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2022-02-05T21:25:29.6922752Z Requested labels: ubuntu-latest
2022-02-05T21:25:29.6922848Z Job defined at: telatin/bamtocov/.github/workflows/docker-image.yml@refs/heads/main
2022-02-05T21:25:29.6922872Z Waiting for a runner to pick up this job...
2022-02-05T21:25:31.1852378Z Job is waiting for a hosted runner to come online.
2022-02-05T21:25:34.6487495Z Job is about to start running on the hosted runner: Hosted Agent (hosted)
2022-02-05T21:25:37.6726181Z Current runner version: '2.287.1'
2022-02-05T21:25:37.6758794Z ##[group]Operating System
2022-02-05T21:25:37.6759444Z Ubuntu
2022-02-05T21:25:37.6759780Z 20.04.3
2022-02-05T21:25:37.6760088Z LTS
2022-02-05T21:25:37.6760358Z ##[endgroup]
2022-02-05T21:25:37.6760735Z ##[group]Virtual Environment
2022-02-05T21:25:37.6761127Z Environment: ubuntu-20.04
2022-02-05T21:25:37.6761500Z Version: 20220131.1
2022-02-05T21:25:37.6762018Z Included Software: https://github.com/actions/virtual-environments/blob/ubuntu20/20220131.1/images/linux/Ubuntu2004-Readme.md
2022-02-05T21:25:37.6762751Z Image Release: https://github.com/actions/virtual-environments/releases/tag/ubuntu20%2F20220131.1
2022-02-05T21:25:37.6763265Z ##[endgroup]
2022-02-05T21:25:37.6763633Z ##[group]Virtual Environment Provisioner
2022-02-05T21:25:37.6764041Z 1.0.0.0-main-20220128-1
2022-02-05T21:25:37.6764331Z ##[endgroup]
2022-02-05T21:25:37.6765395Z ##[group]GITHUB_TOKEN Permissions
2022-02-05T21:25:37.6766066Z Actions: write
2022-02-05T21:25:37.6766548Z Checks: write
2022-02-05T21:25:37.6766901Z Contents: write
2022-02-05T21:25:37.6767273Z Deployments: write
2022-02-05T21:25:37.6767642Z Discussions: write
2022-02-05T21:25:37.6767951Z Issues: write
2022-02-05T21:25:37.6768286Z Metadata: read
2022-02-05T21:25:37.6768642Z Packages: write
2022-02-05T21:25:37.6768935Z Pages: write
2022-02-05T21:25:37.6769314Z PullRequests: write
2022-02-05T21:25:37.6769651Z RepositoryProjects: write
2022-02-05T21:25:37.6770041Z SecurityEvents: write
2022-02-05T21:25:37.6770349Z Statuses: write
2022-02-05T21:25:37.6770707Z ##[endgroup]
2022-02-05T21:25:37.6775219Z Secret source: Actions
2022-02-05T21:25:37.6775912Z Prepare workflow directory
2022-02-05T21:25:37.7715589Z Prepare all required actions
2022-02-05T21:25:37.7922712Z Getting action download info
2022-02-05T21:25:37.9437763Z Download action repository 'actions/checkout@v2' (SHA:ec3a7ce113134d7a93b817d10a8272cb61118579)
2022-02-05T21:25:38.4845573Z ##[group]Run actions/checkout@v2
2022-02-05T21:25:38.4845923Z with:
2022-02-05T21:25:38.4846228Z repository: telatin/bamtocov
2022-02-05T21:25:38.4846784Z token: ***
2022-02-05T21:25:38.4847039Z ssh-strict: true
2022-02-05T21:25:38.4847352Z persist-credentials: true
2022-02-05T21:25:38.4847634Z clean: true
2022-02-05T21:25:38.4847900Z fetch-depth: 1
2022-02-05T21:25:38.4848159Z lfs: false
2022-02-05T21:25:38.4848401Z submodules: false
2022-02-05T21:25:38.4848670Z ##[endgroup]
2022-02-05T21:25:38.7932604Z Syncing repository: telatin/bamtocov
2022-02-05T21:25:38.7935405Z ##[group]Getting Git version info
2022-02-05T21:25:38.7936417Z Working directory is '/home/runner/work/bamtocov/bamtocov'
2022-02-05T21:25:38.7937832Z [command]/usr/bin/git version
2022-02-05T21:25:38.8077076Z git version 2.35.1
2022-02-05T21:25:38.8141572Z ##[endgroup]
2022-02-05T21:25:38.8142192Z Deleting the contents of '/home/runner/work/bamtocov/bamtocov'
2022-02-05T21:25:38.8143563Z ##[group]Initializing the repository
2022-02-05T21:25:38.8143991Z [command]/usr/bin/git init /home/runner/work/bamtocov/bamtocov
2022-02-05T21:25:38.8238425Z hint: Using 'master' as the name for the initial branch. This default branch name
2022-02-05T21:25:38.8239017Z hint: is subject to change. To configure the initial branch name to use in all
2022-02-05T21:25:38.8239553Z hint: of your new repositories, which will suppress this warning, call:
2022-02-05T21:25:38.8239934Z hint:
2022-02-05T21:25:38.8240408Z hint: git config --global init.defaultBranch <name>
2022-02-05T21:25:38.8240766Z hint:
2022-02-05T21:25:38.8241256Z hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and
2022-02-05T21:25:38.8242383Z hint: 'development'. The just-created branch can be renamed via this command:
2022-02-05T21:25:38.8242772Z hint:
2022-02-05T21:25:38.8243118Z hint: git branch -m <name>
2022-02-05T21:25:38.8262045Z Initialized empty Git repository in /home/runner/work/bamtocov/bamtocov/.git/
2022-02-05T21:25:38.8273571Z [command]/usr/bin/git remote add origin https://github.com/telatin/bamtocov
2022-02-05T21:25:38.8350914Z ##[endgroup]
2022-02-05T21:25:38.8351552Z ##[group]Disabling automatic garbage collection
2022-02-05T21:25:38.8354889Z [command]/usr/bin/git config --local gc.auto 0
2022-02-05T21:25:38.8439111Z ##[endgroup]
2022-02-05T21:25:38.8452999Z ##[group]Setting up auth
2022-02-05T21:25:38.8453600Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2022-02-05T21:25:38.8465487Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :
2022-02-05T21:25:38.8901024Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2022-02-05T21:25:38.8936919Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :
2022-02-05T21:25:38.9234269Z [command]/usr/bin/git config --local http.https://github.com/.extraheader AUTHORIZATION: basic ***
2022-02-05T21:25:38.9278263Z ##[endgroup]
2022-02-05T21:25:38.9279215Z ##[group]Fetching the repository
2022-02-05T21:25:38.9287530Z [command]/usr/bin/git -c protocol.version=2 fetch --no-tags --prune --progress --no-recurse-submodules --depth=1 origin +0b0875b74c958ec6e179f29d75077c08f2fe5103:refs/remotes/origin/main
2022-02-05T21:25:39.1075223Z remote: Enumerating objects: 389, done.
2022-02-05T21:25:39.1075750Z remote: Counting objects: 0% (1/389)
2022-02-05T21:25:39.1076161Z remote: Counting objects: 1% (4/389)
2022-02-05T21:25:39.1076621Z remote: Counting objects: 2% (8/389)
2022-02-05T21:25:39.1077056Z remote: Counting objects: 3% (12/389)
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2022-02-05T21:25:39.1082516Z remote: Counting objects: 14% (55/389)
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2022-02-05T21:25:39.1089663Z remote: Counting objects: 30% (117/389)
2022-02-05T21:25:39.1090088Z remote: Counting objects: 31% (121/389)
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2022-02-05T21:25:39.1092030Z remote: Counting objects: 37% (144/389)
2022-02-05T21:25:39.1092316Z remote: Counting objects: 38% (148/389)
2022-02-05T21:25:39.1092582Z remote: Counting objects: 39% (152/389)
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2022-02-05T21:25:39.1093130Z remote: Counting objects: 41% (160/389)
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2022-02-05T21:25:39.1096440Z remote: Counting objects: 53% (207/389)
2022-02-05T21:25:39.1096720Z remote: Counting objects: 54% (211/389)
2022-02-05T21:25:39.1097224Z remote: Counting objects: 55% (214/389)
2022-02-05T21:25:39.1098215Z remote: Counting objects: 56% (218/389)
2022-02-05T21:25:39.1098507Z remote: Counting objects: 57% (222/389)
2022-02-05T21:25:39.1099218Z remote: Counting objects: 58% (226/389)
2022-02-05T21:25:39.1099510Z remote: Counting objects: 59% (230/389)
2022-02-05T21:25:39.1099799Z remote: Counting objects: 60% (234/389)
2022-02-05T21:25:39.1100067Z remote: Counting objects: 61% (238/389)
2022-02-05T21:25:39.1100349Z remote: Counting objects: 62% (242/389)
2022-02-05T21:25:39.1100614Z remote: Counting objects: 63% (246/389)
2022-02-05T21:25:39.1100908Z remote: Counting objects: 64% (249/389)
2022-02-05T21:25:39.1101360Z remote: Counting objects: 65% (253/389)
2022-02-05T21:25:39.1101682Z remote: Counting objects: 66% (257/389)
2022-02-05T21:25:39.1101981Z remote: Counting objects: 67% (261/389)
2022-02-05T21:25:39.1102283Z remote: Counting objects: 68% (265/389)
2022-02-05T21:25:39.1102570Z remote: Counting objects: 69% (269/389)
2022-02-05T21:25:39.1102871Z remote: Counting objects: 70% (273/389)
2022-02-05T21:25:39.1103164Z remote: Counting objects: 71% (277/389)
2022-02-05T21:25:39.1104193Z remote: Counting objects: 72% (281/389)
2022-02-05T21:25:39.1104517Z remote: Counting objects: 73% (284/389)
2022-02-05T21:25:39.1104806Z remote: Counting objects: 74% (288/389)
2022-02-05T21:25:39.1105105Z remote: Counting objects: 75% (292/389)
2022-02-05T21:25:39.1105390Z remote: Counting objects: 76% (296/389)
2022-02-05T21:25:39.1105690Z remote: Counting objects: 77% (300/389)
2022-02-05T21:25:39.1105977Z remote: Counting objects: 78% (304/389)
2022-02-05T21:25:39.1106285Z remote: Counting objects: 79% (308/389)
2022-02-05T21:25:39.1106586Z remote: Counting objects: 80% (312/389)
2022-02-05T21:25:39.1107231Z remote: Counting objects: 81% (316/389)
2022-02-05T21:25:39.1107837Z remote: Counting objects: 82% (319/389)
2022-02-05T21:25:39.1108124Z remote: Counting objects: 83% (323/389)
2022-02-05T21:25:39.1108424Z remote: Counting objects: 84% (327/389)
2022-02-05T21:25:39.1108733Z remote: Counting objects: 85% (331/389)
2022-02-05T21:25:39.1109302Z remote: Counting objects: 86% (335/389)
2022-02-05T21:25:39.1110031Z remote: Counting objects: 87% (339/389)
2022-02-05T21:25:39.1110620Z remote: Counting objects: 88% (343/389)
2022-02-05T21:25:39.1110928Z remote: Counting objects: 89% (347/389)
2022-02-05T21:25:39.1111238Z remote: Counting objects: 90% (351/389)
2022-02-05T21:25:39.1111526Z remote: Counting objects: 91% (354/389)
2022-02-05T21:25:39.1112200Z remote: Counting objects: 92% (358/389)
2022-02-05T21:25:39.1112780Z remote: Counting objects: 93% (362/389)
2022-02-05T21:25:39.1113081Z remote: Counting objects: 94% (366/389)
2022-02-05T21:25:39.1113389Z remote: Counting objects: 95% (370/389)
2022-02-05T21:25:39.1114006Z remote: Counting objects: 96% (374/389)
2022-02-05T21:25:39.1114605Z remote: Counting objects: 97% (378/389)
2022-02-05T21:25:39.1115551Z remote: Counting objects: 98% (382/389)
2022-02-05T21:25:39.1115865Z remote: Counting objects: 99% (386/389)
2022-02-05T21:25:39.1116529Z remote: Counting objects: 100% (389/389)
2022-02-05T21:25:39.1117131Z remote: Counting objects: 100% (389/389), done.
