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March 5, 2020 14:13
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| Mar-05 13:00:04.013 [main] DEBUG nextflow.cli.Launcher - $> nextflow ../../../exolink/demux.nf -resume -ansi-log false | |
| Mar-05 13:00:04.391 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.04.0 | |
| Mar-05 13:00:04.416 [main] INFO nextflow.cli.CmdRun - Launching `../../../exolink/demux.nf` [exotic_stonebraker] - revision: dbdd264a27 | |
| Mar-05 13:00:04.455 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/olavur/experiments/06-11-2019_exolink/tests/demux/181213_NS500347_0048_AHCMT3BGX5/nextflow.config | |
| Mar-05 13:00:04.456 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/olavur/experiments/06-11-2019_exolink/tests/demux/181213_NS500347_0048_AHCMT3BGX5/nextflow.config | |
| Mar-05 13:00:04.544 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` | |
| Mar-05 13:00:06.014 [main] DEBUG nextflow.Session - Session uuid: 1b801422-dc67-4975-9662-61fc90bef576 | |
| Mar-05 13:00:06.015 [main] DEBUG nextflow.Session - Run name: exotic_stonebraker | |
| Mar-05 13:00:06.016 [main] DEBUG nextflow.Session - Executor pool size: 2 | |
| Mar-05 13:00:06.049 [main] DEBUG nextflow.cli.CmdRun - | |
| Version: 19.04.0 build 5069 | |
| Modified: 17-04-2019 06:25 UTC | |
| System: Linux 4.15.0-62-generic | |
| Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 1.8.0_192-b01 | |
| Encoding: UTF-8 (UTF-8) | |
| Process: 18457@hms-beagle-7444bdd5b9-7m8hd [10.42.17.19] | |
| CPUs: 1 - Mem: 503.5 GB (207.8 GB) - Swap: 2 GB (1.9 GB) | |
| Mar-05 13:00:06.146 [main] DEBUG nextflow.Session - Work-dir: /home/olavur/experiments/06-11-2019_exolink/tests/demux/181213_NS500347_0048_AHCMT3BGX5/work [ceph] | |
| Mar-05 13:00:06.533 [main] DEBUG nextflow.Session - Session start invoked | |
| Mar-05 13:00:06.552 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start | |
| Mar-05 13:00:06.552 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing | |
| Mar-05 13:00:07.085 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution | |
| Mar-05 13:00:07.605 [main] DEBUG nextflow.util.CacheHelper - Config settings `withLabel:fatproc` matches label `fatproc` for process with name bcl2fastq | |
| Mar-05 13:00:07.609 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.609 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.614 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.615 [main] INFO nextflow.executor.Executor - [warm up] executor > local | |
| Mar-05 13:00:07.619 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=90; memory=400 GB; capacity=100; pollInterval=100ms; dumpInterval=5m | |
| Mar-05 13:00:07.621 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor | |
| Mar-05 13:00:07.622 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) | |
| Mar-05 13:00:07.624 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local | |
| Mar-05 13:00:07.676 [main] DEBUG nextflow.Session - >>> barrier register (process: bcl2fastq) | |
| Mar-05 13:00:07.681 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bcl2fastq -- maxForks: 2 | |
| Mar-05 13:00:07.772 [main] DEBUG nextflow.util.CacheHelper - Config settings `withLabel:thinproc` matches label `thinproc` for process with name merge | |
| Mar-05 13:00:07.773 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.774 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.774 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.775 [main] DEBUG nextflow.Session - >>> barrier register (process: merge) | |
| Mar-05 13:00:07.775 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge -- maxForks: 2 | |
| Mar-05 13:00:07.800 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.800 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.801 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.804 [main] DEBUG nextflow.Session - >>> barrier register (process: check_merge_sync) | |
| Mar-05 13:00:07.804 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > check_merge_sync -- maxForks: 2 | |
| Mar-05 13:00:07.807 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.807 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.807 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.808 [main] DEBUG nextflow.Session - >>> barrier register (process: extract_adapter) | |
| Mar-05 13:00:07.808 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > extract_adapter -- maxForks: 2 | |
| Mar-05 13:00:07.819 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.820 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.820 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.821 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_adapters) | |
| Mar-05 13:00:07.821 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_adapters -- maxForks: 2 | |
