0s autopkgtest [15:00:30]: starting date and time: 2025-10-18 15:00:30+0000 0s autopkgtest [15:00:30]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:00:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8neh85t3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade bedops --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-6.secgroup --name adt-resolute-arm64-bedops-20251018-150030-juju-7f2275-prod-proposed-migration-environment-2-81729891-cd7a-4e6e-94cb-e2cc5ad30383 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-bedops-20251018-150030-juju-7f2275-prod-proposed-migration-environment-2-81729891-cd7a-4e6e-94cb-e2cc5ad30383 from image adt/ubuntu-resolute-arm64-server-20251018.img (UUID f7a49384-4e4d-4350-9a26-1f59236f89dd)... 62s autopkgtest [15:01:32]: testbed dpkg architecture: arm64 62s autopkgtest [15:01:32]: testbed apt version: 3.1.6ubuntu2 63s autopkgtest [15:01:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s autopkgtest [15:01:33]: testbed release detected to be: None 64s autopkgtest [15:01:34]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 65s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 65s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 65s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 65s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 65s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [81.1 kB] 65s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 65s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [223 kB] 65s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 65s Fetched 831 kB in 1s (857 kB/s) 66s Reading package lists... 67s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 67s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 67s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 67s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 68s Reading package lists... 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade... 70s The following packages will be upgraded: 70s apt flash-kernel gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 70s libpython3-stdlib lto-disabled-list python3 python3-minimal 70s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 2671 kB of archives. 70s After this operation, 66.6 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 70s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 70s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 70s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.8ubuntu1 [1055 kB] 70s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.8ubuntu1 [1373 kB] 70s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgirepository-1.0-1 arm64 1.86.0-6 [84.5 kB] 70s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-girepository-2.0 arm64 1.86.0-6 [25.3 kB] 70s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 flash-kernel arm64 3.109ubuntu7 [58.8 kB] 70s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 lto-disabled-list all 71 [12.5 kB] 71s dpkg-preconfigure: unable to re-open stdin: No such file or directory 71s Fetched 2671 kB in 1s (2942 kB/s) 71s (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 ... 83359 files and directories currently installed.) 71s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 72s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 72s Setting up python3-minimal (3.13.7-2) ... 72s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83359 files and directories currently installed.) 72s Preparing to unpack .../0-python3_3.13.7-2_arm64.deb ... 72s running python pre-rtupdate hooks for python3.13... 72s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 72s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_arm64.deb ... 72s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 72s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_arm64.deb ... 72s Unpacking libapt-pkg7.0:arm64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 73s Preparing to unpack .../3-apt_3.1.8ubuntu1_arm64.deb ... 73s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 73s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_arm64.deb ... 73s Unpacking libgirepository-1.0-1:arm64 (1.86.0-6) over (1.84.0-1) ... 73s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_arm64.deb ... 