2022-02-05T21:25:39.1117492Z remote: Compressing objects: 0% (1/337)
2022-02-05T21:25:39.1118129Z remote: Compressing objects: 1% (4/337)
2022-02-05T21:25:39.1118747Z remote: Compressing objects: 2% (7/337)
2022-02-05T21:25:39.1119083Z remote: Compressing objects: 3% (11/337)
2022-02-05T21:25:39.1119728Z remote: Compressing objects: 4% (14/337)
2022-02-05T21:25:39.1120362Z remote: Compressing objects: 5% (17/337)
2022-02-05T21:25:39.1120677Z remote: Compressing objects: 6% (21/337)
2022-02-05T21:25:39.1121332Z remote: Compressing objects: 7% (24/337)
2022-02-05T21:25:39.1122081Z remote: Compressing objects: 8% (27/337)
2022-02-05T21:25:39.1122393Z remote: Compressing objects: 9% (31/337)
2022-02-05T21:25:39.1122889Z remote: Compressing objects: 10% (34/337)
2022-02-05T21:25:39.1126394Z remote: Compressing objects: 11% (38/337)
2022-02-05T21:25:39.1133523Z remote: Compressing objects: 12% (41/337)
2022-02-05T21:25:39.1201246Z remote: Compressing objects: 13% (44/337)
2022-02-05T21:25:39.1201746Z remote: Compressing objects: 14% (48/337)
2022-02-05T21:25:39.1202176Z remote: Compressing objects: 15% (51/337)
2022-02-05T21:25:39.1205834Z remote: Compressing objects: 16% (54/337)
2022-02-05T21:25:39.1214077Z remote: Compressing objects: 17% (58/337)
2022-02-05T21:25:39.1221100Z remote: Compressing objects: 18% (61/337)
2022-02-05T21:25:39.1224765Z remote: Compressing objects: 19% (65/337)
2022-02-05T21:25:39.1227265Z remote: Compressing objects: 20% (68/337)
2022-02-05T21:25:39.1227664Z remote: Compressing objects: 21% (71/337)
2022-02-05T21:25:39.1228088Z remote: Compressing objects: 22% (75/337)
2022-02-05T21:25:39.1229643Z remote: Compressing objects: 23% (78/337)
2022-02-05T21:25:39.1232143Z remote: Compressing objects: 24% (81/337)
2022-02-05T21:25:39.1240055Z remote: Compressing objects: 25% (85/337)
2022-02-05T21:25:39.1240511Z remote: Compressing objects: 26% (88/337)
2022-02-05T21:25:39.1240839Z remote: Compressing objects: 27% (91/337)
2022-02-05T21:25:39.1243999Z remote: Compressing objects: 28% (95/337)
2022-02-05T21:25:39.1244495Z remote: Compressing objects: 29% (98/337)
2022-02-05T21:25:39.1244939Z remote: Compressing objects: 30% (102/337)
2022-02-05T21:25:39.1245376Z remote: Compressing objects: 31% (105/337)
2022-02-05T21:25:39.1245825Z remote: Compressing objects: 32% (108/337)
2022-02-05T21:25:39.1246241Z remote: Compressing objects: 33% (112/337)
2022-02-05T21:25:39.1246695Z remote: Compressing objects: 34% (115/337)
2022-02-05T21:25:39.1247113Z remote: Compressing objects: 35% (118/337)
2022-02-05T21:25:39.1247840Z remote: Compressing objects: 36% (122/337)
2022-02-05T21:25:39.1248267Z remote: Compressing objects: 37% (125/337)
2022-02-05T21:25:39.1248682Z remote: Compressing objects: 38% (129/337)
2022-02-05T21:25:39.1249101Z remote: Compressing objects: 39% (132/337)
2022-02-05T21:25:39.1249526Z remote: Compressing objects: 40% (135/337)
2022-02-05T21:25:39.1249935Z remote: Compressing objects: 41% (139/337)
2022-02-05T21:25:39.1250356Z remote: Compressing objects: 42% (142/337)
2022-02-05T21:25:39.1250775Z remote: Compressing objects: 43% (145/337)
2022-02-05T21:25:39.1251182Z remote: Compressing objects: 44% (149/337)
2022-02-05T21:25:39.1251602Z remote: Compressing objects: 45% (152/337)
2022-02-05T21:25:39.1252008Z remote: Compressing objects: 46% (156/337)
2022-02-05T21:25:39.1252435Z remote: Compressing objects: 47% (159/337)
2022-02-05T21:25:39.1252858Z remote: Compressing objects: 48% (162/337)
2022-02-05T21:25:39.1253274Z remote: Compressing objects: 49% (166/337)
2022-02-05T21:25:39.1253691Z remote: Compressing objects: 50% (169/337)
2022-02-05T21:25:39.1254248Z remote: Compressing objects: 51% (172/337)
2022-02-05T21:25:39.1254555Z remote: Compressing objects: 52% (176/337)
2022-02-05T21:25:39.1254879Z remote: Compressing objects: 53% (179/337)
2022-02-05T21:25:39.1255184Z remote: Compressing objects: 54% (182/337)
2022-02-05T21:25:39.1255503Z remote: Compressing objects: 55% (186/337)
2022-02-05T21:25:39.1267344Z remote: Compressing objects: 56% (189/337)
2022-02-05T21:25:39.1272884Z remote: Compressing objects: 57% (193/337)
2022-02-05T21:25:39.1273247Z remote: Compressing objects: 58% (196/337)
2022-02-05T21:25:39.1273839Z remote: Compressing objects: 59% (199/337)
2022-02-05T21:25:39.1294661Z remote: Compressing objects: 60% (203/337)
2022-02-05T21:25:39.1295062Z remote: Compressing objects: 61% (206/337)
2022-02-05T21:25:39.1295381Z remote: Compressing objects: 62% (209/337)
2022-02-05T21:25:39.1295712Z remote: Compressing objects: 63% (213/337)
2022-02-05T21:25:39.1296026Z remote: Compressing objects: 64% (216/337)
2022-02-05T21:25:39.1296512Z remote: Compressing objects: 65% (220/337)
2022-02-05T21:25:39.1296850Z remote: Compressing objects: 66% (223/337)
2022-02-05T21:25:39.1297157Z remote: Compressing objects: 67% (226/337)
2022-02-05T21:25:39.1297810Z remote: Compressing objects: 68% (230/337)
2022-02-05T21:25:39.1298170Z remote: Compressing objects: 69% (233/337)
2022-02-05T21:25:39.1298490Z remote: Compressing objects: 70% (236/337)
2022-02-05T21:25:39.1298816Z remote: Compressing objects: 71% (240/337)
2022-02-05T21:25:39.1299131Z remote: Compressing objects: 72% (243/337)
2022-02-05T21:25:39.1299457Z remote: Compressing objects: 73% (247/337)
2022-02-05T21:25:39.1299771Z remote: Compressing objects: 74% (250/337)
2022-02-05T21:25:39.1300238Z remote: Compressing objects: 75% (253/337)
2022-02-05T21:25:39.1301141Z remote: Compressing objects: 76% (257/337)
2022-02-05T21:25:39.1301475Z remote: Compressing objects: 77% (260/337)
2022-02-05T21:25:39.1308522Z remote: Compressing objects: 78% (263/337)
2022-02-05T21:25:39.1311540Z remote: Compressing objects: 79% (267/337)
2022-02-05T21:25:39.1314304Z remote: Compressing objects: 80% (270/337)
2022-02-05T21:25:39.1317222Z remote: Compressing objects: 81% (273/337)
2022-02-05T21:25:39.1323058Z remote: Compressing objects: 82% (277/337)
2022-02-05T21:25:39.1323865Z remote: Compressing objects: 83% (280/337)
2022-02-05T21:25:39.1324163Z remote: Compressing objects: 84% (284/337)
2022-02-05T21:25:39.1324892Z remote: Compressing objects: 85% (287/337)
2022-02-05T21:25:39.1325205Z remote: Compressing objects: 86% (290/337)
2022-02-05T21:25:39.1325682Z remote: Compressing objects: 87% (294/337)
2022-02-05T21:25:39.1329528Z remote: Compressing objects: 88% (297/337)
2022-02-05T21:25:39.1331845Z remote: Compressing objects: 89% (300/337)
2022-02-05T21:25:39.1332662Z remote: Compressing objects: 90% (304/337)
2022-02-05T21:25:39.1332960Z remote: Compressing objects: 91% (307/337)
2022-02-05T21:25:39.1333263Z remote: Compressing objects: 92% (311/337)
2022-02-05T21:25:39.1333702Z remote: Compressing objects: 93% (314/337)
2022-02-05T21:25:39.1334371Z remote: Compressing objects: 94% (317/337)
2022-02-05T21:25:39.1335013Z remote: Compressing objects: 95% (321/337)
2022-02-05T21:25:39.1335298Z remote: Compressing objects: 96% (324/337)
2022-02-05T21:25:39.1335727Z remote: Compressing objects: 97% (327/337)
2022-02-05T21:25:39.1336041Z remote: Compressing objects: 98% (331/337)
2022-02-05T21:25:39.1336347Z remote: Compressing objects: 99% (334/337)
2022-02-05T21:25:39.1339213Z remote: Compressing objects: 100% (337/337)
2022-02-05T21:25:39.1339619Z remote: Compressing objects: 100% (337/337), done.
