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pgx-main from prod added

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Darren Wight
2025-08-18 12:06:58 +02:00
parent fcb0e9aa4c
commit fe48df8676
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Aug-14 12:43:17.201 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf -profile standard --build hg38 --gene cyp2d6
Aug-14 12:43:17.660 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.7
Aug-14 12:43:17.710 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: nf-amazon@1.11.4,nf-azure@0.14.2,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.4,nf-google@1.4.5,nf-tower@1.5.6,nf-wave@0.5.4
Aug-14 12:43:17.754 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-14 12:43:17.755 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-14 12:43:17.762 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-14 12:43:17.782 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Aug-14 12:43:17.816 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /root/pgx-main/nextflow.config
Aug-14 12:43:17.822 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/pgx-main/nextflow.config
Aug-14 12:43:17.889 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Aug-14 12:43:19.612 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Aug-14 12:43:19.668 [main] INFO nextflow.cli.CmdRun - Launching `main.nf` [mighty_brattain] DSL2 - revision: f9254a4b26
Aug-14 12:43:19.671 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-14 12:43:19.671 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Aug-14 12:43:19.729 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Aug-14 12:43:19.742 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2c8c16c0] - activable => nextflow.secret.LocalSecretsProvider@2c8c16c0
Aug-14 12:43:19.935 [main] DEBUG nextflow.Session - Session UUID: 9f6cb1a5-cd74-4ad5-b523-80d635011563
Aug-14 12:43:19.937 [main] DEBUG nextflow.Session - Run name: mighty_brattain
Aug-14 12:43:19.938 [main] DEBUG nextflow.Session - Executor pool size: 2
Aug-14 12:43:19.964 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-14 12:43:20.038 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.10.7 build 5853
Created: 18-02-2023 20:32 UTC
System: Linux 6.10.2-x86_64-linode165
Runtime: Groovy 3.0.13 on OpenJDK 64-Bit Server VM 17.0.15+6
Encoding: UTF-8 (UTF-8)
Process: 1579408@localhost [127.0.0.1]
CPUs: 1 - Mem: 1.9 GB (195.7 MB) - Swap: 512 MB (269.4 MB)
Aug-14 12:43:20.098 [main] DEBUG nextflow.Session - Work-dir: /root/pgx-main/work [ext2/ext3]
Aug-14 12:43:20.100 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /root/pgx-main/bin
Aug-14 12:43:20.123 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-14 12:43:20.145 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-14 12:43:20.253 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-14 12:43:20.364 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 2; maxThreads: 1000
Aug-14 12:43:20.551 [main] DEBUG nextflow.Session - Session start
Aug-14 12:43:24.418 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-14 12:43:24.779 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:24.781 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:24.831 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Aug-14 12:43:24.845 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=1; memory=1.9 GB; capacity=1; pollInterval=100ms; dumpInterval=5m
Aug-14 12:43:25.021 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.027 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.040 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.044 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.066 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.068 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.089 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.090 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.163 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.167 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.193 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.197 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.213 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.216 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.227 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.231 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.247 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.257 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.281 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.281 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.321 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-14 12:43:25.324 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-14 12:43:25.332 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: call_snvs2, format_snvs, analyse_2, call_snvs1, analyse_3, analyse_1, get_depth, save_vcfs, call_sv_del, call_stars, get_core_var, call_sv_dup