73s Unpacking gir1.2-girepository-2.0:arm64 (1.86.0-6) over (1.84.0-1) ... 73s Preparing to unpack .../6-flash-kernel_3.109ubuntu7_arm64.deb ... 73s Unpacking flash-kernel (3.109ubuntu7) over (3.109ubuntu6) ... 73s Preparing to unpack .../7-lto-disabled-list_71_all.deb ... 73s Unpacking lto-disabled-list (71) over (69) ... 73s Setting up lto-disabled-list (71) ... 74s Setting up libgirepository-1.0-1:arm64 (1.86.0-6) ... 74s Setting up libapt-pkg7.0:arm64 (3.1.8ubuntu1) ... 74s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 74s Setting up apt (3.1.8ubuntu1) ... 75s Setting up python3 (3.13.7-2) ... 75s running python rtupdate hooks for python3.13... 75s running python post-rtupdate hooks for python3.13... 75s Setting up gir1.2-girepository-2.0:arm64 (1.86.0-6) ... 75s Setting up flash-kernel (3.109ubuntu7) ... 76s flash-kernel: deferring update (trigger activated) 76s Processing triggers for libc-bin (2.42-0ubuntu3) ... 76s Processing triggers for man-db (2.13.1-1) ... 78s Processing triggers for initramfs-tools (0.150ubuntu3) ... 78s update-initramfs: Generating /boot/initrd.img-6.17.0-5-generic 102s System running in EFI mode, skipping. 102s Processing triggers for flash-kernel (3.109ubuntu7) ... 102s System running in EFI mode, skipping. 103s autopkgtest [15:02:13]: upgrading testbed (apt dist-upgrade and autopurge) 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Solving dependencies... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [15:02:18]: rebooting testbed after setup commands that affected boot 139s autopkgtest [15:02:49]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 142s autopkgtest [15:02:52]: @@@@@@@@@@@@@@@@@@@@ apt-source bedops 146s Get:1 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (dsc) [2227 B] 146s Get:2 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (tar) [13.5 MB] 146s Get:3 http://ftpmaster.internal/ubuntu resolute/universe bedops 2.4.41+dfsg-3 (diff) [10.9 kB] 146s gpgv: Signature made Tue Dec 17 17:01:06 2024 UTC 146s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 146s gpgv: issuer "crusoe@debian.org" 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-3.dsc: no acceptable signature found 146s autopkgtest [15:02:56]: testing package bedops version 2.4.41+dfsg-3 147s autopkgtest [15:02:57]: build not needed 148s autopkgtest [15:02:58]: test run-unit-test: preparing testbed 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Solving dependencies... 149s The following NEW packages will be installed: 149s bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc 149s libjs-underscore tcsh 149s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 31.9 MB of archives. 149s After this operation, 87.1 MB of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu resolute/universe arm64 tcsh arm64 6.24.13-2 [445 kB] 150s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 bedops arm64 2.4.41+dfsg-3 [1269 kB] 150s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 150s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 150s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 150s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 150s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 150s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 bedops-doc all 2.4.41+dfsg-3 [21.8 MB] 152s Fetched 31.9 MB in 2s (13.9 MB/s) 152s Selecting previously unselected package tcsh. 152s (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 ... 83359 files and directories currently installed.) 152s Preparing to unpack .../0-tcsh_6.24.13-2_arm64.deb ... 152s Unpacking tcsh (6.24.13-2) ... 152s Selecting previously unselected package bedops. 152s Preparing to unpack .../1-bedops_2.4.41+dfsg-3_arm64.deb ... 152s Unpacking bedops (2.4.41+dfsg-3) ... 152s Selecting previously unselected package libjs-jquery. 152s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 152s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 152s Selecting previously unselected package libjs-underscore. 152s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 152s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 152s Selecting previously unselected package libjs-sphinxdoc. 