2022-02-05T21:25:39.1391936Z Receiving objects: 0% (1/389)
2022-02-05T21:25:39.1393983Z Receiving objects: 1% (4/389)
2022-02-05T21:25:39.1394415Z Receiving objects: 2% (8/389)
2022-02-05T21:25:39.1396799Z Receiving objects: 3% (12/389)
2022-02-05T21:25:39.1397090Z Receiving objects: 4% (16/389)
2022-02-05T21:25:39.2043546Z Receiving objects: 5% (20/389)
2022-02-05T21:25:39.2046296Z Receiving objects: 6% (24/389)
2022-02-05T21:25:39.2046819Z Receiving objects: 7% (28/389)
2022-02-05T21:25:39.2047200Z Receiving objects: 8% (32/389)
2022-02-05T21:25:39.2047537Z Receiving objects: 9% (36/389)
2022-02-05T21:25:39.2048072Z Receiving objects: 10% (39/389)
2022-02-05T21:25:39.2048498Z Receiving objects: 11% (43/389)
2022-02-05T21:25:39.2050726Z Receiving objects: 12% (47/389)
2022-02-05T21:25:39.2052716Z Receiving objects: 13% (51/389)
2022-02-05T21:25:39.2053117Z Receiving objects: 14% (55/389)
2022-02-05T21:25:39.2054845Z Receiving objects: 15% (59/389)
2022-02-05T21:25:39.2055444Z Receiving objects: 16% (63/389)
2022-02-05T21:25:39.2057207Z Receiving objects: 17% (67/389)
2022-02-05T21:25:39.2057656Z Receiving objects: 18% (71/389)
2022-02-05T21:25:39.2059753Z Receiving objects: 19% (74/389)
2022-02-05T21:25:39.2062655Z Receiving objects: 20% (78/389)
2022-02-05T21:25:39.2064698Z Receiving objects: 21% (82/389)
2022-02-05T21:25:39.2066563Z Receiving objects: 22% (86/389)
2022-02-05T21:25:39.2067003Z Receiving objects: 23% (90/389)
2022-02-05T21:25:39.2069521Z Receiving objects: 24% (94/389)
2022-02-05T21:25:39.2071628Z Receiving objects: 25% (98/389)
2022-02-05T21:25:39.2072077Z Receiving objects: 26% (102/389)
2022-02-05T21:25:39.2074129Z Receiving objects: 27% (106/389)
2022-02-05T21:25:39.2074579Z Receiving objects: 28% (109/389)
2022-02-05T21:25:39.2076554Z Receiving objects: 29% (113/389)
2022-02-05T21:25:39.2076969Z Receiving objects: 30% (117/389)
2022-02-05T21:25:39.2078660Z Receiving objects: 31% (121/389)
2022-02-05T21:25:39.2080494Z Receiving objects: 32% (125/389)
2022-02-05T21:25:39.2080908Z Receiving objects: 33% (129/389)
2022-02-05T21:25:39.2082624Z Receiving objects: 34% (133/389)
2022-02-05T21:25:39.2083013Z Receiving objects: 35% (137/389)
2022-02-05T21:25:39.2085112Z Receiving objects: 36% (141/389)
2022-02-05T21:25:39.2092437Z Receiving objects: 37% (144/389)
2022-02-05T21:25:39.2092916Z Receiving objects: 38% (148/389)
2022-02-05T21:25:39.2093300Z Receiving objects: 39% (152/389)
2022-02-05T21:25:39.2093666Z Receiving objects: 40% (156/389)
2022-02-05T21:25:39.2094032Z Receiving objects: 41% (160/389)
2022-02-05T21:25:39.2094384Z Receiving objects: 42% (164/389)
2022-02-05T21:25:39.2094772Z Receiving objects: 43% (168/389)
2022-02-05T21:25:39.2095143Z Receiving objects: 44% (172/389)
2022-02-05T21:25:39.2100256Z Receiving objects: 45% (176/389)
2022-02-05T21:25:39.2146831Z Receiving objects: 46% (179/389)
2022-02-05T21:25:39.2173074Z Receiving objects: 47% (183/389)
2022-02-05T21:25:39.2177108Z Receiving objects: 48% (187/389)
2022-02-05T21:25:39.2179198Z Receiving objects: 49% (191/389)
2022-02-05T21:25:39.2181722Z Receiving objects: 50% (195/389)
2022-02-05T21:25:39.2184304Z Receiving objects: 51% (199/389)
2022-02-05T21:25:39.2186792Z Receiving objects: 52% (203/389)
2022-02-05T21:25:39.2188874Z Receiving objects: 53% (207/389)
2022-02-05T21:25:39.2192767Z Receiving objects: 54% (211/389)
2022-02-05T21:25:39.2199680Z Receiving objects: 55% (214/389)
2022-02-05T21:25:39.2200159Z Receiving objects: 56% (218/389)
2022-02-05T21:25:39.2200543Z Receiving objects: 57% (222/389)
2022-02-05T21:25:39.2200907Z Receiving objects: 58% (226/389)
2022-02-05T21:25:39.2201439Z Receiving objects: 59% (230/389)
2022-02-05T21:25:39.4338827Z Receiving objects: 60% (234/389)
2022-02-05T21:25:39.4339234Z Receiving objects: 61% (238/389)
2022-02-05T21:25:39.4339559Z Receiving objects: 62% (242/389)
2022-02-05T21:25:39.4351427Z Receiving objects: 63% (246/389)
2022-02-05T21:25:39.4351902Z Receiving objects: 64% (249/389)
2022-02-05T21:25:39.4358606Z Receiving objects: 65% (253/389)
2022-02-05T21:25:39.4382939Z Receiving objects: 66% (257/389)
2022-02-05T21:25:39.4388169Z Receiving objects: 67% (261/389)
2022-02-05T21:25:39.4388509Z Receiving objects: 68% (265/389)
2022-02-05T21:25:39.4388761Z Receiving objects: 69% (269/389)
2022-02-05T21:25:39.4389287Z Receiving objects: 70% (273/389)
2022-02-05T21:25:39.4389589Z Receiving objects: 71% (277/389)
2022-02-05T21:25:39.4396549Z Receiving objects: 72% (281/389)
2022-02-05T21:25:39.4397184Z Receiving objects: 73% (284/389)
2022-02-05T21:25:39.4399565Z Receiving objects: 74% (288/389)
2022-02-05T21:25:39.4400182Z Receiving objects: 75% (292/389)
2022-02-05T21:25:39.4402513Z Receiving objects: 76% (296/389)
2022-02-05T21:25:39.4403070Z Receiving objects: 77% (300/389)
2022-02-05T21:25:39.4404075Z Receiving objects: 78% (304/389)
2022-02-05T21:25:39.4404575Z Receiving objects: 79% (308/389)
2022-02-05T21:25:39.4406824Z Receiving objects: 80% (312/389)
2022-02-05T21:25:39.4407361Z Receiving objects: 81% (316/389)
2022-02-05T21:25:39.4408372Z Receiving objects: 82% (319/389)
2022-02-05T21:25:39.4408875Z Receiving objects: 83% (323/389)
2022-02-05T21:25:39.4409795Z Receiving objects: 84% (327/389)
2022-02-05T21:25:39.4410273Z Receiving objects: 85% (331/389)
2022-02-05T21:25:39.4412514Z Receiving objects: 86% (335/389)
2022-02-05T21:25:39.4413730Z Receiving objects: 87% (339/389)
2022-02-05T21:25:39.4414803Z Receiving objects: 88% (343/389)
2022-02-05T21:25:39.4422672Z Receiving objects: 89% (347/389)
2022-02-05T21:25:39.4425787Z Receiving objects: 90% (351/389)
2022-02-05T21:25:39.4526137Z Receiving objects: 91% (354/389)
2022-02-05T21:25:39.4573067Z Receiving objects: 92% (358/389)
2022-02-05T21:25:39.4573973Z remote: Total 389 (delta 54), reused 295 (delta 38), pack-reused 0
2022-02-05T21:25:39.4585644Z Receiving objects: 93% (362/389)
2022-02-05T21:25:39.4586375Z Receiving objects: 94% (366/389)
2022-02-05T21:25:39.4587245Z Receiving objects: 95% (370/389)
2022-02-05T21:25:39.4587723Z Receiving objects: 96% (374/389)
2022-02-05T21:25:39.4588617Z Receiving objects: 97% (378/389)
2022-02-05T21:25:39.4593695Z Receiving objects: 98% (382/389)
2022-02-05T21:25:39.4594325Z Receiving objects: 99% (386/389)
2022-02-05T21:25:39.4595229Z Receiving objects: 100% (389/389)
2022-02-05T21:25:39.4596026Z Receiving objects: 100% (389/389), 13.06 MiB | 40.76 MiB/s, done.
2022-02-05T21:25:39.4638473Z Resolving deltas: 0% (0/54)
2022-02-05T21:25:39.4639135Z Resolving deltas: 1% (1/54)
2022-02-05T21:25:39.4639521Z Resolving deltas: 3% (2/54)
2022-02-05T21:25:39.4640918Z Resolving deltas: 5% (3/54)
2022-02-05T21:25:39.4641402Z Resolving deltas: 7% (4/54)
2022-02-05T21:25:39.4642562Z Resolving deltas: 9% (5/54)
2022-02-05T21:25:39.4643025Z Resolving deltas: 11% (6/54)
2022-02-05T21:25:39.4644484Z Resolving deltas: 12% (7/54)
2022-02-05T21:25:39.4644955Z Resolving deltas: 14% (8/54)
2022-02-05T21:25:39.4645298Z Resolving deltas: 16% (9/54)
2022-02-05T21:25:39.4646361Z Resolving deltas: 18% (10/54)
2022-02-05T21:25:39.4646832Z Resolving deltas: 20% (11/54)
2022-02-05T21:25:39.4648175Z Resolving deltas: 22% (12/54)
2022-02-05T21:25:39.4648636Z Resolving deltas: 24% (13/54)
2022-02-05T21:25:39.4650039Z Resolving deltas: 25% (14/54)
2022-02-05T21:25:39.4650480Z Resolving deltas: 27% (15/54)
2022-02-05T21:25:39.4651728Z Resolving deltas: 29% (16/54)
2022-02-05T21:25:39.4652138Z Resolving deltas: 31% (17/54)
2022-02-05T21:25:39.4652472Z Resolving deltas: 33% (18/54)
2022-02-05T21:25:39.4653408Z Resolving deltas: 35% (19/54)
2022-02-05T21:25:39.4653836Z Resolving deltas: 37% (20/54)
2022-02-05T21:25:39.4655259Z Resolving deltas: 38% (21/54)
2022-02-05T21:25:39.4655668Z Resolving deltas: 40% (22/54)
2022-02-05T21:25:39.4656006Z Resolving deltas: 42% (23/54)
2022-02-05T21:25:39.4657099Z Resolving deltas: 44% (24/54)
2022-02-05T21:25:39.4657560Z Resolving deltas: 46% (25/54)
2022-02-05T21:25:39.4658748Z Resolving deltas: 48% (26/54)
2022-02-05T21:25:39.4659163Z Resolving deltas: 50% (27/54)
2022-02-05T21:25:39.4660040Z Resolving deltas: 51% (28/54)
2022-02-05T21:25:39.4660553Z Resolving deltas: 53% (29/54)
2022-02-05T21:25:39.4662703Z Resolving deltas: 55% (30/54)
2022-02-05T21:25:39.4663458Z Resolving deltas: 57% (31/54)
2022-02-05T21:25:39.4664002Z Resolving deltas: 59% (32/54)
2022-02-05T21:25:39.4664367Z Resolving deltas: 61% (33/54)
2022-02-05T21:25:39.4665686Z Resolving deltas: 62% (34/54)
2022-02-05T21:25:39.4666144Z Resolving deltas: 64% (35/54)
2022-02-05T21:25:39.4667593Z Resolving deltas: 66% (36/54)
2022-02-05T21:25:39.4668082Z Resolving deltas: 68% (37/54)
2022-02-05T21:25:39.4669239Z Resolving deltas: 70% (38/54)
2022-02-05T21:25:39.4670613Z Resolving deltas: 72% (39/54)
2022-02-05T21:25:39.4671222Z Resolving deltas: 74% (40/54)
2022-02-05T21:25:39.4672756Z Resolving deltas: 75% (41/54)
2022-02-05T21:25:39.4673552Z Resolving deltas: 77% (42/54)
2022-02-05T21:25:39.4675173Z Resolving deltas: 79% (43/54)
2022-02-05T21:25:39.4677021Z Resolving deltas: 81% (44/54)
2022-02-05T21:25:39.4677441Z Resolving deltas: 83% (45/54)
2022-02-05T21:25:39.4678190Z Resolving deltas: 85% (46/54)
2022-02-05T21:25:39.4678646Z Resolving deltas: 87% (47/54)
2022-02-05T21:25:39.4680555Z Resolving deltas: 88% (48/54)
2022-02-05T21:25:39.4681690Z Resolving deltas: 90% (49/54)
2022-02-05T21:25:39.4683545Z Resolving deltas: 92% (50/54)
2022-02-05T21:25:39.4766026Z Resolving deltas: 94% (51/54)
2022-02-05T21:25:39.4799462Z Resolving deltas: 96% (52/54)
2022-02-05T21:25:39.4836878Z Resolving deltas: 98% (53/54)
2022-02-05T21:25:39.4840740Z Resolving deltas: 100% (54/54)
2022-02-05T21:25:39.4841206Z Resolving deltas: 100% (54/54), done.