| Mar-05 13:00:07.826 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.826 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.826 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.827 [main] DEBUG nextflow.Session - >>> barrier register (process: bctrim) | |
| Mar-05 13:00:07.827 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bctrim -- maxForks: 2 | |
| Mar-05 13:00:07.833 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.833 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.833 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.837 [main] DEBUG nextflow.Session - >>> barrier register (process: check_bctrim_sync) | |
| Mar-05 13:00:07.838 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > check_bctrim_sync -- maxForks: 2 | |
| Mar-05 13:00:07.845 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.845 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.845 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.847 [main] DEBUG nextflow.Session - >>> barrier register (process: polyG_trim) | |
| Mar-05 13:00:07.847 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > polyG_trim -- maxForks: 2 | |
| Mar-05 13:00:07.854 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.854 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.854 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.856 [main] DEBUG nextflow.Session - >>> barrier register (process: quality_trim_read1) | |
| Mar-05 13:00:07.858 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > quality_trim_read1 -- maxForks: 2 | |
| Mar-05 13:00:07.866 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.866 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.866 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.867 [main] DEBUG nextflow.Session - >>> barrier register (process: quality_trim_read2) | |
| Mar-05 13:00:07.868 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > quality_trim_read2 -- maxForks: 2 | |
| Mar-05 13:00:07.881 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.881 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.881 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.882 [main] DEBUG nextflow.Session - >>> barrier register (process: sync_qtrim_reads) | |
| Mar-05 13:00:07.882 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sync_qtrim_reads -- maxForks: 2 | |
| Mar-05 13:00:07.888 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local | |
| Mar-05 13:00:07.888 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' | |
| Mar-05 13:00:07.889 [main] DEBUG nextflow.executor.Executor - Initializing executor: local | |
| Mar-05 13:00:07.890 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc_analysis) | |
| Mar-05 13:00:07.890 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc_analysis -- maxForks: 2 | |
| Mar-05 13:00:07.891 [main] DEBUG nextflow.script.ScriptRunner - > Await termination | |
| Mar-05 13:00:07.891 [main] DEBUG nextflow.Session - Session await | |
| Mar-05 13:00:07.921 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [23/2da0e3] Cached process > extract_adapter | |
| Mar-05 13:00:07.937 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: extract_adapter) | |
| Mar-05 13:00:07.958 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [b9/c161f8] Cached process > bcl2fastq | |
| Mar-05 13:00:08.126 [Actor Thread 3] DEBUG nextflow.Session - <<< barrier arrive (process: bcl2fastq) | |
| Mar-05 13:00:08.249 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.255 [Task submitter] INFO nextflow.Session - [a9/5db2b2] Submitted process > merge (2) | |
| Mar-05 13:00:08.290 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.291 [Task submitter] INFO nextflow.Session - [57/876946] Submitted process > merge (1) | |
| Mar-05 13:00:08.335 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.336 [Task submitter] INFO nextflow.Session - [95/e58dd2] Submitted process > merge (3) | |
| Mar-05 13:00:08.362 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.363 [Task submitter] INFO nextflow.Session - [13/2ca86c] Submitted process > merge (4) | |
| Mar-05 13:00:08.389 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.389 [Task submitter] INFO nextflow.Session - [39/736878] Submitted process > merge (5) | |
| Mar-05 13:00:08.396 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.396 [Task submitter] INFO nextflow.Session - [06/fd5204] Submitted process > merge (6) | |
| Mar-05 13:00:08.402 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.403 [Task submitter] INFO nextflow.Session - [67/30ee8a] Submitted process > merge (8) | |
| Mar-05 13:00:08.413 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.413 [Task submitter] INFO nextflow.Session - [63/e5cc55] Submitted process > merge (7) | |