152s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 152s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 152s Selecting previously unselected package fonts-mathjax. 152s Preparing to unpack .../5-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 152s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 153s Selecting previously unselected package libjs-mathjax. 153s Preparing to unpack .../6-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 153s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 153s Selecting previously unselected package bedops-doc. 153s Preparing to unpack .../7-bedops-doc_2.4.41+dfsg-3_all.deb ... 153s Unpacking bedops-doc (2.4.41+dfsg-3) ... 153s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 153s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 153s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 153s Setting up tcsh (6.24.13-2) ... 153s update-alternatives: using /bin/tcsh to provide /bin/csh (csh) in auto mode 153s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 153s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 153s Setting up bedops (2.4.41+dfsg-3) ... 153s Setting up bedops-doc (2.4.41+dfsg-3) ... 153s Processing triggers for man-db (2.13.1-1) ... 154s Processing triggers for debianutils (5.23.2) ... 155s autopkgtest [15:03:05]: test run-unit-test: [----------------------- 156s Testing bedops 156s Testing binary [bedops] and build type [] 156s make[1]: Entering directory '/tmp/autopkgtest.U989Su/autopkgtest_tmp/tests/bedops' 156s Missing binary [bedops] for build type [] 156s Writing to [/tmp/tmp.89VPeSBiqT] 156s bedops --version 156s bedops 156s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 156s https://doi.org/10.1093/bioinformatics/bts277 156s version: 2.4.41 (typical) 156s authors: Shane Neph & Scott Kuehn 156s [bedops- --merge] - [Test 001] ...passed! 156s [bedops- --merge] - [Test 002] ...passed! 156s [bedops- --merge] - [Test 003] ...passed! 156s [bedops- --merge] - [Test 004] ...passed! 156s [bedops- --merge] - [Test 005] ...passed! 156s [bedops- --merge] - [Test 006] ...passed! 156s [bedops- --merge] - [Test 007] ...passed! 156s [bedops- --merge] - [Test 008] ...passed! 156s [bedops- --merge] - [Test 009] ...passed! 156s [bedops- --complement] - [Test 001] ...passed! 156s [bedops- --complement] - [Test 002] ...passed! 156s [bedops- --complement] - [Test 003] ...passed! 156s [bedops- --complement] - [Test 004] ...passed! 156s [bedops- --complement] - [Test 005] ...passed! 156s [bedops- --complement] - [Test 006] ...passed! 156s [bedops- --complement] - [Test 007] ...passed! 156s [bedops- --complement] - [Test 008] ...passed! 156s [bedops- --complement] - [Test 009] ...passed! 156s [bedops- --intersection] - [Test 001] ...passed! 156s [bedops- --intersection] - [Test 002] ...passed! 156s [bedops- --intersection] - [Test 003] ...passed! 156s [bedops- --intersection] - [Test 004] ...passed! 156s [bedops- --difference] - [Test 001] ...passed! 156s [bedops- --difference] - [Test 002] ...passed! 156s [bedops- --difference] - [Test 003] ...passed! 156s [bedops- --difference] - [Test 004] ...passed! 156s [bedops- --difference] - [Test 005] ...passed! 156s [bedops- --difference] - [Test 006] ...passed! 156s [bedops- --difference] - [Test 007] ...passed! 156s [bedops- --symdiff] - [Test 001] ...passed! 156s [bedops- --symdiff] - [Test 002] ...passed! 156s [bedops- --symdiff] - [Test 003] ...passed! 156s [bedops- --symdiff] - [Test 004] ...passed! 156s [bedops- --symdiff] - [Test 005] ...passed! 156s [bedops- --element-of] - [Test 001] ...passed! 156s [bedops- --element-of] - [Test 002] ...passed! 156s [bedops- --element-of] - [Test 003] ...passed! 156s [bedops- --element-of] - [Test 004] ...passed! 156s [bedops- --not-element-of] - [Test 001] ...passed! 156s [bedops- --not-element-of] - [Test 002] ...passed! 156s [bedops- --not-element-of] - [Test 003] ...passed! 156s [bedops- --union] - [Test 001] ...passed! 156s [bedops- --union] - [Test 002] ...passed! 156s [bedops- --union] - [Test 003] ...passed! 156s [bedops- --union] - [Test 004] ...passed! 156s [bedops- --union] - [Test 005] ...passed! 156s [bedops- --union] - [Test 006] ...passed! 156s [bedops- --union] - [Test 007] ...passed! 156s [bedops- --union] - [Test 008] ...passed! 156s [bedops- --union] - [Test 009] ...passed! 