2022-02-05T21:25:39.5161293Z From https://github.com/telatin/bamtocov
2022-02-05T21:25:39.5162719Z * [new ref] 0b0875b74c958ec6e179f29d75077c08f2fe5103 -> origin/main
2022-02-05T21:25:39.5183243Z ##[endgroup]
2022-02-05T21:25:39.5183772Z ##[group]Determining the checkout info
2022-02-05T21:25:39.5185384Z ##[endgroup]
2022-02-05T21:25:39.5185812Z ##[group]Checking out the ref
2022-02-05T21:25:39.5190403Z [command]/usr/bin/git checkout --progress --force -B main refs/remotes/origin/main
2022-02-05T21:25:39.5819799Z Switched to a new branch 'main'
2022-02-05T21:25:39.5825660Z branch 'main' set up to track 'origin/main'.
2022-02-05T21:25:39.5834405Z ##[endgroup]
2022-02-05T21:25:39.5902910Z [command]/usr/bin/git log -1 --format='%H'
2022-02-05T21:25:39.5935899Z '0b0875b74c958ec6e179f29d75077c08f2fe5103'
2022-02-05T21:25:39.6142736Z ##[group]Run docker build . --file benchmark/Dockerfile --tag my-image-name:$(date +%s)
2022-02-05T21:25:39.6143206Z [36;1mdocker build . --file benchmark/Dockerfile --tag my-image-name:$(date +%s)[0m
2022-02-05T21:25:39.6198686Z shell: /usr/bin/bash -e {0}
2022-02-05T21:25:39.6199173Z ##[endgroup]
2022-02-05T21:25:40.0814283Z Sending build context to Docker daemon 30.86MB
2022-02-05T21:25:40.0814995Z
2022-02-05T21:25:40.0866323Z Step 1/9 : FROM nfcore/base:1.9
2022-02-05T21:25:40.3560339Z 1.9: Pulling from nfcore/base
2022-02-05T21:25:40.3569434Z b8f262c62ec6: Pulling fs layer
2022-02-05T21:25:40.3569728Z 0a43c0154f16: Pulling fs layer
2022-02-05T21:25:40.3569986Z 906d7b5da8fb: Pulling fs layer
2022-02-05T21:25:40.3570754Z 067a79e18102: Pulling fs layer
2022-02-05T21:25:40.3570987Z 067a79e18102: Waiting
2022-02-05T21:25:40.8268293Z b8f262c62ec6: Verifying Checksum
2022-02-05T21:25:40.8269260Z b8f262c62ec6: Download complete
2022-02-05T21:25:41.1385192Z 906d7b5da8fb: Verifying Checksum
2022-02-05T21:25:41.1385863Z 906d7b5da8fb: Download complete
2022-02-05T21:25:41.2376588Z 067a79e18102: Verifying Checksum
2022-02-05T21:25:41.2376990Z 067a79e18102: Download complete
2022-02-05T21:25:41.3178264Z 0a43c0154f16: Verifying Checksum
2022-02-05T21:25:41.3179057Z 0a43c0154f16: Download complete
2022-02-05T21:25:42.2307289Z b8f262c62ec6: Pull complete
2022-02-05T21:25:46.6904586Z 0a43c0154f16: Pull complete
2022-02-05T21:25:49.4810910Z 906d7b5da8fb: Pull complete
2022-02-05T21:25:49.7965561Z 067a79e18102: Pull complete
2022-02-05T21:25:49.8013091Z Digest: sha256:bebedcb30fc6e93492e01fcedfba8a3d76930f98ffef816000eaa1e31ad2a237
2022-02-05T21:25:49.8036696Z Status: Downloaded newer image for nfcore/base:1.9
2022-02-05T21:25:49.8050980Z ---> f1c63ec29383
2022-02-05T21:25:49.8053187Z Step 2/9 : LABEL authors="Andrea Telatin" description="Docker image containing all software requirements for the telatin/nextflow-example project"
2022-02-05T21:25:49.8264070Z ---> Running in 2d05d354f85f
2022-02-05T21:25:50.5256752Z Removing intermediate container 2d05d354f85f
2022-02-05T21:25:50.5257676Z ---> 9bf431bac459
2022-02-05T21:25:50.5258503Z Step 3/9 : COPY benchmark/env.yaml /environment.yml
2022-02-05T21:25:51.2505134Z ---> adabcba5b351
2022-02-05T21:25:51.2505467Z Step 4/9 : COPY benchmark/compare.sh /usr/local/bin/
2022-02-05T21:25:52.0498968Z ---> 11bcd8d39256
2022-02-05T21:25:52.0502183Z Step 5/9 : RUN conda install -q -y -c conda-forge mamba && mamba env create -q -n env -f /environment.yml && conda clean -a
2022-02-05T21:25:52.0760624Z ---> Running in afec3f130c60
2022-02-05T21:26:02.1954526Z Collecting package metadata (current_repodata.json): ...working... done
2022-02-05T21:26:04.4714271Z Solving environment: ...working... done
2022-02-05T21:26:14.0749915Z
2022-02-05T21:26:14.0750272Z ## Package Plan ##
2022-02-05T21:26:14.0750505Z
2022-02-05T21:26:14.0750672Z environment location: /opt/conda
2022-02-05T21:26:14.0750907Z
2022-02-05T21:26:14.0751042Z added / updated specs:
2022-02-05T21:26:14.0751630Z - mamba
2022-02-05T21:26:14.0751802Z
2022-02-05T21:26:14.0751810Z
2022-02-05T21:26:14.0751993Z The following packages will be downloaded:
2022-02-05T21:26:14.0752236Z
2022-02-05T21:26:14.0752390Z package | build
2022-02-05T21:26:14.0752887Z ---------------------------|-----------------
2022-02-05T21:26:14.0753488Z _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
2022-02-05T21:26:14.0754055Z _openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
2022-02-05T21:26:14.0754624Z bzip2-1.0.8 | h7f98852_4 484 KB conda-forge
2022-02-05T21:26:14.0755186Z c-ares-1.18.1 | h7f98852_0 113 KB conda-forge
2022-02-05T21:26:14.0755761Z ca-certificates-2021.10.8 | ha878542_0 139 KB conda-forge
2022-02-05T21:26:14.0756367Z certifi-2021.10.8 | py37h89c1867_1 145 KB conda-forge
2022-02-05T21:26:14.0757235Z conda-4.11.0 | py37h89c1867_0 16.9 MB conda-forge
2022-02-05T21:26:14.0757816Z icu-68.2 | h9c3ff4c_0 13.1 MB conda-forge
2022-02-05T21:26:14.0758370Z krb5-1.19.2 | hcc1bbae_3 1.4 MB conda-forge
2022-02-05T21:26:14.0759064Z libarchive-3.5.2 | hccf745f_1 1.6 MB conda-forge
2022-02-05T21:26:14.0759614Z libcurl-7.80.0 | h0b77cf5_0 339 KB
2022-02-05T21:26:14.0760160Z libedit-3.1.20191231 | h46ee950_2 121 KB conda-forge
2022-02-05T21:26:14.0760714Z libev-4.33 | h516909a_1 104 KB conda-forge
2022-02-05T21:26:14.0761280Z libgcc-ng-11.2.0 | h1d223b6_12 904 KB conda-forge
2022-02-05T21:26:14.0761831Z libgomp-11.2.0 | h1d223b6_12 426 KB conda-forge
2022-02-05T21:26:14.0762395Z libiconv-1.16 | h516909a_0 1.4 MB conda-forge
2022-02-05T21:26:14.0762946Z libnghttp2-1.46.0 | hce63b2e_0 680 KB
2022-02-05T21:26:14.0763501Z libsolv-0.7.19 | h780b84a_5 445 KB conda-forge
2022-02-05T21:26:14.0764054Z libssh2-1.10.0 | ha56f1ee_2 233 KB conda-forge
2022-02-05T21:26:14.0764614Z libstdcxx-ng-11.2.0 | he4da1e4_12 4.2 MB conda-forge
2022-02-05T21:26:14.0765183Z libxml2-2.9.12 | h72842e0_0 772 KB conda-forge
2022-02-05T21:26:14.0765719Z lz4-c-1.9.3 | h9c3ff4c_1 179 KB conda-forge
2022-02-05T21:26:14.0766260Z lzo-2.10 | h516909a_1000 314 KB conda-forge
2022-02-05T21:26:14.0766815Z mamba-0.15.3 | py37h7f483ca_0 741 KB conda-forge
2022-02-05T21:26:14.0767351Z openssl-1.1.1l | h7f98852_0 2.1 MB conda-forge
2022-02-05T21:26:14.0767913Z python_abi-3.7 | 2_cp37m 4 KB conda-forge
2022-02-05T21:26:14.0768503Z reproc-14.2.3 | h7f98852_0 28 KB conda-forge
2022-02-05T21:26:14.0769070Z reproc-cpp-14.2.3 | h9c3ff4c_0 20 KB conda-forge
2022-02-05T21:26:14.0769628Z tk-8.6.11 | h27826a3_1 3.3 MB conda-forge
2022-02-05T21:26:14.0770139Z xz-5.2.5 | h516909a_1 343 KB conda-forge
2022-02-05T21:26:14.0770640Z zstd-1.5.0 | ha4553b6_1 524 KB
2022-02-05T21:26:14.0771166Z ------------------------------------------------------------
2022-02-05T21:26:14.0771575Z Total: 50.9 MB
2022-02-05T21:26:14.0771787Z
2022-02-05T21:26:14.0771976Z The following NEW packages will be INSTALLED:
2022-02-05T21:26:14.0772202Z
2022-02-05T21:26:14.0795027Z _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
2022-02-05T21:26:14.0795839Z bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
2022-02-05T21:26:14.0796503Z c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
2022-02-05T21:26:14.0797123Z icu conda-forge/linux-64::icu-68.2-h9c3ff4c_0
2022-02-05T21:26:14.0798428Z krb5 conda-forge/linux-64::krb5-1.19.2-hcc1bbae_3
2022-02-05T21:26:14.0799132Z libarchive conda-forge/linux-64::libarchive-3.5.2-hccf745f_1
2022-02-05T21:26:14.0799806Z libcurl pkgs/main/linux-64::libcurl-7.80.0-h0b77cf5_0
2022-02-05T21:26:14.0800450Z libev conda-forge/linux-64::libev-4.33-h516909a_1
2022-02-05T21:26:14.0801087Z libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_12
2022-02-05T21:26:14.0801752Z libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0
2022-02-05T21:26:14.0802413Z libnghttp2 pkgs/main/linux-64::libnghttp2-1.46.0-hce63b2e_0
2022-02-05T21:26:14.0803085Z libsolv conda-forge/linux-64::libsolv-0.7.19-h780b84a_5
2022-02-05T21:26:14.0804001Z libssh2 conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
2022-02-05T21:26:14.0804653Z libxml2 conda-forge/linux-64::libxml2-2.9.12-h72842e0_0
2022-02-05T21:26:14.0805291Z lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
2022-02-05T21:26:14.0806034Z lzo conda-forge/linux-64::lzo-2.10-h516909a_1000
2022-02-05T21:26:14.0806656Z mamba conda-forge/linux-64::mamba-0.15.3-py37h7f483ca_0
2022-02-05T21:26:14.0807310Z python_abi conda-forge/linux-64::python_abi-3.7-2_cp37m
2022-02-05T21:26:14.0808005Z reproc conda-forge/linux-64::reproc-14.2.3-h7f98852_0
2022-02-05T21:26:14.0808691Z reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.3-h9c3ff4c_0
2022-02-05T21:26:14.0809350Z zstd pkgs/main/linux-64::zstd-1.5.0-ha4553b6_1
2022-02-05T21:26:14.0809587Z
2022-02-05T21:26:14.0810581Z The following packages will be UPDATED:
2022-02-05T21:26:14.0810843Z
2022-02-05T21:26:14.0811511Z ca-certificates pkgs/main::ca-certificates-2019.8.28-0 --> conda-forge::ca-certificates-2021.10.8-ha878542_0
2022-02-05T21:26:14.0812405Z certifi pkgs/main::certifi-2019.9.11-py37_0 --> conda-forge::certifi-2021.10.8-py37h89c1867_1
2022-02-05T21:26:14.0815797Z conda pkgs/main::conda-4.7.12-py37_0 --> conda-forge::conda-4.11.0-py37h89c1867_0
2022-02-05T21:26:14.0816640Z libedit pkgs/main::libedit-3.1.20181209-hc058~ --> conda-forge::libedit-3.1.20191231-h46ee950_2
2022-02-05T21:26:14.0817519Z libgcc-ng pkgs/main::libgcc-ng-9.1.0-hdf63c60_0 --> conda-forge::libgcc-ng-11.2.0-h1d223b6_12
2022-02-05T21:26:14.0818407Z libstdcxx-ng pkgs/main::libstdcxx-ng-9.1.0-hdf63c6~ --> conda-forge::libstdcxx-ng-11.2.0-he4da1e4_12
2022-02-05T21:26:14.0819243Z openssl pkgs/main::openssl-1.1.1d-h7b6447c_2 --> conda-forge::openssl-1.1.1l-h7f98852_0
2022-02-05T21:26:14.0819966Z tk pkgs/main::tk-8.6.8-hbc83047_0 --> conda-forge::tk-8.6.11-h27826a3_1
2022-02-05T21:26:14.0820732Z xz pkgs/main::xz-5.2.4-h14c3975_4 --> conda-forge::xz-5.2.5-h516909a_1
2022-02-05T21:26:14.0820968Z
2022-02-05T21:26:14.0821280Z The following packages will be SUPERSEDED by a higher-priority channel:
2022-02-05T21:26:14.0821531Z
2022-02-05T21:26:14.0821890Z _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge
2022-02-05T21:26:14.0822159Z
2022-02-05T21:26:14.0822165Z
2022-02-05T21:26:14.3936706Z Preparing transaction: ...working... done
2022-02-05T21:26:14.7311151Z Verifying transaction: ...working... done
2022-02-05T21:26:16.4368322Z Executing transaction: ...working... done
2022-02-05T21:26:45.0402345Z Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.
