ok
177s     general.t43...ok
177s     general.t44...ok
177s     general.t45...ok
177s     general.t46...ok
177s Testing bedtools genomecov:
177s     genomecov.t1...ok
177s     genomecov.t2...ok
177s     genomecov.t3...ok
177s     genomecov.t4...ok
177s     genomecov.t5...ok
177s     genomecov.t6...ok
177s     genomecov.t7...ok
177s     genomecov.t8...ok
177s     genomecov.t9...ok
177s     genomecov.t10...ok
177s     genomecov.t11...ok
177s     genomecov.t12...ok
177s     genomecov.t13...ok
177s     genomecov.t14...ok
177s     genomecov.t15...ok
177s     genomecov.t16...ok
177s     genomecov.t17...ok
179s     genomecov.t18...ok
179s Testing bedtools getfasta:
179s     getfasta.t01...ok
179s     getfasta.t02...ok
179s     getfasta.t03...ok
179s     getfasta.t04...ok
179s     getfasta.t05...ok
179s     getfasta.t06...ok
179s     getfasta.t07...ok
179s     getfasta.t08...ok
179s     getfasta.t09...ok
180s     getfasta.t10...ok
180s     getfasta.t11...ok
180s     getfasta.t12a...ok
180s     getfasta.t12a...ok
180s     getfasta.t12b...ok
180s     getfasta.t13a...ok
180s     getfasta.t13b...ok
180s     getfasta.t13c...ok
180s     getfasta.t14...ok
180s     getfasta.t15...ok
180s     getfasta.t134..ok
180s     getfasta.t16..ok
180s     getfasta.t17..ok
180s     getfasta.t18...ok
180s Testing bedtools groupby:
180s     groupby.t1...ok
180s     groupby.t2...ok
180s     groupby.t3...ok
180s     groupby.t4...ok
180s     groupby.t5...ok
180s     groupby.t6...ok
180s     groupby.t7...ok
180s     groupby.t8...ok
180s     groupby.t9...ok
180s     groupby.t10...ok
180s     groupby.t11...ok
180s     groupby.t12...ok
180s     groupby.t13...ok
180s     groupby.t14...ok
180s     groupby.t16...ok
180s     groupby.t17...ok
180s     groupby.t18...ok
180s     groupby.t19...\c
180s ok
180s     groupby.t20...\c
180s ok
180s Testing bedtools intersect:
180s     intersect.t01...ok
180s     intersect.t02...ok
180s     intersect.t03...ok
180s     intersect.t04...ok
180s     intersect.t05...ok
180s     intersect.t06...ok
181s     intersect.t07...ok
181s     intersect.t08...ok
181s     intersect.t09...ok
181s     intersect.t10...ok
181s     intersect.t11...ok
181s     intersect.t12...ok
181s     intersect.t13...ok
181s     intersect.t14...ok
181s     intersect.t15...ok
181s     intersect.t16...ok
181s     intersect.t17...ok
181s     intersect.t18...ok
181s     intersect.t19...ok
181s     intersect.t20...ok
181s     intersect.t21...ok
181s     intersect.t22...ok
181s     intersect.t22.a...ok
181s     intersect.t22.b...ok
181s     intersect.t22.c...ok
181s     intersect.t22.d...ok
181s     intersect.t22.e...ok
181s     intersect.t22.f...ok
181s     intersect.t22.g...ok
181s     intersect.t22.h...ok
181s     intersect.t22.i...ok
181s     intersect.t22.j...ok
181s     intersect.t22.j...ok
181s     intersect.t22.k...ok
181s     intersect.t22.l...ok
181s     intersect.t22.m...ok
181s     intersect.t22.n...ok
181s     intersect.t22.o...ok
181s     intersect.t22.p...ok
181s     intersect.t22.q...ok
181s     intersect.t22.r...ok
181s     intersect.t22.s...ok
181s     intersect.t22.t...ok
181s     intersect.t22.u...ok
181s     intersect.t22.v...ok
181s     intersect.t22.w...ok
181s     intersect.t23...ok
181s     intersect.t24...ok