156s [bedops- --partition] - [Test 001] ...passed! 156s [bedops- --partition] - [Test 002] ...passed! 156s [bedops- --partition] - [Test 003] ...passed! 156s [bedops- --partition] - [Test 004] ...passed! 156s [bedops- --partition] - [Test 005] ...passed! 156s [bedops- --chrom] - [Test 001] ...passed! 156s [bedops- --chrom] - [Test 002] ...passed! 156s [bedops- --chrom] - [Test 003] ...passed! 156s [bedops- --chrom] - [Test 004] ...passed! 156s [bedops- --chop] - [Test 001] ...passed! 156s [bedops- --chop] - [Test 002] ...passed! 157s [bedops- --chop] - [Test 003] ...passed! 157s [bedops- --chop] - [Test 004] ...passed! 157s [bedops- --chop] - [Test 005] ...passed! 157s [bedops- --stdin] - [Test 001] ...passed! 157s [bedops- --named-pipe] - [Test 001] ...passed! 157s [bedops- --ec] - [Test 001] ...passed! (not expected to pass) 157s make[1]: Leaving directory '/tmp/autopkgtest.U989Su/autopkgtest_tmp/tests/bedops' 157s make[1]: *** [Makefile:380: ec] Error 1 157s Testing starch 157s make: *** [Makefile:10: all] Error 2 157s Testing binary group [starch] and build type [] 157s make[1]: Entering directory '/tmp/autopkgtest.U989Su/autopkgtest_tmp/tests/starch' 157s Missing binary [unstarch] for build type [] 157s Writing to [/tmp/tmp.JeLhwaL7WQ] 157s unstarch --version 157s unstarch 157s binary version: 2.4.41 (typical) (extracts archive version: 2.2.0 or older) 157s [starch-unstarch- --signature] - [Test 001] ...passed! 157s [starch-unstarch- --signature] - [Test 002] ...passed! 157s Missing binary [bedops-starch] for build type [] 157s bedops-starch --version 157s starch 157s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 157s Writing to [/tmp/tmp.JeLhwaL7WQ] 157s Missing binary [bedmap] for build type [] 157s bedmap --help 157s bedmap 157s citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract 157s https://doi.org/10.1093/bioinformatics/bts277 157s version: 2.4.41 (typical) 157s authors: Shane Neph & Scott Kuehn 157s 157s USAGE: bedmap [process-flags] [overlap-option] [map-file] 157s Any input file must be sorted per the sort-bed utility. 157s The program accepts BED and Starch file formats. 157s You may use '-' for a BED file to indicate the input comes from stdin. 157s 157s Traverse , while applying on qualified, overlapping elements from 157s . Output is one line for each line in , sent to standard output. There 157s is no limit on the number of operations you can specify to compute in one bedmap call. 157s If is omitted, the given file is treated as both the and . 157s This usage is more efficient than specifying the same file twice. 157s Arguments may be given in any order before the input file(s). 157s 157s Process Flags: 157s -------- 157s --chrom Jump to and process data for given only. 157s --delim Change output delimiter from '|' to between columns (e.g. '\t'). 157s --ec Error check all input files (slower). 157s --faster (advanced) Strong input assumptions are made. Compatible with: 157s --bp-ovr, --range, --fraction-both, and --exact overlap options only. 157s --header Accept headers (VCF, GFF, SAM, BED, WIG) in any input file. 157s --help Print this message and exit successfully. 157s --min-memory Minimize memory usage (slower). 157s --multidelim Change delimiter of multi-value output columns from ';' to . 157s --prec Change the post-decimal precision of scores to . 0 <= . 157s --sci Use scientific notation for score outputs. 157s --skip-unmapped Print no output for a row with no mapped elements. 157s --sweep-all Ensure is read completely (helps to prevent broken pipes). 157s --unmapped-val Print on unmapped --echo-map* and --min/max-element* operations. 157s The default is to print nothing. 157s --version Print program information. 157s 157s 157s Overlap Options (At most, one may be selected. By default, --bp-ovr 1 is used): 157s -------- 157s --bp-ovr Require bp overlap between elements of input files. 157s --exact First 3 fields from must be identical to 's. 157s --fraction-both Both --fraction-ref and --fraction-map must be true to 157s qualify as overlapping. Expect 0 < val <= 1. 157s --fraction-either Either --fraction-ref or --fraction-map must be true to 157s qualify as overlapping. Expect 0 < val <= 1. 