2022-02-05T21:26:45.3401905Z Preparing transaction: ...working... done
2022-02-05T21:26:48.0689442Z Verifying transaction: ...working... done
2022-02-05T21:26:49.0490486Z Executing transaction: ...working... done
2022-02-05T21:26:50.5034787Z Installing pip dependencies: ...working... done
2022-02-05T21:26:50.8543424Z Cache location: /opt/conda/pkgs
2022-02-05T21:26:50.8544627Z Will remove the following tarballs:
2022-02-05T21:26:50.8644244Z
2022-02-05T21:26:50.8644557Z /opt/conda/pkgs
2022-02-05T21:26:50.8645062Z ---------------
2022-02-05T21:26:50.8645473Z libffi-3.4.2-h7f98852_5.tar.bz2 57 KB
2022-02-05T21:26:50.8646022Z libev-4.33-h516909a_1.tar.bz2 104 KB
2022-02-05T21:26:50.8646663Z setuptools-58.0.4-py310h06a4308_0.conda 782 KB
2022-02-05T21:26:50.8647224Z mosdepth-0.3.3-hdfd78af_1.tar.bz2 3.4 MB
2022-02-05T21:26:50.8647671Z pip-21.2.4-py310h06a4308_0.conda 1.8 MB
2022-02-05T21:26:50.8648467Z libdeflate-1.9-h7f98852_0.tar.bz2 77 KB
2022-02-05T21:26:50.8648920Z pcre-8.45-h9c3ff4c_0.tar.bz2 253 KB
2022-02-05T21:26:50.8649414Z reproc-14.2.3-h7f98852_0.tar.bz2 28 KB
2022-02-05T21:26:50.8649849Z libbigwig-0.4.6-h1b8c3c0_1.tar.bz2 331 KB
2022-02-05T21:26:50.8650533Z python_abi-3.7-2_cp37m.tar.bz2 4 KB
2022-02-05T21:26:50.8651028Z _libgcc_mutex-0.1-conda_forge.tar.bz2 3 KB
2022-02-05T21:26:50.8651476Z libgomp-11.2.0-h1d223b6_12.tar.bz2 426 KB
2022-02-05T21:26:50.8652037Z libstdcxx-ng-11.2.0-he4da1e4_12.tar.bz2 4.2 MB
2022-02-05T21:26:50.8652473Z xz-5.2.5-h516909a_1.tar.bz2 343 KB
2022-02-05T21:26:50.8653030Z certifi-2021.10.8-py37h89c1867_1.tar.bz2 145 KB
2022-02-05T21:26:50.8653531Z mamba-0.15.3-py37h7f483ca_0.tar.bz2 741 KB
2022-02-05T21:26:50.8653969Z bamtocov-2.5.0-h38613fd_1.tar.bz2 778 KB
2022-02-05T21:26:50.8654470Z libedit-3.1.20191231-h46ee950_2.tar.bz2 121 KB
2022-02-05T21:26:50.8654920Z wheel-0.37.1-pyhd3eb1b0_0.conda 33 KB
2022-02-05T21:26:50.8655437Z bzip2-1.0.8-h7f98852_4.tar.bz2 484 KB
2022-02-05T21:26:50.8655862Z readline-8.1-h46c0cb4_0.tar.bz2 295 KB
2022-02-05T21:26:50.8656351Z libxml2-2.9.12-h72842e0_0.tar.bz2 772 KB
2022-02-05T21:26:50.8656840Z libedit-3.1.20191231-he28a2e2_2.tar.bz2 121 KB
2022-02-05T21:26:50.8657297Z libnghttp2-1.46.0-hce63b2e_0.conda 680 KB
2022-02-05T21:26:50.8657835Z libnghttp2-1.46.0-h812cca2_0.tar.bz2 806 KB
2022-02-05T21:26:50.8658277Z bedtools-2.30.0-h7d7f7ad_2.tar.bz2 17.9 MB
2022-02-05T21:26:50.8658863Z ncurses-6.2-h58526e2_4.tar.bz2 985 KB
2022-02-05T21:26:50.8659329Z libsolv-0.7.19-h780b84a_5.tar.bz2 445 KB
2022-02-05T21:26:50.8659724Z libssh2-1.10.0-ha56f1ee_2.tar.bz2 233 KB
2022-02-05T21:26:50.8660205Z c-ares-1.18.1-h7f98852_0.tar.bz2 113 KB
2022-02-05T21:26:50.8660613Z libarchive-3.5.2-hccf745f_1.tar.bz2 1.6 MB
2022-02-05T21:26:50.8661187Z ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2 667 KB
2022-02-05T21:26:50.8661607Z megadepth-1.1.3-h00214ad_1.tar.bz2 104 KB
2022-02-05T21:26:50.8662085Z libiconv-1.16-h516909a_0.tar.bz2 1.4 MB
2022-02-05T21:26:50.8662655Z lzo-2.10-h516909a_1000.tar.bz2 314 KB
2022-02-05T21:26:50.8663006Z tomli-2.0.0-pyhd8ed1ab_1.tar.bz2 15 KB
2022-02-05T21:26:50.8663436Z ca-certificates-2021.10.8-ha878542_0.tar.bz2 139 KB
2022-02-05T21:26:50.8663823Z libcurl-7.80.0-h0b77cf5_0.conda 339 KB
2022-02-05T21:26:50.8664227Z libgcc-ng-11.2.0-h1d223b6_12.tar.bz2 904 KB
2022-02-05T21:26:50.8664665Z certifi-2021.5.30-py310h06a4308_0.conda 148 KB
2022-02-05T21:26:50.8665027Z reproc-cpp-14.2.3-h9c3ff4c_0.tar.bz2 20 KB
2022-02-05T21:26:50.8665433Z bamtools-2.5.1-h9a82719_9.tar.bz2 1012 KB
2022-02-05T21:26:50.8665794Z libzlib-1.2.11-h36c2ea0_1013.tar.bz2 59 KB
2022-02-05T21:26:50.8666189Z libcurl-7.81.0-h2574ce0_0.tar.bz2 338 KB
2022-02-05T21:26:50.8666559Z krb5-1.19.2-hcc1bbae_3.tar.bz2 1.4 MB
2022-02-05T21:26:50.8667351Z lz4-c-1.9.3-h9c3ff4c_1.tar.bz2 179 KB
2022-02-05T21:26:50.8667844Z tzdata-2021e-he74cb21_0.tar.bz2 121 KB
2022-02-05T21:26:50.8668275Z libnsl-2.0.0-h7f98852_0.tar.bz2 31 KB
2022-02-05T21:26:50.8668751Z openssl-1.1.1l-h7f98852_0.tar.bz2 2.1 MB
2022-02-05T21:26:50.8669339Z zstd-1.5.0-ha4553b6_1.conda 524 KB
2022-02-05T21:26:50.8669847Z python-3.10.2-h62f1059_0_cpython.tar.bz2 30.0 MB
2022-02-05T21:26:50.8670383Z _openmp_mutex-4.5-1_gnu.tar.bz2 22 KB
2022-02-05T21:26:50.8670811Z libuuid-2.32.1-h14c3975_1000.tar.bz2 26 KB
2022-02-05T21:26:50.8671289Z samtools-1.14-hb421002_0.tar.bz2 411 KB
2022-02-05T21:26:50.8671746Z curl-7.81.0-h2574ce0_0.tar.bz2 90 KB
2022-02-05T21:26:50.8672360Z htslib-1.14-h5138463_1.tar.bz2 2.2 MB
2022-02-05T21:26:50.8672806Z sqlite-3.37.0-h9cd32fc_0.tar.bz2 1.5 MB
2022-02-05T21:26:50.8673300Z conda-4.11.0-py37h89c1867_0.tar.bz2 16.9 MB
2022-02-05T21:26:50.8673784Z icu-68.2-h9c3ff4c_0.tar.bz2 13.1 MB
2022-02-05T21:26:50.8674235Z tk-8.6.11-h27826a3_1.tar.bz2 3.3 MB
2022-02-05T21:26:50.8674820Z zlib-1.2.11-h36c2ea0_1013.tar.bz2 86 KB
2022-02-05T21:26:50.8675238Z python_abi-3.10-2_cp310.tar.bz2 4 KB
2022-02-05T21:26:50.8675730Z hyperfine-1.12.0-habb4d0f_0.tar.bz2 624 KB
2022-02-05T21:26:50.8676224Z covtobed-1.3.5-h36a6f06_0.tar.bz2 67 KB
2022-02-05T21:26:50.8676399Z
2022-02-05T21:26:50.8676705Z ---------------------------------------------------
2022-02-05T21:26:50.8677102Z Total: 115.9 MB
2022-02-05T21:26:50.8677303Z
2022-02-05T21:26:50.8677388Z Proceed ([y]/n)?