181s     intersect.t25...ok
181s     intersect.t26...ok
181s     intersect.t27...ok
181s     intersect.t28...ok
181s     intersect.t29...ok
181s     intersect.t30...ok
181s     intersect.t31...ok
181s     intersect.t32...ok
181s     intersect.t33...ok
181s     intersect.t34...ok
181s     intersect.t35...ok
181s     intersect.t36...ok
181s     intersect.t37...ok
182s     intersect.t38...ok
182s     intersect.t39...ok
182s     intersect.t40...ok
182s     intersect.t41...ok
182s     intersect.t42...ok
182s     intersect.t43...ok
182s     intersect.t44...ok
182s     intersect.t45...ok
182s     intersect.t46...ok
182s     intersect.t47...ok
182s     intersect.t48...ok
182s     intersect.t49...ok
182s     intersect.t50...ok
182s     intersect.t51...ok
182s     intersect.t52...ok
182s     intersect.t53...ok
182s     intersect.t54...ok
182s     intersect.t55...ok
182s     intersect.t56...ok
182s     intersect.t57...ok
182s     intersect.t58...ok
182s     intersect.t59...ok
182s     intersect.t60...ok
182s     intersect.t61...ok
182s     intersect.t62...ok
182s     intersect.t63...ok
182s     intersect.t64...ok
182s     intersect.t65...ok
182s     intersect.t66...ok
182s     intersect.t67...ok
182s     intersect.t68...ok
182s     intersect.t69...ok
182s     intersect.t70...ok
182s     intersect.t71...ok
182s     intersect.t72...ok
182s     intersect.t73...ok
182s     intersect.t74...ok
182s     intersect.t75...ok
182s     intersect.t76...ok
182s     intersect.t77...ok
182s     intersect.t78...ok
182s     intersect.t79...ok
182s     intersect.t80...ok
182s     intersect.t81...ok
182s     intersect.t82...ok
182s     intersect.t83...ok
182s     intersect.new.t01...ok
182s     intersect.new.t02...ok
182s     intersect.new.t03...ok
182s     intersect.new.t04...ok
182s     intersect.new.t05...ok
182s     intersect.new.t06...ok
182s     intersect.new.t07...ok
182s     intersect.new.t08...ok
182s     intersect.new.t09...ok
182s     intersect.new.t10...ok
183s     intersect.new.t11...ok
183s     intersect.new.t12...ok
183s     intersect.new.t13...ok
183s     intersect.new.t14...ok
183s     intersect.new.t15...ok
183s     intersect.new.t16...ok
183s     intersect.new.t17...ok
183s     intersect.new.t18...ok
183s     intersect.new.t19...ok
183s     intersect.new.t20...ok
183s     intersect.new.t20.b...ok
183s     intersect.new.t20.c...ok
183s     intersect.new.t21...ok
183s     intersect.new.t22...ok
183s     intersect.new.t23...ok
183s     intersect.new.t24...ok
183s     intersect.new.t25...ok
183s     intersect.new.t26...ok
184s     intersect.new.t27...ok
184s     intersect.new.t28...ok
184s     intersect.new.t29...ok
184s     intersect.new.t30...ok
184s     intersect.new.t31...ok
184s     intersect.new.t32...ok
184s     intersect.new.t33...ok
185s     intersect.new.t34...ok
185s     intersect.new.t35...ok
185s     intersect.new.t36...ok
185s     intersect.new.t37...ok
185s     intersect.new.t38...ok
185s     intersect.new.t39...ok
185s     intersect.new.t40...ok
186s     intersect.new.t41...ok
186s     intersect.new.t42...ok
186s     intersect.new.t43...ok
186s     intersect.new.t44...ok
186s     intersect.new.t45...ok
186s     intersect.new.t46...ok
186s     intersect.new.t47...ok