| Mar-05 13:00:08.421 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.421 [Task submitter] INFO nextflow.Session - [f3/8126d6] Submitted process > merge (9) | |
| Mar-05 13:00:08.445 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.446 [Task submitter] INFO nextflow.Session - [44/5e1756] Submitted process > merge (10) | |
| Mar-05 13:00:08.453 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.454 [Task submitter] INFO nextflow.Session - [5f/1c7ad2] Submitted process > merge (12) | |
| Mar-05 13:00:08.459 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.460 [Task submitter] INFO nextflow.Session - [3e/d5cbba] Submitted process > merge (11) | |
| Mar-05 13:00:08.466 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.466 [Task submitter] INFO nextflow.Session - [dc/bf8851] Submitted process > merge (13) | |
| Mar-05 13:00:08.473 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.474 [Task submitter] INFO nextflow.Session - [9f/42fab5] Submitted process > merge (14) | |
| Mar-05 13:00:08.482 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.482 [Task submitter] INFO nextflow.Session - [a3/02d1f5] Submitted process > merge (15) | |
| Mar-05 13:00:08.498 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.499 [Task submitter] INFO nextflow.Session - [9f/fef86d] Submitted process > merge (16) | |
| Mar-05 13:00:08.505 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.506 [Task submitter] INFO nextflow.Session - [9f/b3ffe7] Submitted process > merge (18) | |
| Mar-05 13:00:08.511 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.511 [Task submitter] INFO nextflow.Session - [b8/8295e7] Submitted process > merge (17) | |
| Mar-05 13:00:08.517 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.517 [Task submitter] INFO nextflow.Session - [02/60cac3] Submitted process > merge (20) | |
| Mar-05 13:00:08.523 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.523 [Task submitter] INFO nextflow.Session - [2b/a66798] Submitted process > merge (19) | |
| Mar-05 13:00:08.528 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.529 [Task submitter] INFO nextflow.Session - [a1/72be62] Submitted process > merge (21) | |
| Mar-05 13:00:08.533 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.534 [Task submitter] INFO nextflow.Session - [7c/da6a09] Submitted process > merge (22) | |
| Mar-05 13:00:08.538 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.539 [Task submitter] INFO nextflow.Session - [00/cfebf4] Submitted process > merge (24) | |
| Mar-05 13:00:08.547 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.547 [Task submitter] INFO nextflow.Session - [f0/3e6241] Submitted process > merge (23) | |
| Mar-05 13:00:08.552 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Mar-05 13:00:08.552 [Task submitter] INFO nextflow.Session - [19/ef8d23] Submitted process > merge (25) | |
| Mar-05 13:01:20.485 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT | |
| Mar-05 13:01:20.491 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) | |
| Mar-05 13:01:20.506 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active: | |
| [process] check_merge_sync | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] trim_adapters | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] bctrim | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] check_bctrim_sync | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] polyG_trim | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] quality_trim_read1 | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] quality_trim_read2 | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] sync_qtrim_reads | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| [process] fastqc_analysis | |
| status=ACTIVE | |
| port 0: (queue) OPEN ; channel: - | |
| port 1: (cntrl) - ; channel: $ | |
| Mar-05 13:01:20.508 [main] DEBUG nextflow.Session - Session await > all process finished | |
| Mar-05 13:01:20.509 [main] DEBUG nextflow.Session - Session await > all barriers passed | |
| Mar-05 13:01:20.514 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (25) | |
| Mar-05 13:01:20.528 [main] DEBUG nextflow.executor.LocalTaskHandler - Unable to kill merge (2) -- command: kill -TERM 18518; exit: 1 | |
| bash: line 0: kill: (18518) - No such process | |
| Mar-05 13:01:20.544 [main] DEBUG nextflow.executor.LocalTaskHandler - Unable to kill merge (1) -- command: kill -TERM 18521; exit: 1 | |
| bash: line 0: kill: (18521) - No such process | |
| Mar-05 13:01:20.563 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=25; ignoredCount=0; cachedCount=2; succeedDuration=0ms; failedDuration=0ms; cachedDuration=1d 10h 32m 23s] | |
| Mar-05 13:01:20.603 [main] DEBUG nextflow.CacheDB - Closing CacheDB done | |
| Mar-05 13:01:20.621 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye |
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