157s --fraction-map The fraction of the element's size from that must overlap 157s the element in . Expect 0 < val <= 1. 157s --fraction-ref The fraction of the element's size from that must overlap 157s an element in . Expect 0 < val <= 1. 157s --range Grab elements within bp of 's element, 157s where 0 <= int. --range 0 is an alias for --bp-ovr 1. 157s 157s 157s Operations: (Any number of operations may be used any number of times.) 157s ---------- 157s SCORE: 157s must have at least 3 columns and 5 columns. 157s 157s --cv The result of --stdev divided by the result of --mean. 157s --kth Generalized median. Report the value, x, such that the fraction 157s of overlapping elements' scores from is less than x, 157s and the fraction 1- of scores is greater than x. 0 < val <= 1. 157s --mad The median absolute deviation of overlapping elements in . 157s Multiply mad score by . 0 < mult, and mult is 1 by default. 157s --max The highest score from overlapping elements in . 157s --max-element A (non-random) highest-scoring and overlapping element in . 157s --max-element-rand A random highest-scoring and overlapping element in . 157s --mean The average score from overlapping elements in . 157s --median The median score from overlapping elements in . 157s --min The lowest score from overlapping elements in . 157s --min-element A (non-random) lowest-scoring and overlapping element in . 157s --min-element-rand A random lowest-scoring and overlapping element in . 157s --stdev The square root of the result of --variance. 157s --sum Accumulated scores from overlapping elements in . 157s --tmean The mean score from overlapping elements in , after 157s ignoring the bottom and top fractions of those scores. 157s 0 <= low <= 1. 0 <= hi <= 1. low+hi <= 1. 157s --variance The variance of scores from overlapping elements in . 157s --wmean Weighted mean, scaled in proportion to the coverage of the 157s element by each overlapping element. 157s 157s ---------- 157s NON-SCORE: 157s must have at least 3 columns. 157s For --echo-map-id/echo-map-id-uniq, must have at least 4 columns. 157s For --echo-map-score, must have at least 5 columns. 157s For all others, requires at least 3 columns. 157s 157s --bases The total number of overlapping bases from . 157s --bases-uniq The number of distinct bases from 's element covered by 157s overlapping elements in . 157s --bases-uniq-f The fraction of distinct bases from 's element covered by 157s overlapping elements in . 157s --count The number of overlapping elements in . 157s --echo Print each line from . 157s --echo-map List all overlapping elements from . 157s --echo-map-id List IDs from all overlapping elements. 157s --echo-map-id-uniq List unique IDs from overlapping elements. 157s --echo-map-range Print genomic range of overlapping elements from . 157s --echo-map-score List scores from overlapping elements. 157s --echo-map-size List the full length of every overlapping element. 157s --echo-overlap-size List lengths of overlaps. 157s --echo-ref-name Print the first 3 fields of using chrom:start-end format. 157s --echo-ref-row-id Print 'id-' followed by the line number of . 157s --echo-ref-size Print the length of each line from . 157s --indicator Print 1 if there exists an overlapping element in , 0 otherwise. 157s 157s 157s [starch-starch-API- --starch_api_bedmap] - [Test 001] ...passed! 157s Missing binary [bedops-starch] for build type [] 157s Writing to [/tmp/tmp.JeLhwaL7WQ] 157s bedops-starch --version 157s starch 157s binary version: 2.4.41 (typical) (creates archive version: 2.2.0) 157s Generating random intervals... 157s ./generate_random_intervals.sh /tmp/autopkgtest.U989Su/autopkgtest_tmp/tests/starch/data/hg38.bed 3 10000 | sort-bed - > /tmp/tmp.JeLhwaL7WQ/random_intervals.bed 159s [starch-starch- --deflate_and_inflate_bzip2] - [Test 001] ...passed! 159s [starch-starch- --deflate_and_inflate_gz] - [Test 001] ...passed! 159s Removing [/tmp/tmp.JeLhwaL7WQ] 159s make[1]: Leaving directory '/tmp/autopkgtest.U989Su/autopkgtest_tmp/tests/starch' 159s autopkgtest [15:03:09]: test run-unit-test: -----------------------] 160s run-unit-test PASS 160s autopkgtest [15:03:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 160s autopkgtest [15:03:10]: @@@@@@@@@@@@@@@@@@@@ summary 160s run-unit-test PASS