186s     intersect.new.t48...ok
186s     intersect.new.t49...ok
186s     intersect.new.t50...ok
186s     intersect.new.t51...ok
186s     intersect.new.t52...ok
186s     intersect.new.t53...ok
187s     intersect.new.t54...ok
187s     intersect.new.t55...ok
187s     intersect.new.t56...ok
187s     intersect.new.t57...ok
187s     intersect.new.t58...ok
187s     intersect.new.t59...ok
187s     intersect.new.t60...ok
187s     intersect.new.t61...ok
187s     intersect.new.t62...ok
187s     intersect.new.t63...ok
187s     intersect.new.t64...ok
187s     intersect.new.t65...ok
187s     intersect.new.t66...ok
187s     intersect.new.t67a...ok
187s     intersect.new.t67b...ok
187s     intersect.new.t68a...ok
187s     intersect.new.t68b...ok
187s     intersect.new.t69...ok
187s     intersect.new.t70...ok
187s     intersect.new.t71...ok
187s     intersect.new.t72...ok
187s     intersect.new.t73...ok
187s     intersect.new.t74...ok
187s     intersect.new.t75...ok
187s     intersect.new.t76...ok
187s     intersect.new.t77...ok
187s     intersect.new.t78...ok
187s     intersect.new.t79...ok
188s     intersect.new.t80...ok
188s     intersect.new.t81...ok
188s 
188s ###########################################################
188s #  
188s #  MULTIPLE DATABASE INTERSECTION
188s #
188s ###########################################################
188s 
188s     intersect.t01...ok
188s     intersect.t02...ok
188s     intersect.t03...ok
188s     intersect.t04...ok
188s     intersect.t05...ok
188s     intersect.t06...ok
188s     intersect.t07...ok
188s     intersect.t08...ok
188s     intersect.t09...ok
188s     intersect.t10...ok
188s     intersect.t11...ok
188s     intersect.t12...ok
188s     intersect.t13...ok
188s     intersect.t14...ok
188s     intersect.t15...ok
188s     intersect.t16...ok
188s     intersect.t17...ok
188s     intersect.t18...ok
188s     intersect.t13...ok
188s     intersect.t19...ok
188s     intersect.t20...ok
188s     intersect.t21...ok
188s     intersect.t22...ok
188s     intersect.t23...ok
188s     intersect.t24...ok
188s 
188s ###########################################################
188s #  
188s #  CHROMOSOME SORT ORDER AND NAMING CONVENTIONS 
188s #
188s ###########################################################
188s 
188s     intersect.t01...ok
188s     intersect.t02...ok
188s     intersect.t03...ok
188s     intersect.t04...ok
188s     intersect.t05...ok
189s     intersect.t06...ok
189s     intersect.t07...ok
189s     intersect.t08...ok
189s     intersect.t09...ok
189s     intersect.t10...ok
189s     intersect.t11...ok
189s     intersect.t12...ok
189s     intersect.t13...ok
189s     intersect.t14...ok
189s     intersect.t15...ok
189s     intersect.t16...ok
189s     intersect.t17...ok
189s     intersect.t18...ok
189s     intersect.t19...ok
189s     intersect.20...ok
189s     intersect.21...ok
190s     intersect.22...ok
190s     intersect.23...ok
190s Testing bedtools jaccard:
190s     jaccard.t01...ok
190s     jaccard.t02...ok
190s     jaccard.t03...ok
190s     jaccard.t05...ok
190s     jaccard.t06...ok
190s     jaccard.t07...ok
190s     jaccard.t08...ok
190s     jaccard.t09...ok
190s     jaccard.t10...ok
190s     jaccard.t11...ok
190s     jaccard.t12...ok
190s     jaccard.t13...ok