Aug-14 12:43:25.336 [main] DEBUG nextflow.Session - Igniting dataflow network (14)
Aug-14 12:43:25.351 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /root/pgx-main/data/; pattern: *{bam,bai}; options: [type:file]
Aug-14 12:43:25.355 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > call_snvs1
Aug-14 12:43:25.357 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > call_snvs2
Aug-14 12:43:25.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > call_sv_del
Aug-14 12:43:25.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > call_sv_dup
Aug-14 12:43:25.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > get_depth
Aug-14 12:43:25.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > format_snvs
Aug-14 12:43:25.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > save_vcfs
Aug-14 12:43:25.377 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > get_core_var
Aug-14 12:43:25.377 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > analyse_1
Aug-14 12:43:25.377 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > analyse_2
Aug-14 12:43:25.385 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > analyse_3
Aug-14 12:43:25.385 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > call_stars
Aug-14 12:43:25.385 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Aug-14 12:43:25.385 [main] DEBUG nextflow.Session - Session await
Aug-14 12:43:25.962 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:25.968 [Task submitter] INFO nextflow.Session - [13/3c2971] Submitted process > call_snvs1 (1)
Aug-14 12:43:28.482 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: call_snvs1 (1); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/13/3c2971a84f60469002ad24c1e88030]
Aug-14 12:43:28.554 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:28.557 [Task submitter] INFO nextflow.Session - [f5/b26de9] Submitted process > get_depth (2)
Aug-14 12:43:33.814 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: get_depth (2); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/f5/b26de950d2ba6d2746e73b90aafe5b]
Aug-14 12:43:33.849 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:33.851 [Task submitter] INFO nextflow.Session - [6d/97cd67] Submitted process > call_snvs1 (2)
Aug-14 12:43:35.768 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: call_snvs1 (2); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/6d/97cd67728ee5397390dced1315530d]
Aug-14 12:43:35.819 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:35.828 [Task submitter] INFO nextflow.Session - [6f/968fc9] Submitted process > call_sv_del (1)
Aug-14 12:43:40.126 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: call_sv_del (1); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/6f/968fc9927dad5c83c3a50b014af984]
Aug-14 12:43:40.146 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:40.149 [Task submitter] INFO nextflow.Session - [dc/49271e] Submitted process > call_snvs2 (2)
Aug-14 12:43:42.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: call_snvs2 (2); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/dc/49271e3604a0b8a5b518492ee85221]
Aug-14 12:43:42.417 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:42.430 [Task submitter] INFO nextflow.Session - [96/b55669] Submitted process > call_sv_dup (1)
Aug-14 12:43:47.151 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: call_sv_dup (1); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/96/b5566900152fcc727fe0b76df43321]
Aug-14 12:43:47.201 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:47.201 [Task submitter] INFO nextflow.Session - [b6/43bbde] Submitted process > call_sv_dup (2)
Aug-14 12:43:51.898 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: call_sv_dup (2); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/b6/43bbde7de04201528411748786900b]
Aug-14 12:43:51.928 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:51.929 [Task submitter] INFO nextflow.Session - [6b/3ceacf] Submitted process > get_depth (1)
Aug-14 12:43:54.748 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: get_depth (1); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/6b/3ceacfedb27d4b4ee748ef0eb3b8e1]
Aug-14 12:43:54.758 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:54.761 [Task submitter] INFO nextflow.Session - [e0/66fb20] Submitted process > call_snvs2 (1)
Aug-14 12:43:56.619 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: call_snvs2 (1); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/e0/66fb2053791cc120739b0c72264d68]
Aug-14 12:43:56.627 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:43:56.641 [Task submitter] INFO nextflow.Session - [aa/83e3f4] Submitted process > call_sv_del (2)
Aug-14 12:44:01.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: call_sv_del (2); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/aa/83e3f47a663c63b1377b0df7ff9aa6]
