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| Aug-09 13:56:37.157 [main] DEBUG nextflow.cli.Launcher - $> nextflow run 07_assembly.nf | |
| Aug-09 13:56:37.320 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.10.6 | |
| Aug-09 13:56:37.359 [main] INFO nextflow.cli.CmdRun - Launching `07_assembly.nf` [scruffy_archimedes] - revision: c0bb013155 | |
| Aug-09 13:56:37.489 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/subudhak/.nextflow/plugins | |
| Aug-09 13:56:37.491 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] | |
| Aug-09 13:56:37.507 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] | |
| Aug-09 13:56:37.509 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] | |
| Aug-09 13:56:37.514 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode | |
| Aug-09 13:56:37.532 [main] INFO org.pf4j.AbstractPluginManager - No plugins | |
| Aug-09 13:56:37.619 [main] DEBUG nextflow.Session - Session uuid: 45fb3b1d-e701-4c3c-a3ab-ab9308099447 | |
| Aug-09 13:56:37.620 [main] DEBUG nextflow.Session - Run name: scruffy_archimedes | |
| Aug-09 13:56:37.622 [main] DEBUG nextflow.Session - Executor pool size: 112 | |
| Aug-09 13:56:37.659 [main] DEBUG nextflow.cli.CmdRun - | |
| Version: 21.10.6 build 5660 | |
| Created: 21-12-2021 16:55 UTC (19:55 ADT) | |
| System: Linux 5.4.0-122-generic | |
| Runtime: Groovy 3.0.9 on OpenJDK 64-Bit Server VM 1.8.0_332-b09 | |
| Encoding: UTF-8 (UTF-8) | |
| Process: 826041@KW61216 [127.0.1.1] | |
| CPUs: 112 - Mem: 251.5 GB (202.6 GB) - Swap: 16 GB (16 GB) | |
| Aug-09 13:56:37.691 [main] DEBUG nextflow.Session - Work-dir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work [ext2/ext3] | |
| Aug-09 13:56:37.691 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/bin | |
| Aug-09 13:56:37.841 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] | |
| Aug-09 13:56:37.863 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory | |
| Aug-09 13:56:37.936 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 113; maxThreads: 1000 | |
| Aug-09 13:56:38.165 [main] DEBUG nextflow.Session - Session start invoked | |
| Aug-09 13:56:39.312 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution | |
| Aug-09 13:56:39.456 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 113; maxThreads: 1000 | |
| Aug-09 13:56:39.597 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null | |
| Aug-09 13:56:39.597 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' | |
| Aug-09 13:56:39.605 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local | |
| Aug-09 13:56:39.613 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=112; memory=251.5 GB; capacity=112; pollInterval=100ms; dumpInterval=5m | |
| Aug-09 13:56:39.775 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: COV | |
| Aug-09 13:56:39.776 [main] DEBUG nextflow.Session - Ignite dataflow network (2) | |
| Aug-09 13:56:39.796 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > COV | |
| Aug-09 13:56:39.798 [main] DEBUG nextflow.script.ScriptRunner - > Await termination | |
| Aug-09 13:56:39.798 [main] DEBUG nextflow.Session - Session await | |
| Aug-09 13:56:39.804 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: results/06_gatkresults/vcfs/; pattern: *.vcf.gz; options: [:] | |
| Aug-09 13:56:40.500 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.507 [Task submitter] INFO nextflow.Session - [89/7121b5] Submitted process > COV (12) | |
| Aug-09 13:56:40.514 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.515 [Task submitter] INFO nextflow.Session - [ed/95f4ac] Submitted process > COV (9) | |
| Aug-09 13:56:40.525 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.526 [Task submitter] INFO nextflow.Session - [7d/48b740] Submitted process > COV (8) | |
| Aug-09 13:56:40.535 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.536 [Task submitter] INFO nextflow.Session - [8a/3442fa] Submitted process > COV (4) | |
| Aug-09 13:56:40.540 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.541 [Task submitter] INFO nextflow.Session - [87/a78bf1] Submitted process > COV (11) | |
| Aug-09 13:56:40.547 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.548 [Task submitter] INFO nextflow.Session - [3a/c8054e] Submitted process > COV (5) | |
| Aug-09 13:56:40.552 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.553 [Task submitter] INFO nextflow.Session - [b2/8db2b6] Submitted process > COV (10) | |
| Aug-09 13:56:40.558 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.558 [Task submitter] INFO nextflow.Session - [5c/18d886] Submitted process > COV (2) | |
| Aug-09 13:56:40.563 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.564 [Task submitter] INFO nextflow.Session - [81/ced80e] Submitted process > COV (6) | |
| Aug-09 13:56:40.569 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.569 [Task submitter] INFO nextflow.Session - [a2/c6c221] Submitted process > COV (7) | |
| Aug-09 13:56:40.577 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.578 [Task submitter] INFO nextflow.Session - [88/e76d99] Submitted process > COV (3) | |
| Aug-09 13:56:40.583 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run | |
| Aug-09 13:56:40.584 [Task submitter] INFO nextflow.Session - [97/70b728] Submitted process > COV (1) | |
| Aug-09 13:56:40.631 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: COV (12); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/89/7121b58fb40e5f5902c30ed7b5365b] | |
| Aug-09 13:56:40.690 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: COV (9); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/ed/95f4ac6c2f18ed1a22d98618a95cc2] | |
| Aug-09 13:56:40.695 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: COV (8); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/7d/48b7408d6e1439edb44686edf4386e] | |
| Aug-09 13:56:40.704 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: COV (4); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/8a/3442faa2ab5491ee21bba187ceb1ff] | |
| Aug-09 13:56:40.713 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: COV (11); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/87/a78bf198a988d2c9e03f642107e312] | |
| Aug-09 13:56:40.721 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: COV (5); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/3a/c8054ea62fa625bd39b296e99dc2a0] | |
| Aug-09 13:56:40.731 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: COV (10); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/b2/8db2b6e1017edb4fa8d2c3858824fe] | |
| Aug-09 13:56:40.742 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: COV (2); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/5c/18d8865157aecf27192016352873bf] | |
| Aug-09 13:56:40.752 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: COV (6); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/81/ced80ee9cc806f261f297e69623bba] | |
| Aug-09 13:56:40.764 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: COV (7); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/a2/c6c2210ebbe821aee62101b79fe107] | |
| Aug-09 13:56:40.771 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: COV (3); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/88/e76d9964eca856182003f19d10765a] | |
| Aug-09 13:56:40.777 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: COV (1); status: COMPLETED; exit: 0; error: -; workDir: /home/subudhak/Documents/Illumina_ONT_ARTIC_Comparison/illumina/work/97/70b7289e2fe3e610cc78bcec598048] | |
| Aug-09 13:56:40.786 [main] DEBUG nextflow.Session - Session await > all process finished | |
| Aug-09 13:56:40.883 [main] DEBUG nextflow.Session - Session await > all barriers passed | |
| Aug-09 13:56:40.897 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=12; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=423ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=3; peakMemory=0; ] | |
| Aug-09 13:56:41.071 [main] DEBUG nextflow.CacheDB - Closing CacheDB done | |
| Aug-09 13:56:41.093 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye |
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