2022-02-05T21:26:50.9571887Z Removed libffi-3.4.2-h7f98852_5.tar.bz2
2022-02-05T21:26:50.9572936Z Removed libev-4.33-h516909a_1.tar.bz2
2022-02-05T21:26:50.9573844Z Removed setuptools-58.0.4-py310h06a4308_0.conda
2022-02-05T21:26:50.9574633Z Removed mosdepth-0.3.3-hdfd78af_1.tar.bz2
2022-02-05T21:26:50.9575492Z Removed pip-21.2.4-py310h06a4308_0.conda
2022-02-05T21:26:50.9576507Z Removed libdeflate-1.9-h7f98852_0.tar.bz2
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2022-02-05T21:26:50.9578839Z Removed libbigwig-0.4.6-h1b8c3c0_1.tar.bz2
2022-02-05T21:26:50.9579682Z Removed python_abi-3.7-2_cp37m.tar.bz2
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2022-02-05T21:26:50.9582199Z Removed libstdcxx-ng-11.2.0-he4da1e4_12.tar.bz2
2022-02-05T21:26:50.9582914Z Removed xz-5.2.5-h516909a_1.tar.bz2
2022-02-05T21:26:50.9583774Z Removed certifi-2021.10.8-py37h89c1867_1.tar.bz2
2022-02-05T21:26:50.9584545Z Removed mamba-0.15.3-py37h7f483ca_0.tar.bz2
2022-02-05T21:26:50.9585415Z Removed bamtocov-2.5.0-h38613fd_1.tar.bz2
2022-02-05T21:26:50.9586179Z Removed libedit-3.1.20191231-h46ee950_2.tar.bz2
2022-02-05T21:26:50.9586998Z Removed wheel-0.37.1-pyhd3eb1b0_0.conda
2022-02-05T21:26:50.9587811Z Removed bzip2-1.0.8-h7f98852_4.tar.bz2
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2022-02-05T21:26:50.9591754Z Removed libnghttp2-1.46.0-hce63b2e_0.conda
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2022-02-05T21:26:50.9606361Z Removed bamtools-2.5.1-h9a82719_9.tar.bz2
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2022-02-05T21:26:50.9607716Z Removed libcurl-7.81.0-h2574ce0_0.tar.bz2
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2022-02-05T21:26:50.9608564Z Removed lz4-c-1.9.3-h9c3ff4c_1.tar.bz2
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2022-02-05T21:26:50.9609425Z Removed libnsl-2.0.0-h7f98852_0.tar.bz2
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2022-02-05T21:26:50.9610326Z Removed zstd-1.5.0-ha4553b6_1.conda
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2022-02-05T21:26:50.9611213Z Removed _openmp_mutex-4.5-1_gnu.tar.bz2
2022-02-05T21:26:50.9611691Z Removed libuuid-2.32.1-h14c3975_1000.tar.bz2
2022-02-05T21:26:50.9612071Z Removed samtools-1.14-hb421002_0.tar.bz2
2022-02-05T21:26:50.9612487Z Removed curl-7.81.0-h2574ce0_0.tar.bz2
2022-02-05T21:26:50.9612850Z Removed htslib-1.14-h5138463_1.tar.bz2
2022-02-05T21:26:50.9613285Z Removed sqlite-3.37.0-h9cd32fc_0.tar.bz2
2022-02-05T21:26:50.9613710Z Removed conda-4.11.0-py37h89c1867_0.tar.bz2
2022-02-05T21:26:50.9614134Z Removed icu-68.2-h9c3ff4c_0.tar.bz2
2022-02-05T21:26:50.9614539Z Removed tk-8.6.11-h27826a3_1.tar.bz2
2022-02-05T21:26:50.9614944Z Removed zlib-1.2.11-h36c2ea0_1013.tar.bz2
2022-02-05T21:26:50.9615371Z Removed python_abi-3.10-2_cp310.tar.bz2
2022-02-05T21:26:50.9615795Z Removed hyperfine-1.12.0-habb4d0f_0.tar.bz2
2022-02-05T21:26:50.9616235Z Removed covtobed-1.3.5-h36a6f06_0.tar.bz2
2022-02-05T21:26:50.9616600Z WARNING: /root/.conda/pkgs does not exist
2022-02-05T21:26:50.9617091Z Cache location: /opt/conda/pkgs
2022-02-05T21:26:50.9617473Z Will remove the following packages:
2022-02-05T21:26:50.9617796Z /opt/conda/pkgs
2022-02-05T21:26:50.9618157Z ---------------
2022-02-05T21:26:50.9618349Z
2022-02-05T21:26:50.9618559Z python_abi-3.10-2_cp310 11 KB
2022-02-05T21:26:50.9619040Z _openmp_mutex-4.5-1_gnu 93 KB
2022-02-05T21:26:50.9619516Z _libgcc_mutex-0.1-conda_forge 6 KB
2022-02-05T21:26:50.9619964Z python_abi-3.7-2_cp37m 11 KB
2022-02-05T21:26:50.9620188Z
2022-02-05T21:26:50.9620461Z ---------------------------------------------------
2022-02-05T21:26:50.9620789Z Total: 120 KB
2022-02-05T21:26:50.9620989Z
2022-02-05T21:26:50.9621139Z Proceed ([y]/n)?
2022-02-05T21:26:51.1827393Z removing python_abi-3.10-2_cp310
2022-02-05T21:26:51.1828427Z removing _openmp_mutex-4.5-1_gnu
2022-02-05T21:26:51.1829645Z removing _libgcc_mutex-0.1-conda_forge
2022-02-05T21:26:51.1830349Z removing python_abi-3.7-2_cp37m
2022-02-05T21:27:02.5994076Z Removing intermediate container afec3f130c60
2022-02-05T21:27:02.5994750Z ---> da36f032743c
2022-02-05T21:27:02.5995143Z Step 6/9 : ENV PATH /opt/conda/envs/env/bin:$PATH
2022-02-05T21:27:02.6352448Z ---> Running in 8677a7565ce6
2022-02-05T21:27:04.2140954Z Removing intermediate container 8677a7565ce6
2022-02-05T21:27:04.2141801Z ---> d391a4147c45
2022-02-05T21:27:04.2143157Z Step 7/9 : RUN conda env export --name env > workflow.yml
2022-02-05T21:27:04.2292409Z ---> Running in 5ede275076ab
2022-02-05T21:27:06.8472794Z Removing intermediate container 5ede275076ab
2022-02-05T21:27:06.8473826Z ---> 02a3b3fcf418
2022-02-05T21:27:06.8474497Z Step 8/9 : RUN compare.sh all
2022-02-05T21:27:06.8688924Z ---> Running in c7df37499bf1
2022-02-05T21:27:07.1414458Z covtobed : 1.3.5
2022-02-05T21:27:07.1415210Z bamtocov : 2.5.0
2022-02-05T21:27:07.1415809Z megadepth : 1.1.2
2022-02-05T21:27:07.1416189Z mosdepth : 0.3.3
2022-02-05T21:27:20.2851964Z Benchmark 1: covtobed 'cpara-illumina-noseq.bam' #1.3.5
2022-02-05T21:28:33.0522200Z Time (mean ± σ): 14.553 s ± 0.246 s [User: 12.598 s, System: 1.953 s]
2022-02-05T21:28:33.0716300Z Range (min … max): 14.289 s … 14.895 s 5 runs
2022-02-05T21:28:33.0716595Z
2022-02-05T21:28:33.0716985Z Benchmark 2: bamtocov 'cpara-illumina-noseq.bam' #2.5.0
2022-02-05T21:29:26.9236341Z Time (mean ± σ): 10.774 s ± 0.144 s [User: 10.845 s, System: 2.251 s]
2022-02-05T21:29:26.9237700Z Range (min … max): 10.550 s … 10.939 s 5 runs
2022-02-05T21:29:26.9350384Z
2022-02-05T21:29:26.9355176Z Benchmark 3: megadepth --coverage 'cpara-illumina-noseq.bam' #1.1.2
2022-02-05T21:29:46.5926729Z Time (mean ± σ): 3.932 s ± 0.077 s [User: 3.882 s, System: 0.049 s]
2022-02-05T21:29:46.5928687Z Range (min … max): 3.842 s … 4.030 s 5 runs
2022-02-05T21:29:46.5929275Z
2022-02-05T21:29:46.5929730Z Benchmark 4: megadepth --coverage --longreads 'cpara-illumina-noseq.bam' #1.1.2
2022-02-05T21:30:07.2379282Z Time (mean ± σ): 4.129 s ± 0.112 s [User: 4.050 s, System: 0.077 s]
2022-02-05T21:30:07.2381235Z Range (min … max): 4.012 s … 4.313 s 5 runs
2022-02-05T21:30:07.2473047Z
2022-02-05T21:30:07.2473622Z Benchmark 5: mosdepth mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3
2022-02-05T21:31:02.6897285Z Time (mean ± σ): 11.090 s ± 0.135 s [User: 10.770 s, System: 0.275 s]
2022-02-05T21:31:02.6904337Z Range (min … max): 10.908 s … 11.289 s 5 runs
2022-02-05T21:31:02.6904765Z
2022-02-05T21:31:02.6905668Z Benchmark 6: mosdepth --fast-mode mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3
2022-02-05T21:31:02.6906362Z [91m
2022-02-05T21:31:02.6907659Z Warning: Statistical outliers were detected. Consider re-running this benchmark on a quiet PC without any interferences from other programs. It might help to use the '--warmup' or '--prepare' options.
2022-02-05T21:31:49.6312897Z [0m Time (mean ± σ): 9.387 s ± 0.074 s [User: 9.041 s, System: 0.288 s]
2022-02-05T21:31:49.6322364Z Range (min … max): 9.291 s … 9.468 s 5 runs
2022-02-05T21:31:49.6322968Z
2022-02-05T21:31:49.6323432Z Summary
2022-02-05T21:31:49.6324115Z 'megadepth --coverage 'cpara-illumina-noseq.bam' #1.1.2' ran
2022-02-05T21:31:49.6325098Z 1.05 ± 0.04 times faster than 'megadepth --coverage --longreads 'cpara-illumina-noseq.bam' #1.1.2'
2022-02-05T21:31:49.6326038Z 2.39 ± 0.05 times faster than 'mosdepth --fast-mode mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3'
2022-02-05T21:31:49.6326894Z 2.74 ± 0.07 times faster than 'bamtocov 'cpara-illumina-noseq.bam' #2.5.0'
2022-02-05T21:31:49.6370818Z 2.82 ± 0.07 times faster than 'mosdepth mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3'
2022-02-05T21:31:49.6371382Z 3.70 ± 0.10 times faster than 'covtobed 'cpara-illumina-noseq.bam' #1.3.5'
2022-02-05T21:31:52.2830199Z Benchmark 1: covtobed 'cpara-ont-noseq.bam' #1.3.5
2022-02-05T21:31:55.2528184Z Time (mean ± σ): 494.1 ms ± 14.3 ms [User: 465.9 ms, System: 27.7 ms]
2022-02-05T21:31:55.2529022Z Range (min … max): 479.1 ms … 512.8 ms 6 runs
2022-02-05T21:31:55.2529455Z
2022-02-05T21:31:55.2530117Z Benchmark 2: bamtocov 'cpara-ont-noseq.bam' #2.5.0
2022-02-05T21:31:58.0957769Z Time (mean ± σ): 236.3 ms ± 10.7 ms [User: 368.3 ms, System: 42.9 ms]
2022-02-05T21:31:58.0958285Z Range (min … max): 224.2 ms … 253.5 ms 12 runs
2022-02-05T21:31:58.0958529Z
2022-02-05T21:31:58.0958962Z Benchmark 3: megadepth --coverage 'cpara-ont-noseq.bam' #1.1.2
2022-02-05T21:32:00.9029776Z Time (mean ± σ): 400.3 ms ± 11.5 ms [User: 391.2 ms, System: 9.0 ms]
2022-02-05T21:32:00.9030648Z Range (min … max): 387.4 ms … 419.2 ms 7 runs
2022-02-05T21:32:00.9031077Z
2022-02-05T21:32:00.9031873Z Benchmark 4: megadepth --coverage --longreads 'cpara-ont-noseq.bam' #1.1.2
2022-02-05T21:32:03.7532557Z Time (mean ± σ): 406.4 ms ± 11.4 ms [User: 394.2 ms, System: 11.7 ms]
2022-02-05T21:32:03.7533385Z Range (min … max): 392.1 ms … 424.8 ms 7 runs
2022-02-05T21:32:03.7533826Z
2022-02-05T21:32:03.7534583Z Benchmark 5: mosdepth mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3
2022-02-05T21:32:07.0810157Z Time (mean ± σ): 664.9 ms ± 29.3 ms [User: 643.4 ms, System: 20.9 ms]
2022-02-05T21:32:07.0810621Z Range (min … max): 629.0 ms … 687.7 ms 5 runs
2022-02-05T21:32:07.0810865Z
2022-02-05T21:32:07.0811290Z Benchmark 6: mosdepth --fast-mode mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3
2022-02-05T21:32:07.0811648Z [91m
2022-02-05T21:32:07.0814029Z Warning: Statistical outliers were detected. Consider re-running this benchmark on a quiet PC without any interferences from other programs. It might help to use the '--warmup' or '--prepare' options.