Aug-14 12:44:01.239 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:01.246 [Task submitter] INFO nextflow.Session - [b5/932863] Submitted process > call_snvs1 (3)
Aug-14 12:44:02.966 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: call_snvs1 (3); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/b5/93286339dc616cee999e1266ef283b]
Aug-14 12:44:02.990 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:02.990 [Task submitter] INFO nextflow.Session - [a8/3360d6] Submitted process > call_snvs2 (4)
Aug-14 12:44:04.514 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: call_snvs2 (4); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/a8/3360d6043aee6b842d69c829ade53e]
Aug-14 12:44:04.531 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:04.532 [Task submitter] INFO nextflow.Session - [fb/20d100] Submitted process > call_sv_dup (3)
Aug-14 12:44:08.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: call_sv_dup (3); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/fb/20d100d8af0727ab4446d0ef85673d]
Aug-14 12:44:08.513 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:08.516 [Task submitter] INFO nextflow.Session - [21/dc0d4d] Submitted process > call_sv_dup (4)
Aug-14 12:44:12.523 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: call_sv_dup (4); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/21/dc0d4d6511aefb9efd5778100e2b57]
Aug-14 12:44:12.543 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:12.545 [Task submitter] INFO nextflow.Session - [58/475879] Submitted process > call_snvs2 (3)
Aug-14 12:44:14.080 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: call_snvs2 (3); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/58/475879af155be406e2e36cf26cd84f]
Aug-14 12:44:14.118 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:14.120 [Task submitter] INFO nextflow.Session - [c7/b885a8] Submitted process > call_snvs1 (4)
Aug-14 12:44:15.675 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: call_snvs1 (4); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/c7/b885a8443642a49c0fe932f7b28091]
Aug-14 12:44:15.688 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:15.697 [Task submitter] INFO nextflow.Session - [98/8af20b] Submitted process > call_sv_del (3)
Aug-14 12:44:20.285 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: call_sv_del (3); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/98/8af20b31b1fb741436d4c74d17c5bb]
Aug-14 12:44:20.310 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:20.318 [Task submitter] INFO nextflow.Session - [94/4a1754] Submitted process > get_depth (4)
Aug-14 12:44:23.510 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: get_depth (4); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/94/4a1754149cfd765b9415ec19eb7868]
Aug-14 12:44:23.532 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:23.537 [Task submitter] INFO nextflow.Session - [3b/5153f9] Submitted process > call_snvs1 (5)
Aug-14 12:44:25.114 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: call_snvs1 (5); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/3b/5153f946698ac27efa6a47181ea98d]
Aug-14 12:44:25.126 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:25.134 [Task submitter] INFO nextflow.Session - [ed/174b1f] Submitted process > call_snvs2 (5)
Aug-14 12:44:27.050 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: call_snvs2 (5); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/ed/174b1fb7786ecf09f99df45bcf41a7]
Aug-14 12:44:27.073 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:27.079 [Task submitter] INFO nextflow.Session - [bb/84e511] Submitted process > get_depth (5)
Aug-14 12:44:29.839 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: get_depth (5); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/bb/84e5113bcbee224cfabada48e6b8c0]
Aug-14 12:44:29.862 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:29.863 [Task submitter] INFO nextflow.Session - [96/17a481] Submitted process > call_sv_del (4)
Aug-14 12:44:33.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: call_sv_del (4); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/96/17a4814ad78a600ddb8b1980d23b5d]
Aug-14 12:44:33.886 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:33.891 [Task submitter] INFO nextflow.Session - [ad/7c9eeb] Submitted process > get_depth (3)
Aug-14 12:44:36.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: get_depth (3); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/ad/7c9eebd7e9fe186182609674927dc4]
Aug-14 12:44:36.904 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:36.906 [Task submitter] INFO nextflow.Session - [e4/baa91c] Submitted process > call_sv_dup (5)
Aug-14 12:44:40.465 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: call_sv_dup (5); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/e4/baa91c3d6965063da6cb9fa5dc28bd]