190s     jaccard.t14...ok
190s     jaccard.t15...ok
190s     jaccard.t16...ok
190s Testing bedtools makewindows:
190s     makewindows.t01...ok
191s     makewindows.t02...ok
191s     makewindows.t03...ok
191s     makewindows.t04...ok
191s     makewindows.t05...ok
191s     makewindows.t06...ok
191s     makewindows.t07...ok
191s     makewindows.t08...ok
191s     makewindows.t09...ok
191s Testing bedtools map:
191s     map.t01...ok
191s     map.t02...ok
191s     map.t03...ok
191s     map.t04...ok
191s     map.t05...ok
191s     map.t06...ok
192s     map.t07...ok
192s     map.t08...ok
192s     map.t09...ok
192s     map.t10...ok
192s     map.t11...ok
192s     map.t12...ok
192s     map.t13...ok
192s     map.t14...ok
192s     map.t15...ok
192s     map.t16...ok
192s     map.t17...ok
192s     map.t18...ok
192s     map.t19...ok
192s     map.t20...ok
192s     map.t21...ok
192s     map.t22..ok
192s     map.t23..ok
192s     map.t24..ok
192s     map.t25..ok
192s     map.t26..ok
192s     map.t27..ok
192s     map.t28..ok
192s     map.t29..ok
192s     map.t30..ok
192s     map.t31..ok
192s     map.t32..ok
193s     map.t33..ok
193s     map.t33..ok
193s     map.t33..ok
193s     map.t34..ok
193s     map.t35..ok
193s     map.t36..ok
193s     map.t37..ok
193s     map.t38..ok
193s     map.t39..ok
193s     map.t40..ok
193s     map.t41..ok
193s     map.t42..ok
193s     map.t43..ok
193s     map.t44...ok
193s     map.t45...ok
193s     map.t46...ok
193s     map.t47...ok
193s     map.t48...ok
193s     map.t49...ok
193s     map.t50...ok
193s     map.t51...ok
193s     map.t52...ok
193s     map.t53...ok
193s     map.t54...ok
193s     map.t55...ok
193s Testing bedtools merge:
193s     merge.t1...ok
193s     merge.t2...ok
193s     merge.t3...ok
193s     merge.t4...ok
193s     merge.t5...ok
193s     merge.t6...ok
193s     merge.t7...ok
193s     merge.t8...ok
193s     merge.t9a...ok
193s     merge.t9b...ok
193s     merge.t10...ok
193s     merge.t11...ok
193s     merge.t12...ok
193s     merge.t13...ok
193s     merge.t14...ok
193s     merge.t15...ok
193s     merge.t16...ok
193s     merge.t17...ok
193s     merge.t18...ok
193s     merge.t19...ok
193s     merge.t20...ok
193s     merge.t21...ok
193s     merge.t22...ok
193s     merge.t23a...ok
193s     merge.t23b...ok
193s     merge.t24...ok
193s     merge.t25...ok
193s     merge.t26...ok
193s     merge.t27...ok
193s     merge.t28...ok
193s     merge.t29...ok
193s     merge.t30...ok
193s     merge.t31...ok
193s     merge.t32...ok
193s     merge.t33...ok
193s     merge.t34...ok
193s     merge.t35...ok
193s     merge.t36...ok
193s     merge.t37...ok
193s     merge.t38...ok
194s     merge.t39...ok
194s     merge.t40...ok
194s     merge.t41...ok
194s     merge.t42...ok
194s     merge.t43...ok
194s     merge.t44a...ok
194s     merge.t44b...skipped - could not find vcfSVtest.2.vcf
194s     merge.t45...ok
194s     merge.t46...ok
194s     merge.t47...ok
194s     merge.t48...ok
194s     merge.t49...ok
194s     merge.t50...ok
194s Testing bedtools multicov:
194s     multicov.t1...ok
194s     multicov.t2...ok
194s     multicov.t3...ok
194s     multicov.t4...ok
194s     multicov.t5...ok
194s     multicov.t6...ok
194s     multicov.t7...ok
194s     multicov.t8...ok
194s     multicov.t9...ok