2022-02-05T21:32:09.7992032Z [0m Time (mean ± σ): 542.8 ms ± 10.0 ms [User: 534.0 ms, System: 8.7 ms]
2022-02-05T21:32:09.7992857Z Range (min … max): 535.5 ms … 560.0 ms 5 runs
2022-02-05T21:32:09.7993120Z
2022-02-05T21:32:09.7993305Z Summary
2022-02-05T21:32:09.7993675Z 'bamtocov 'cpara-ont-noseq.bam' #2.5.0' ran
2022-02-05T21:32:09.7994290Z 1.69 ± 0.09 times faster than 'megadepth --coverage 'cpara-ont-noseq.bam' #1.1.2'
2022-02-05T21:32:09.7994852Z 1.72 ± 0.09 times faster than 'megadepth --coverage --longreads 'cpara-ont-noseq.bam' #1.1.2'
2022-02-05T21:32:09.7995433Z 2.09 ± 0.11 times faster than 'covtobed 'cpara-ont-noseq.bam' #1.3.5'
2022-02-05T21:32:09.7995899Z 2.30 ± 0.11 times faster than 'mosdepth --fast-mode mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3'
2022-02-05T21:32:09.7996454Z 2.81 ± 0.18 times faster than 'mosdepth mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3'
2022-02-05T21:41:48.7574036Z Benchmark 1: covtobed 'HG00258.bam' #1.3.5
2022-02-05T22:28:45.3939644Z Time (mean ± σ): 563.326 s ± 8.611 s [User: 489.595 s, System: 73.595 s]
2022-02-05T22:28:45.3940160Z Range (min … max): 555.070 s … 574.771 s 5 runs
2022-02-05T22:28:45.3940385Z
2022-02-05T22:28:45.3940699Z Benchmark 2: bamtocov 'HG00258.bam' #2.5.0
2022-02-05T22:59:04.4592656Z Time (mean ± σ): 363.811 s ± 8.651 s [User: 386.928 s, System: 92.597 s]
2022-02-05T22:59:04.4593516Z Range (min … max): 350.075 s … 373.599 s 5 runs
2022-02-05T22:59:04.4593846Z
2022-02-05T22:59:04.4594316Z Benchmark 3: megadepth --coverage 'HG00258.bam' #1.1.2
2022-02-05T23:13:32.0623968Z Time (mean ± σ): 173.520 s ± 0.228 s [User: 164.764 s, System: 8.327 s]
2022-02-05T23:13:32.0625104Z Range (min … max): 173.290 s … 173.810 s 5 runs
2022-02-05T23:13:32.0625675Z
2022-02-05T23:13:32.0626705Z Benchmark 4: megadepth --coverage --longreads 'HG00258.bam' #1.1.2
2022-02-05T23:27:58.4713914Z Time (mean ± σ): 173.281 s ± 0.478 s [User: 164.471 s, System: 8.422 s]
2022-02-05T23:27:58.4715047Z Range (min … max): 172.890 s … 173.919 s 5 runs
2022-02-05T23:27:58.4715610Z
2022-02-05T23:27:58.4716616Z Benchmark 5: mosdepth mosdepth.pMD4Cm 'HG00258.bam' #0.3.3
2022-02-06T00:07:06.4949935Z Time (mean ± σ): 469.604 s ± 0.839 s [User: 453.589 s, System: 14.500 s]
2022-02-06T00:07:06.4950464Z Range (min … max): 468.725 s … 471.000 s 5 runs
2022-02-06T00:07:06.4950702Z
2022-02-06T00:07:06.4950941Z [91m
2022-02-06T00:07:06.4951699Z Warning: Statistical outliers were detected. Consider re-running this benchmark on a quiet PC without any interferences from other programs. It might help to use the '--warmup' or '--prepare' options.
2022-02-06T00:07:06.4952435Z [0mBenchmark 6: mosdepth --fast-mode mosdepth.pMD4Cm 'HG00258.bam' #0.3.3
2022-02-06T00:45:23.3983978Z Time (mean ± σ): 459.380 s ± 1.134 s [User: 440.636 s, System: 16.454 s]
2022-02-06T00:45:23.3984819Z Range (min … max): 458.283 s … 461.134 s 5 runs
2022-02-06T00:45:23.3987191Z
2022-02-06T00:45:23.3988525Z Summary
2022-02-06T00:45:23.3989766Z 'megadepth --coverage --longreads 'HG00258.bam' #1.1.2' ran
2022-02-06T00:45:23.3990687Z 1.00 ± 0.00 times faster than 'megadepth --coverage 'HG00258.bam' #1.1.2'
2022-02-06T00:45:23.3991573Z 2.10 ± 0.05 times faster than 'bamtocov 'HG00258.bam' #2.5.0'
2022-02-06T00:45:23.3992620Z 2.65 ± 0.01 times faster than 'mosdepth --fast-mode mosdepth.pMD4Cm 'HG00258.bam' #0.3.3'
2022-02-06T00:45:23.3993590Z 2.71 ± 0.01 times faster than 'mosdepth mosdepth.pMD4Cm 'HG00258.bam' #0.3.3'
2022-02-06T00:45:23.3994404Z 3.25 ± 0.05 times faster than 'covtobed 'HG00258.bam' #1.3.5'
2022-02-06T00:45:26.4487256Z Benchmark 1: covtobed 'panel_01.bam' #1.3.5
2022-02-06T00:45:29.4121273Z Time (mean ± σ): 422.6 ms ± 3.7 ms [User: 416.2 ms, System: 5.5 ms]
2022-02-06T00:45:29.4121908Z Range (min … max): 417.5 ms … 427.5 ms 7 runs
2022-02-06T00:45:29.4122210Z
2022-02-06T00:45:29.4122631Z Benchmark 2: bamtocov 'panel_01.bam' #2.5.0
2022-02-06T00:45:32.2932084Z Time (mean ± σ): 191.3 ms ± 4.9 ms [User: 277.7 ms, System: 37.4 ms]
2022-02-06T00:45:32.2932921Z Range (min … max): 185.7 ms … 204.4 ms 15 runs
2022-02-06T00:45:32.2933151Z
2022-02-06T00:45:32.2933518Z Benchmark 3: megadepth --coverage 'panel_01.bam' #1.1.2
2022-02-06T00:46:02.6513542Z Time (mean ± σ): 6.069 s ± 0.037 s [User: 5.655 s, System: 0.411 s]
2022-02-06T00:46:02.6514019Z Range (min … max): 6.021 s … 6.122 s 5 runs
2022-02-06T00:46:02.6514279Z
2022-02-06T00:46:02.6584654Z Benchmark 4: megadepth --coverage --longreads 'panel_01.bam' #1.1.2
2022-02-06T00:46:32.8964360Z Time (mean ± σ): 6.050 s ± 0.020 s [User: 5.642 s, System: 0.407 s]
2022-02-06T00:46:32.8965737Z Range (min … max): 6.023 s … 6.079 s 5 runs
2022-02-06T00:46:32.8966489Z
2022-02-06T00:46:32.8967353Z Benchmark 5: mosdepth mosdepth.zCQZhW 'panel_01.bam' #0.3.3
2022-02-06T00:50:06.5607735Z Time (mean ± σ): 42.687 s ± 7.201 s [User: 24.145 s, System: 4.893 s]
2022-02-06T00:50:06.5628666Z Range (min … max): 35.746 s … 51.458 s 5 runs
2022-02-06T00:50:06.5636168Z
2022-02-06T00:50:06.5647780Z Benchmark 6: mosdepth --fast-mode mosdepth.zCQZhW 'panel_01.bam' #0.3.3
2022-02-06T00:52:15.9523319Z Time (mean ± σ): 25.917 s ± 0.166 s [User: 23.335 s, System: 2.565 s]
2022-02-06T00:52:16.0655400Z Range (min … max): 25.730 s … 26.144 s 5 runs
2022-02-06T00:52:16.0656490Z
2022-02-06T00:52:16.0657837Z Summary
2022-02-06T00:52:16.0659229Z 'bamtocov 'panel_01.bam' #2.5.0' ran
2022-02-06T00:52:16.0660186Z 2.21 ± 0.06 times faster than 'covtobed 'panel_01.bam' #1.3.5'
2022-02-06T00:52:16.0661265Z 31.63 ± 0.81 times faster than 'megadepth --coverage --longreads 'panel_01.bam' #1.1.2'
2022-02-06T00:52:16.0664013Z 31.72 ± 0.83 times faster than 'megadepth --coverage 'panel_01.bam' #1.1.2'
2022-02-06T00:52:16.0696463Z 135.47 ± 3.55 times faster than 'mosdepth --fast-mode mosdepth.zCQZhW 'panel_01.bam' #0.3.3'
2022-02-06T00:52:16.0698271Z 223.14 ± 38.07 times faster than 'mosdepth mosdepth.zCQZhW 'panel_01.bam' #0.3.3'
2022-02-06T00:52:40.0440055Z Benchmark 1: covtobed 'w1118_f_hd_R1.junc.bam' #1.3.5
2022-02-06T00:52:47.6994038Z Time (mean ± σ): 1.530 s ± 0.021 s [User: 1.220 s, System: 0.307 s]
2022-02-06T00:52:47.7011982Z Range (min … max): 1.502 s … 1.556 s 5 runs
2022-02-06T00:52:47.7012595Z
2022-02-06T00:52:47.7016158Z Benchmark 2: bamtocov 'w1118_f_hd_R1.junc.bam' #2.5.0
2022-02-06T00:52:54.8627425Z Time (mean ± σ): 1.432 s ± 0.074 s [User: 1.223 s, System: 0.396 s]
2022-02-06T00:52:54.8627903Z Range (min … max): 1.375 s … 1.523 s 5 runs
2022-02-06T00:52:54.8628164Z
2022-02-06T00:52:54.8628386Z [91m
2022-02-06T00:52:54.8629461Z Warning: Statistical outliers were detected. Consider re-running this benchmark on a quiet PC without any interferences from other programs. It might help to use the '--warmup' or '--prepare' options.