Aug-14 12:44:40.488 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:40.489 [Task submitter] INFO nextflow.Session - [11/a8f3ae] Submitted process > call_sv_del (5)
Aug-14 12:44:44.474 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: call_sv_del (5); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/11/a8f3ae457de79bb30dde749bb9f7d9]
Aug-14 12:44:44.506 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:44.508 [Task submitter] INFO nextflow.Session - [29/a91100] Submitted process > analyse_1 (CAN-NA12003-29Mar2025_S25)
Aug-14 12:44:45.715 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: analyse_1 (CAN-NA12003-29Mar2025_S25); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/29/a91100e79a2e9ee92ca382846d7abf]
Aug-14 12:44:45.722 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:45.727 [Task submitter] INFO nextflow.Session - [8f/ef4c81] Submitted process > format_snvs (1)
Aug-14 12:44:47.088 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: format_snvs (1); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/8f/ef4c816b44fff9cd3855b9df6db9ad]
Aug-14 12:44:47.113 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:47.113 [Task submitter] INFO nextflow.Session - [ab/d3beb6] Submitted process > format_snvs (2)
Aug-14 12:44:48.624 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: format_snvs (2); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/ab/d3beb6bc270ea875c238810b15718b]
Aug-14 12:44:48.642 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:48.642 [Task submitter] INFO nextflow.Session - [21/c30bc0] Submitted process > analyse_1 (CAN-NA19226-29Mar2025_S29)
Aug-14 12:44:50.696 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: analyse_1 (CAN-NA19226-29Mar2025_S29); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/21/c30bc0df08de8e38d238107b6fd759]
Aug-14 12:44:50.721 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:50.722 [Task submitter] INFO nextflow.Session - [eb/9507bd] Submitted process > format_snvs (3)
Aug-14 12:44:52.182 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: format_snvs (3); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/eb/9507bd0cf41a3aef8f8c18fb934ddd]
Aug-14 12:44:52.215 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:52.215 [Task submitter] INFO nextflow.Session - [99/52d03e] Submitted process > format_snvs (4)
Aug-14 12:44:53.553 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: format_snvs (4); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/99/52d03e9cb22c485cc9353ca9522a33]
Aug-14 12:44:53.575 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:53.575 [Task submitter] INFO nextflow.Session - [16/663f27] Submitted process > analyse_1 (CAN-NA24385-2-29Mar2025_S23)
Aug-14 12:44:54.839 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: analyse_1 (CAN-NA24385-2-29Mar2025_S23); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/16/663f27a6c2bb4a1809a31f33f066b4]
Aug-14 12:44:54.856 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:54.857 [Task submitter] INFO nextflow.Session - [3d/215a55] Submitted process > format_snvs (5)
Aug-14 12:44:56.295 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: format_snvs (5); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/3d/215a553f9712059dd415956b5f4f48]
Aug-14 12:44:56.313 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:56.314 [Task submitter] INFO nextflow.Session - [fb/cca38b] Submitted process > analyse_1 (CAN-NA12878-1-29Mar2025_S20)
Aug-14 12:44:57.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: analyse_1 (CAN-NA12878-1-29Mar2025_S20); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/fb/cca38bb95a55accc8bfd05ce6f035d]
Aug-14 12:44:57.591 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:57.591 [Task submitter] INFO nextflow.Session - [53/c4171c] Submitted process > analyse_1 (CAN-NA19239-29Mar2025_S32)
Aug-14 12:44:58.799 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: analyse_1 (CAN-NA19239-29Mar2025_S32); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/53/c4171ccea22c6f72ecaba97b9ca05c]
Aug-14 12:44:58.811 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:44:58.815 [Task submitter] INFO nextflow.Session - [4e/a5b3f3] Submitted process > save_vcfs (CAN-NA19226-29Mar2025_S29)
Aug-14 12:45:00.068 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: save_vcfs (CAN-NA19226-29Mar2025_S29); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/4e/a5b3f310925aae6bf8581c71d54835]
Aug-14 12:45:00.078 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:00.084 [Task submitter] INFO nextflow.Session - [64/9e0134] Submitted process > get_core_var (CAN-NA19226-29Mar2025_S29)
Aug-14 12:45:00.123 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-14 12:45:06.159 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: get_core_var (CAN-NA19226-29Mar2025_S29); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/64/9e013499e37272517604cc12a7b3bf]