194s     multicov.t10...ok
194s Testing bedtools negativecontrol:
194s Testing bedtools reldist:
194s     reldist.t01...ok
194s     reldist.t02...ok
194s     reldist.t03...ok
194s     reldist.t02...ok
194s Testing bedtools sample:
195s     sample.t01...ok
195s     sample.new.t02...ok
195s     sample.new.t03...ok
195s     sample.new.t04...ok
195s     sample.new.t05...ok
195s     sample.new.t06...ok
195s     sample.new.t07...ok
195s     sample.new.t08...ok
195s     sample.new.t09...ok
195s Testing bedtools shift:
195s     shift.t1...ok
195s     shift.t2...ok
195s     shift.t3...ok
195s     shift.t3...ok
195s     shift.t4...ok
195s     shift.t5...ok
196s     shift.t6...ok
196s     shift.t7...ok
196s     shift.t8...ok
196s     shift.t9...ok
196s     shift.t10...ok
196s     shift.t11...ok
196s Testing bedtools shuffle:
196s     shuffle.t1...ok
196s     shuffle.t2...ok
196s     shuffle.t3...ok
196s     shuffle.t4...ok
196s     shuffle.t5...ok
196s     shuffle.t6...ok
196s Testing bedtools slop:
196s     slop.t1...ok
196s     slop.t2...ok
196s     slop.t3...ok
196s     slop.t4...ok
196s     slop.t5...ok
196s     slop.t6...ok
196s     slop.t7...ok
196s     slop.t8...ok
196s     slop.t9...ok
196s     slop.t10...ok
196s     slop.t11...ok
196s     slop.t12...ok
196s     slop.t13...ok
196s     slop.t14...ok
196s     slop.t15...ok
196s     slop.t16...ok
196s     slop.t17...ok
196s     slop.t18...ok
196s     slop.t19...ok
196s     slop.t20...ok
196s     slop.t21...ok
196s     slop.t22...ok
196s Testing bedtools sort:
196s     sort.t01...ok
196s     sort.t02...ok
196s     sort.t03...ok
196s     sort.t04...ok
196s     sort.t05...ok
196s     sort.t06...ok
196s     sort.t07...ok
196s     sort.t08...ok
196s     sort.t09...ok
196s     sort.t10...ok
196s Testing bedtools spacing:
196s     spacing.t01...ok
196s Testing bedtools split:
196s     split.01.size...ok
196s     split.02.simple...ok
197s     spliit.03.simple...ok
197s Testing bedtools subtract:
197s     subtract.t1...ok
197s     subtract.t2...ok
197s     subtract.t3...ok
197s     subtract.t4...ok
197s     subtract.t5...ok
197s     subtract.t6...ok
197s     subtract.t7...ok
197s     subtract.t8...ok
197s     subtract.t9...ok
197s     subtract.t10...ok
197s     subtract.t11...ok
197s     subtract.t12...ok
197s     subtract.t13...ok
197s     subtract.t14...ok
197s     subtract.t15...ok
197s     subtract.t16...ok
197s     subtract.t17...ok
197s     subtract.t18...ok
197s     subtract.t19...ok
197s     subtract.t20...ok
197s     subtract.t21...ok
197s 
197s 
197s --------------------------
197s  Test Results             
197s --------------------------
197s 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
197s Tools failing:  negativecontrol
197s NB: the 'negativecontrol' test is supposed to fail. If it wasn't caught, 
197s something went wrong with this test script.
198s autopkgtest [17:13:49]: test run-unit-test: -----------------------]
199s autopkgtest [17:13:50]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
199s run-unit-test        PASS
200s autopkgtest [17:13:51]: @@@@@@@@@@@@@@@@@@@@ summary
200s run-unit-test        PASS
211s Creating nova instance adt-noble-arm64-bedtools-20240316-171030-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...