2022-02-06T00:52:54.8630322Z [0mBenchmark 3: megadepth --coverage 'w1118_f_hd_R1.junc.bam' #1.1.2
2022-02-06T00:52:57.9310988Z Time (mean ± σ): 613.0 ms ± 12.5 ms [User: 521.3 ms, System: 86.5 ms]
2022-02-06T00:52:57.9311953Z Range (min … max): 604.0 ms … 634.4 ms 5 runs
2022-02-06T00:52:57.9312399Z
2022-02-06T00:52:57.9313199Z Benchmark 4: megadepth --coverage --longreads 'w1118_f_hd_R1.junc.bam' #1.1.2
2022-02-06T00:53:01.0045904Z Time (mean ± σ): 613.9 ms ± 3.4 ms [User: 535.9 ms, System: 77.8 ms]
2022-02-06T00:53:01.0046525Z Range (min … max): 609.2 ms … 617.5 ms 5 runs
2022-02-06T00:53:01.0046754Z
2022-02-06T00:53:01.0047161Z Benchmark 5: mosdepth mosdepth.7dbdyA 'w1118_f_hd_R1.junc.bam' #0.3.3
2022-02-06T00:53:15.7044388Z Time (mean ± σ): 2.939 s ± 0.017 s [User: 2.721 s, System: 0.213 s]
2022-02-06T00:53:15.7048588Z Range (min … max): 2.913 s … 2.958 s 5 runs
2022-02-06T00:53:15.7049068Z
2022-02-06T00:53:15.7049845Z Benchmark 6: mosdepth --fast-mode mosdepth.7dbdyA 'w1118_f_hd_R1.junc.bam' #0.3.3
2022-02-06T00:53:30.2471724Z Time (mean ± σ): 2.907 s ± 0.030 s [User: 2.681 s, System: 0.219 s]
2022-02-06T00:53:30.2476544Z Range (min … max): 2.881 s … 2.953 s 5 runs
2022-02-06T00:53:30.2476802Z
2022-02-06T00:53:30.2476985Z Summary
2022-02-06T00:53:30.2477391Z 'megadepth --coverage 'w1118_f_hd_R1.junc.bam' #1.1.2' ran
2022-02-06T00:53:30.2478068Z 1.00 ± 0.02 times faster than 'megadepth --coverage --longreads 'w1118_f_hd_R1.junc.bam' #1.1.2'
2022-02-06T00:53:30.2478620Z 2.34 ± 0.13 times faster than 'bamtocov 'w1118_f_hd_R1.junc.bam' #2.5.0'
2022-02-06T00:53:30.2479131Z 2.50 ± 0.06 times faster than 'covtobed 'w1118_f_hd_R1.junc.bam' #1.3.5'
2022-02-06T00:53:30.2479737Z 4.74 ± 0.11 times faster than 'mosdepth --fast-mode mosdepth.7dbdyA 'w1118_f_hd_R1.junc.bam' #0.3.3'
2022-02-06T00:53:30.2480344Z 4.80 ± 0.10 times faster than 'mosdepth mosdepth.7dbdyA 'w1118_f_hd_R1.junc.bam' #0.3.3'
2022-02-06T00:54:42.1090704Z [91m[E::hts_idx_push] NO_COOR reads not in a single block at the end 35 -1
2022-02-06T00:54:42.1091915Z [E::sam_index] Read 'Z7KPB:01332:11615' with ref_name='chr13_random', ref_length=608348, flags=16, pos=439846 cannot be indexed
2022-02-06T00:54:42.1092741Z samtools index: failed to create index for "Library_01.bam"
2022-02-06T00:54:42.1466816Z [0mBenchmark 1: covtobed 'Library_01.bam' #1.3.5
2022-02-06T00:54:42.1499847Z [91mError: Command terminated with non-zero exit code: 2. Use the '-i'/'--ignore-failure' option if you want to ignore this. Alternatively, use the '--show-output' option to debug what went wrong.
2022-02-06T00:57:04.3995536Z [0mRemoving intermediate container c7df37499bf1
2022-02-06T00:57:04.3996259Z ---> b970b865f6b5
2022-02-06T00:57:04.3996682Z Step 9/9 : RUN cat *md
2022-02-06T00:57:04.4336258Z ---> Running in 9a74681f4d5f
2022-02-06T00:57:04.8433884Z | Command | Mean [s] | Min [s] | Max [s] | Relative |
2022-02-06T00:57:04.8444846Z |:---|---:|---:|---:|---:|
2022-02-06T00:57:04.8447727Z | `covtobed 'HG00258.bam' #1.3.5` | 563.326 ± 8.611 | 555.070 | 574.771 | 3.25 ± 0.05 |
2022-02-06T00:57:04.8448280Z | `bamtocov 'HG00258.bam' #2.5.0` | 363.811 ± 8.651 | 350.075 | 373.599 | 2.10 ± 0.05 |
2022-02-06T00:57:04.8448810Z | `megadepth --coverage 'HG00258.bam' #1.1.2` | 173.520 ± 0.228 | 173.290 | 173.810 | 1.00 ± 0.00 |
2022-02-06T00:57:04.8449345Z | `megadepth --coverage --longreads 'HG00258.bam' #1.1.2` | 173.281 ± 0.478 | 172.890 | 173.919 | 1.00 |
2022-02-06T00:57:04.8449872Z | `mosdepth mosdepth.pMD4Cm 'HG00258.bam' #0.3.3` | 469.604 ± 0.839 | 468.725 | 471.000 | 2.71 ± 0.01 |
2022-02-06T00:57:04.8450430Z | `mosdepth --fast-mode mosdepth.pMD4Cm 'HG00258.bam' #0.3.3` | 459.380 ± 1.134 | 458.283 | 461.134 | 2.65 ± 0.01 |
2022-02-06T00:57:04.8450781Z | Command | Mean [s] | Min [s] | Max [s] | Relative |
2022-02-06T00:57:04.8451114Z |:---|---:|---:|---:|---:|
2022-02-06T00:57:04.8451572Z | `covtobed 'cpara-illumina-noseq.bam' #1.3.5` | 14.553 ± 0.246 | 14.289 | 14.895 | 3.70 ± 0.10 |
2022-02-06T00:57:04.8452076Z | `bamtocov 'cpara-illumina-noseq.bam' #2.5.0` | 10.774 ± 0.144 | 10.550 | 10.939 | 2.74 ± 0.07 |
2022-02-06T00:57:04.8452628Z | `megadepth --coverage 'cpara-illumina-noseq.bam' #1.1.2` | 3.932 ± 0.077 | 3.842 | 4.030 | 1.00 |
2022-02-06T00:57:04.8453220Z | `megadepth --coverage --longreads 'cpara-illumina-noseq.bam' #1.1.2` | 4.129 ± 0.112 | 4.012 | 4.313 | 1.05 ± 0.04 |
2022-02-06T00:57:04.8453823Z | `mosdepth mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3` | 11.090 ± 0.135 | 10.908 | 11.289 | 2.82 ± 0.07 |
2022-02-06T00:57:04.8454440Z | `mosdepth --fast-mode mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3` | 9.387 ± 0.074 | 9.291 | 9.468 | 2.39 ± 0.05 |
2022-02-06T00:57:04.8454824Z | Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
2022-02-06T00:57:04.8455143Z |:---|---:|---:|---:|---:|
2022-02-06T00:57:04.8455849Z | `covtobed 'cpara-ont-noseq.bam' #1.3.5` | 494.1 ± 14.3 | 479.1 | 512.8 | 2.09 ± 0.11 |
2022-02-06T00:57:04.8456332Z | `bamtocov 'cpara-ont-noseq.bam' #2.5.0` | 236.3 ± 10.7 | 224.2 | 253.5 | 1.00 |
2022-02-06T00:57:04.8456850Z | `megadepth --coverage 'cpara-ont-noseq.bam' #1.1.2` | 400.3 ± 11.5 | 387.4 | 419.2 | 1.69 ± 0.09 |
2022-02-06T00:57:04.8457548Z | `megadepth --coverage --longreads 'cpara-ont-noseq.bam' #1.1.2` | 406.4 ± 11.4 | 392.1 | 424.8 | 1.72 ± 0.09 |
2022-02-06T00:57:04.8458179Z | `mosdepth mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3` | 664.9 ± 29.3 | 629.0 | 687.7 | 2.81 ± 0.18 |
2022-02-06T00:57:04.8458789Z | `mosdepth --fast-mode mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3` | 542.8 ± 10.0 | 535.5 | 560.0 | 2.30 ± 0.11 |
2022-02-06T00:57:04.8459160Z | Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
2022-02-06T00:57:04.8459479Z |:---|---:|---:|---:|---:|
2022-02-06T00:57:04.8459863Z | `covtobed 'panel_01.bam' #1.3.5` | 422.6 ± 3.7 | 417.5 | 427.5 | 2.21 ± 0.06 |
2022-02-06T00:57:04.8460308Z | `bamtocov 'panel_01.bam' #2.5.0` | 191.3 ± 4.9 | 185.7 | 204.4 | 1.00 |
2022-02-06T00:57:04.8460784Z | `megadepth --coverage 'panel_01.bam' #1.1.2` | 6068.9 ± 36.9 | 6021.0 | 6121.8 | 31.72 ± 0.83 |
2022-02-06T00:57:04.8461307Z | `megadepth --coverage --longreads 'panel_01.bam' #1.1.2` | 6050.0 ± 19.7 | 6023.0 | 6078.5 | 31.63 ± 0.81 |
2022-02-06T00:57:04.8461857Z | `mosdepth mosdepth.zCQZhW 'panel_01.bam' #0.3.3` | 42686.6 ± 7201.3 | 35745.8 | 51457.9 | 223.14 ± 38.07 |
2022-02-06T00:57:04.8462402Z | `mosdepth --fast-mode mosdepth.zCQZhW 'panel_01.bam' #0.3.3` | 25916.5 ± 166.2 | 25730.0 | 26144.3 | 135.47 ± 3.55 |
2022-02-06T00:57:04.8462766Z | Command | Mean [s] | Min [s] | Max [s] | Relative |
2022-02-06T00:57:04.8463080Z |:---|---:|---:|---:|---:|
2022-02-06T00:57:04.8463504Z | `covtobed 'w1118_f_hd_R1.junc.bam' #1.3.5` | 1.530 ± 0.021 | 1.502 | 1.556 | 2.50 ± 0.06 |
2022-02-06T00:57:04.8463971Z | `bamtocov 'w1118_f_hd_R1.junc.bam' #2.5.0` | 1.432 ± 0.074 | 1.375 | 1.523 | 2.34 ± 0.13 |
2022-02-06T00:57:04.8464620Z | `megadepth --coverage 'w1118_f_hd_R1.junc.bam' #1.1.2` | 0.613 ± 0.013 | 0.604 | 0.634 | 1.00 |
2022-02-06T00:57:04.8465230Z | `megadepth --coverage --longreads 'w1118_f_hd_R1.junc.bam' #1.1.2` | 0.614 ± 0.003 | 0.609 | 0.618 | 1.00 ± 0.02 |
2022-02-06T00:57:04.8465827Z | `mosdepth mosdepth.7dbdyA 'w1118_f_hd_R1.junc.bam' #0.3.3` | 2.939 ± 0.017 | 2.913 | 2.958 | 4.80 ± 0.10 |
2022-02-06T00:57:04.8466517Z | `mosdepth --fast-mode mosdepth.7dbdyA 'w1118_f_hd_R1.junc.bam' #0.3.3` | 2.907 ± 0.030 | 2.881 | 2.953 | 4.74 ± 0.11 |
2022-02-06T00:57:06.6404780Z Removing intermediate container 9a74681f4d5f
2022-02-06T00:57:06.6408198Z ---> 77c98ce4cabf
2022-02-06T00:57:06.6711398Z Successfully built 77c98ce4cabf
2022-02-06T00:57:06.6816003Z Successfully tagged my-image-name:1644096339
2022-02-06T00:57:06.7821800Z Post job cleanup.
2022-02-06T00:57:07.0178945Z [command]/usr/bin/git version
2022-02-06T00:57:07.0292003Z git version 2.35.1
2022-02-06T00:57:07.0348067Z [command]/usr/bin/git config --local --name-only --get-regexp core\.sshCommand
2022-02-06T00:57:07.0403438Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'core\.sshCommand' && git config --local --unset-all 'core.sshCommand' || :
2022-02-06T00:57:07.0809252Z [command]/usr/bin/git config --local --name-only --get-regexp http\.https\:\/\/github\.com\/\.extraheader
2022-02-06T00:57:07.0863062Z http.https://github.com/.extraheader
2022-02-06T00:57:07.0864090Z [command]/usr/bin/git config --local --unset-all http.https://github.com/.extraheader
2022-02-06T00:57:07.0896537Z [command]/usr/bin/git submodule foreach --recursive git config --local --name-only --get-regexp 'http\.https\:\/\/github\.com\/\.extraheader' && git config --local --unset-all 'http.https://github.com/.extraheader' || :
2022-02-06T00:57:07.1528202Z Cleaning up orphan processes