Aug-14 12:45:06.197 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:06.231 [Task submitter] INFO nextflow.Session - [b0/adad81] Submitted process > save_vcfs (CAN-NA12003-29Mar2025_S25)
Aug-14 12:45:07.490 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: save_vcfs (CAN-NA12003-29Mar2025_S25); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/b0/adad81b858b62dcdb0e9638e84a709]
Aug-14 12:45:07.499 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:07.499 [Task submitter] INFO nextflow.Session - [dd/644a02] Submitted process > get_core_var (CAN-NA12003-29Mar2025_S25)
Aug-14 12:45:12.656 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: get_core_var (CAN-NA12003-29Mar2025_S25); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/dd/644a02684827efc5389e0b841e8824]
Aug-14 12:45:12.680 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:12.681 [Task submitter] INFO nextflow.Session - [13/10763a] Submitted process > save_vcfs (CAN-NA24385-2-29Mar2025_S23)
Aug-14 12:45:14.037 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: save_vcfs (CAN-NA24385-2-29Mar2025_S23); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/13/10763a5029a5c8df36d747267b0533]
Aug-14 12:45:14.047 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:14.047 [Task submitter] INFO nextflow.Session - [54/7e8178] Submitted process > get_core_var (CAN-NA24385-2-29Mar2025_S23)
Aug-14 12:45:19.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: get_core_var (CAN-NA24385-2-29Mar2025_S23); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/54/7e8178efb557b8ac7ade68fbb02f89]
Aug-14 12:45:19.202 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:19.202 [Task submitter] INFO nextflow.Session - [a2/78d779] Submitted process > save_vcfs (CAN-NA12878-1-29Mar2025_S20)
Aug-14 12:45:20.294 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: save_vcfs (CAN-NA12878-1-29Mar2025_S20); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/a2/78d77938d11241e4469c943005a95a]
Aug-14 12:45:20.318 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:20.319 [Task submitter] INFO nextflow.Session - [9c/3dd8c3] Submitted process > get_core_var (CAN-NA12878-1-29Mar2025_S20)
Aug-14 12:45:26.353 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: get_core_var (CAN-NA12878-1-29Mar2025_S20); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/9c/3dd8c36ec173b80825a166220c4834]
Aug-14 12:45:26.378 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:26.381 [Task submitter] INFO nextflow.Session - [4b/7051b2] Submitted process > save_vcfs (CAN-NA19239-29Mar2025_S32)
Aug-14 12:45:27.557 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: save_vcfs (CAN-NA19239-29Mar2025_S32); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/4b/7051b2011ca128229e1d15dbe2e4d7]
Aug-14 12:45:27.566 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:27.567 [Task submitter] INFO nextflow.Session - [a4/3f73e7] Submitted process > get_core_var (CAN-NA19239-29Mar2025_S32)
Aug-14 12:45:32.665 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: get_core_var (CAN-NA19239-29Mar2025_S32); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/a4/3f73e7e1505d6c8aebaa5fceefe27e]
Aug-14 12:45:32.698 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:32.699 [Task submitter] INFO nextflow.Session - [67/70c0da] Submitted process > analyse_3 (CAN-NA19226-29Mar2025_S29)
Aug-14 12:45:33.975 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: analyse_3 (CAN-NA19226-29Mar2025_S29); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/67/70c0daea7ca3681e5824ade4e6641d]
Aug-14 12:45:33.986 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:33.988 [Task submitter] INFO nextflow.Session - [4f/c883c1] Submitted process > analyse_2 (CAN-NA19226-29Mar2025_S29)
Aug-14 12:45:35.171 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: analyse_2 (CAN-NA19226-29Mar2025_S29); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/4f/c883c1e240ab982fc62f8d39ec5e3e]
Aug-14 12:45:35.189 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:35.191 [Task submitter] INFO nextflow.Session - [37/b9461c] Submitted process > analyse_3 (CAN-NA12003-29Mar2025_S25)
Aug-14 12:45:36.361 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: analyse_3 (CAN-NA12003-29Mar2025_S25); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/37/b9461c873bc14cb1c06c323c80f262]
Aug-14 12:45:36.374 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:36.374 [Task submitter] INFO nextflow.Session - [dd/9012fe] Submitted process > analyse_2 (CAN-NA12003-29Mar2025_S25)
Aug-14 12:45:37.499 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: analyse_2 (CAN-NA12003-29Mar2025_S25); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/dd/9012fe64a40ed03b8c725adfcde68f]
Aug-14 12:45:37.510 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:37.510 [Task submitter] INFO nextflow.Session - [54/77dc4e] Submitted process > analyse_2 (CAN-NA24385-2-29Mar2025_S23)
Aug-14 12:45:38.675 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: analyse_2 (CAN-NA24385-2-29Mar2025_S23); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/54/77dc4e835bc666d92ae251c7816d31]
Aug-14 12:45:38.679 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:38.683 [Task submitter] INFO nextflow.Session - [a2/2af8a1] Submitted process > analyse_3 (CAN-NA24385-2-29Mar2025_S23)
Aug-14 12:45:39.935 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: analyse_3 (CAN-NA24385-2-29Mar2025_S23); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/a2/2af8a10fa59d07cea2d0fbd8a47ae3]
Aug-14 12:45:39.939 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:39.948 [Task submitter] INFO nextflow.Session - [0f/d33c71] Submitted process > analyse_3 (CAN-NA12878-1-29Mar2025_S20)
Aug-14 12:45:41.099 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: analyse_3 (CAN-NA12878-1-29Mar2025_S20); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/0f/d33c7148b3e5473df169545a7f5330]
Aug-14 12:45:41.106 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:41.108 [Task submitter] INFO nextflow.Session - [1f/eca63f] Submitted process > analyse_2 (CAN-NA12878-1-29Mar2025_S20)
Aug-14 12:45:42.273 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: analyse_2 (CAN-NA12878-1-29Mar2025_S20); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/1f/eca63f24bc433c4ea8f2e21f0b044c]
Aug-14 12:45:42.291 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:42.291 [Task submitter] INFO nextflow.Session - [8f/f34ccc] Submitted process > analyse_2 (CAN-NA19239-29Mar2025_S32)
Aug-14 12:45:43.511 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: analyse_2 (CAN-NA19239-29Mar2025_S32); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/8f/f34cccae4ea8e8006fb5660ba30841]
Aug-14 12:45:43.519 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:43.520 [Task submitter] INFO nextflow.Session - [ee/d4b2b6] Submitted process > analyse_3 (CAN-NA19239-29Mar2025_S32)
Aug-14 12:45:44.660 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: analyse_3 (CAN-NA19239-29Mar2025_S32); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/ee/d4b2b6feeafcdfe3ed1051cb881fae]
Aug-14 12:45:44.676 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:44.676 [Task submitter] INFO nextflow.Session - [34/a93e76] Submitted process > call_stars (CAN-NA19226-29Mar2025_S29)
Aug-14 12:45:46.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: call_stars (CAN-NA19226-29Mar2025_S29); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/34/a93e76842db859098d5a7d946b3fdf]
Aug-14 12:45:46.106 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:46.111 [Task submitter] INFO nextflow.Session - [f9/381431] Submitted process > call_stars (CAN-NA12003-29Mar2025_S25)
Aug-14 12:45:47.343 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: call_stars (CAN-NA12003-29Mar2025_S25); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/f9/38143178f71e5169ebf934d30589d8]
Aug-14 12:45:47.356 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:47.357 [Task submitter] INFO nextflow.Session - [62/b59df7] Submitted process > call_stars (CAN-NA24385-2-29Mar2025_S23)
Aug-14 12:45:48.581 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: call_stars (CAN-NA24385-2-29Mar2025_S23); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/62/b59df754ccea843ba36f4a92cf6896]
Aug-14 12:45:48.589 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:48.589 [Task submitter] INFO nextflow.Session - [7c/3698c3] Submitted process > call_stars (CAN-NA12878-1-29Mar2025_S20)
Aug-14 12:45:50.016 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: call_stars (CAN-NA12878-1-29Mar2025_S20); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/7c/3698c331aab671806b698958475df0]
Aug-14 12:45:50.034 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Aug-14 12:45:50.034 [Task submitter] INFO nextflow.Session - [dc/8e683b] Submitted process > call_stars (CAN-NA19239-29Mar2025_S32)
Aug-14 12:45:51.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: call_stars (CAN-NA19239-29Mar2025_S32); status: COMPLETED; exit: 0; error: -; workDir: /root/pgx-main/work/dc/8e683b427396eeaff38bfd23bb2266]
Aug-14 12:45:51.407 [main] DEBUG nextflow.Session - Session await > all processes finished
Aug-14 12:45:51.412 [main] DEBUG nextflow.Session - Session await > all barriers passed
Aug-14 12:45:51.427 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Aug-14 12:45:51.439 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=60; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=2m 19s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Aug-14 12:45:51.604 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Aug-14 12:45:51.626 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Aug-14 12:45:51.631 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye