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1
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Jun-04 15:33:28.563 [main] DEBUG nextflow.cli.Launcher - $> /opt/exp_soft/cbio/nextflow/nextflow run kviljoen/16S-rDNA-dada2-pipeline -r dev --trimFor 24 --trimRev 25 --reference ./gg_13_8_train_set_97.fa.gz --email katieviljoen@gmail.com -profile uct_hex --reads /researchdata/fhgfs/katie/dada2-test/raw_testdata/*{R1,R2}.fastq -with-singularity /scratch/DB/bio/singularity-containers/1a32017e5935-2018-05-31-db3a9cebe9fc.img -resume
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2
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Jun-04 15:33:28.802 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.28.0
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3
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Jun-04 15:33:29.531 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/kviljoen/.nextflow/assets/kviljoen/16S-rDNA-dada2-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/kviljoen/16S-rDNA-dada2-pipeline.git
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4
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Jun-04 15:33:29.673 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/kviljoen/.nextflow/assets/kviljoen/16S-rDNA-dada2-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/kviljoen/16S-rDNA-dada2-pipeline.git
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5
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Jun-04 15:33:30.309 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/kviljoen/.nextflow/assets/kviljoen/16S-rDNA-dada2-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/kviljoen/16S-rDNA-dada2-pipeline.git
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6
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Jun-04 15:33:30.310 [main] INFO nextflow.cli.CmdRun - Launching `kviljoen/16S-rDNA-dada2-pipeline` [berserk_legentil] - revision: f859e828fa [dev]
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7
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Jun-04 15:33:31.890 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/kviljoen/.nextflow/assets/kviljoen/16S-rDNA-dada2-pipeline/nextflow.config
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8
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Jun-04 15:33:31.894 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/kviljoen/.nextflow/assets/kviljoen/16S-rDNA-dada2-pipeline/nextflow.config
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Jun-04 15:33:31.909 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `uct_hex`
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Jun-04 15:33:32.119 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [uct_hex, none]
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Jun-04 15:33:32.147 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by cli option `-with-singularity null`
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Jun-04 15:33:32.187 [main] DEBUG nextflow.Session - Session uuid: 7efc3a47-0237-4a71-8b24-f118fbb9945c
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Jun-04 15:33:32.188 [main] DEBUG nextflow.Session - Run name: berserk_legentil
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Jun-04 15:33:32.192 [main] DEBUG nextflow.Session - Executor pool size: 64
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Jun-04 15:33:32.214 [main] DEBUG nextflow.cli.CmdRun -
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Version: 0.28.0 build 4779
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17
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Modified: 10-03-2018 12:13 UTC (14:13 SAST)
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System: Linux 3.0.101-108.13-default
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Runtime: Groovy 2.4.13 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13
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Encoding: UTF-8 (UTF-8)
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Process: 12052@srvslshpc603.uct.ac.za [137.158.155.222]
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CPUs: 64 - Mem: 126 GB (83.8 GB) - Swap: 0 (0)
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Jun-04 15:33:32.261 [main] DEBUG nextflow.Session - Work-dir: /researchdata/fhgfs/katie/dada2-test/work [UNKNOWN (0x19830326)]
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24
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Jun-04 15:33:32.262 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/kviljoen/.nextflow/assets/kviljoen/16S-rDNA-dada2-pipeline/bin
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Jun-04 15:33:32.474 [main] DEBUG nextflow.Session - Session start invoked
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Jun-04 15:33:32.481 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
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Jun-04 15:33:32.482 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /researchdata/fhgfs/katie/dada2-test/2018-06-04-dada2/pipeline_info/dada2_trace.txt
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Jun-04 15:33:32.493 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
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Jun-04 15:33:32.956 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
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Jun-04 15:33:32.976 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: /researchdata/fhgfs/katie/dada2-test/raw_testdata/; pattern: *{R1,R2}.fastq; options: null
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Jun-04 15:33:33.315 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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Jun-04 15:33:33.316 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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33
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Jun-04 15:33:33.333 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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34
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Jun-04 15:33:33.337 [main] INFO nextflow.executor.Executor - [warm up] executor > pbs
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Jun-04 15:33:33.348 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbs' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
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Jun-04 15:33:33.353 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
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Jun-04 15:33:33.355 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: pbs)
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Jun-04 15:33:33.360 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: pbs
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Jun-04 15:33:33.361 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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40
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Jun-04 15:33:33.419 [main] DEBUG nextflow.Session - >>> barrier register (process: plotQual)
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Jun-04 15:33:33.424 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > plotQual -- maxForks: 64
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Jun-04 15:33:33.500 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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Jun-04 15:33:33.501 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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44
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Jun-04 15:33:33.502 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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Jun-04 15:33:33.504 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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46
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Jun-04 15:33:33.509 [main] DEBUG nextflow.Session - >>> barrier register (process: filterAndTrim)
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Jun-04 15:33:33.511 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > filterAndTrim -- maxForks: 64
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Jun-04 15:33:33.540 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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Jun-04 15:33:33.541 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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Jun-04 15:33:33.541 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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Jun-04 15:33:33.542 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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52
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Jun-04 15:33:33.545 [main] DEBUG nextflow.Session - >>> barrier register (process: mergeTrimmedTable)
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Jun-04 15:33:33.546 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > mergeTrimmedTable -- maxForks: 64
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Jun-04 15:33:33.562 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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Jun-04 15:33:33.563 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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Jun-04 15:33:33.563 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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57
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Jun-04 15:33:33.564 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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58
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Jun-04 15:33:33.568 [main] DEBUG nextflow.Session - >>> barrier register (process: LearnErrorsFor)
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Jun-04 15:33:33.569 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > LearnErrorsFor -- maxForks: 64
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60
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Jun-04 15:33:33.587 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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61
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Jun-04 15:33:33.591 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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62
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Jun-04 15:33:33.592 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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63
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Jun-04 15:33:33.593 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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64
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Jun-04 15:33:33.595 [main] DEBUG nextflow.Session - >>> barrier register (process: LearnErrorsRev)
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65
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Jun-04 15:33:33.596 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > LearnErrorsRev -- maxForks: 64
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66
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Jun-04 15:33:33.606 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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67
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Jun-04 15:33:33.606 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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68
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Jun-04 15:33:33.607 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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69
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Jun-04 15:33:33.608 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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70
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Jun-04 15:33:33.611 [main] DEBUG nextflow.Session - >>> barrier register (process: SampleInferDerepAndMerge)
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71
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Jun-04 15:33:33.612 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > SampleInferDerepAndMerge -- maxForks: 64
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72
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Jun-04 15:33:33.638 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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73
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Jun-04 15:33:33.639 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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74
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Jun-04 15:33:33.641 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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75
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Jun-04 15:33:33.644 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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76
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Jun-04 15:33:33.646 [main] DEBUG nextflow.Session - >>> barrier register (process: mergeDadaRDS)
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77
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Jun-04 15:33:33.648 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > mergeDadaRDS -- maxForks: 64
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78
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Jun-04 15:33:33.658 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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79
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Jun-04 15:33:33.663 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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80
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Jun-04 15:33:33.666 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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81
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Jun-04 15:33:33.667 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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82
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Jun-04 15:33:33.672 [main] DEBUG nextflow.Session - >>> barrier register (process: SequenceTable)
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83
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Jun-04 15:33:33.675 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > SequenceTable -- maxForks: 64
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84
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Jun-04 15:33:33.688 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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85
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Jun-04 15:33:33.688 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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86
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Jun-04 15:33:33.689 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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87
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Jun-04 15:33:33.690 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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88
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Jun-04 15:33:33.692 [main] DEBUG nextflow.Session - >>> barrier register (process: ChimeraTaxonomy)
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89
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Jun-04 15:33:33.692 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > ChimeraTaxonomy -- maxForks: 64
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90
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Jun-04 15:33:33.702 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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91
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Jun-04 15:33:33.702 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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92
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Jun-04 15:33:33.703 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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93
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Jun-04 15:33:33.704 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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94
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Jun-04 15:33:33.706 [main] DEBUG nextflow.Session - >>> barrier register (process: AlignAndGenerateTree)
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95
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Jun-04 15:33:33.706 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > AlignAndGenerateTree -- maxForks: 64
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96
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Jun-04 15:33:33.713 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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97
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Jun-04 15:33:33.714 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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98
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Jun-04 15:33:33.715 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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99
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Jun-04 15:33:33.719 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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100
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Jun-04 15:33:33.721 [main] DEBUG nextflow.Session - >>> barrier register (process: BiomFile)
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101
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Jun-04 15:33:33.721 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BiomFile -- maxForks: 64
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102
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Jun-04 15:33:33.728 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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103
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Jun-04 15:33:33.728 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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104
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Jun-04 15:33:33.729 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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105
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Jun-04 15:33:33.730 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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106
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Jun-04 15:33:33.731 [main] DEBUG nextflow.Session - >>> barrier register (process: ReadTracking)
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107
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Jun-04 15:33:33.731 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > ReadTracking -- maxForks: 64
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108
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Jun-04 15:33:33.735 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
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109
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Jun-04 15:33:33.736 [main] DEBUG nextflow.Session - Session await
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110
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Jun-04 15:33:33.820 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [85/e79dfe] Cached process > plotQual (plotQ)
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111
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Jun-04 15:33:33.853 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [98/b4759f] Cached process > filterAndTrim (filterAndTrim)
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112
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Jun-04 15:33:33.857 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [f6/6fffc0] Cached process > filterAndTrim (filterAndTrim)
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113
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Jun-04 15:33:33.889 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: plotQual)
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114
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Jun-04 15:33:33.890 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: filterAndTrim)
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115
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Jun-04 15:33:33.925 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [05/c98492] Cached process > mergeTrimmedTable (dada2-nextflow-pipeline.mergTrimmedTable)
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116
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Jun-04 15:33:33.930 [Actor Thread 13] DEBUG nextflow.Session - <<< barrier arrive (process: mergeTrimmedTable)
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117
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Jun-04 15:33:34.082 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process LearnErrorsRev > jobId: 1921069.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/22/401dabcd96c74b4296d2b1f8cd471b
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118
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Jun-04 15:33:34.090 [Task submitter] INFO nextflow.Session - [22/401dab] Submitted process > LearnErrorsRev
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119
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Jun-04 15:33:34.149 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process LearnErrorsFor > jobId: 1921070.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/34/b3d3815feeab2ed545eb57c87848dc
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120
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Jun-04 15:33:34.150 [Task submitter] INFO nextflow.Session - [34/b3d381] Submitted process > LearnErrorsFor
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121
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Jun-04 15:38:38.395 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 2 -- pending tasks are shown below
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122
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~> TaskHandler[jobId: 1921069.srvslshpc001; id: 6; name: LearnErrorsRev; status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/22/401dabcd96c74b4296d2b1f8cd471b started: 1528119388377; exited: -; ]
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123
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~> TaskHandler[jobId: 1921070.srvslshpc001; id: 4; name: LearnErrorsFor; status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/34/b3d3815feeab2ed545eb57c87848dc started: 1528119393372; exited: 2018-06-04T13:38:34Z; ]
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124
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Jun-04 15:38:38.399 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921070.srvslshpc001; id: 4; name: LearnErrorsFor; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/34/b3d3815feeab2ed545eb57c87848dc started: 1528119393372; exited: 2018-06-04T13:38:34Z; ]
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125
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Jun-04 15:38:38.410 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: LearnErrorsFor)
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126
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Jun-04 15:41:48.413 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921069.srvslshpc001; id: 6; name: LearnErrorsRev; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/22/401dabcd96c74b4296d2b1f8cd471b started: 1528119388377; exited: 2018-06-04T13:41:47Z; ]
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127
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Jun-04 15:41:48.417 [Actor Thread 12] DEBUG nextflow.Session - <<< barrier arrive (process: LearnErrorsRev)
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128
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Jun-04 15:41:48.493 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process SampleInferDerepAndMerge (2) > jobId: 1921114.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/80/9d7416506b95b8bdfb79b313e76565
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129
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Jun-04 15:41:48.494 [Task submitter] INFO nextflow.Session - [80/9d7416] Submitted process > SampleInferDerepAndMerge (2)
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130
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Jun-04 15:41:48.531 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process SampleInferDerepAndMerge (1) > jobId: 1921115.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/9c/a010ee685a7a2e717339851e7d5fce
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131
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Jun-04 15:41:48.532 [Task submitter] INFO nextflow.Session - [9c/a010ee] Submitted process > SampleInferDerepAndMerge (1)
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132
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Jun-04 15:43:13.421 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921115.srvslshpc001; id: 7; name: SampleInferDerepAndMerge (1); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/9c/a010ee685a7a2e717339851e7d5fce started: 1528119748417; exited: 2018-06-04T13:43:11Z; ]
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133
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Jun-04 15:43:38.420 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
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134
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~> TaskHandler[jobId: 1921114.srvslshpc001; id: 8; name: SampleInferDerepAndMerge (2); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/80/9d7416506b95b8bdfb79b313e76565 started: 1528119748413; exited: -; ]
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135
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Jun-04 15:44:13.426 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921114.srvslshpc001; id: 8; name: SampleInferDerepAndMerge (2); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/80/9d7416506b95b8bdfb79b313e76565 started: 1528119748413; exited: 2018-06-04T13:44:10Z; ]
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136
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Jun-04 15:44:13.455 [Actor Thread 19] DEBUG nextflow.Session - <<< barrier arrive (process: SampleInferDerepAndMerge)
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137
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Jun-04 15:44:18.720 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process SequenceTable > jobId: 1921161.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/f3/b4927e4067b7387645c6d922010c9b
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138
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Jun-04 15:44:18.722 [Task submitter] INFO nextflow.Session - [f3/b4927e] Submitted process > SequenceTable
|
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139
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Jun-04 15:44:18.755 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process mergeDadaRDS > jobId: 1921162.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/34/042015e125d1679697416ece93da11
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140
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Jun-04 15:44:18.757 [Task submitter] INFO nextflow.Session - [34/042015] Submitted process > mergeDadaRDS
|
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141
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Jun-04 15:45:43.429 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921161.srvslshpc001; id: 10; name: SequenceTable; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/f3/b4927e4067b7387645c6d922010c9b started: 1528119928426; exited: 2018-06-04T13:45:41Z; ]
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Jun-04 15:45:43.441 [Actor Thread 24] DEBUG nextflow.Session - <<< barrier arrive (process: SequenceTable)
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Jun-04 15:45:43.447 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921162.srvslshpc001; id: 9; name: mergeDadaRDS; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/34/042015e125d1679697416ece93da11 started: 1528119928448; exited: 2018-06-04T13:45:42Z; ]
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Jun-04 15:45:43.451 [Actor Thread 29] DEBUG nextflow.Session - <<< barrier arrive (process: mergeDadaRDS)
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Jun-04 15:45:43.493 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process ChimeraTaxonomy > jobId: 1921178.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/65/ed492478a7b7550a0a215378139afa
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Jun-04 15:45:43.494 [Task submitter] INFO nextflow.Session - [65/ed4924] Submitted process > ChimeraTaxonomy
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Jun-04 15:48:38.436 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
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~> TaskHandler[jobId: 1921178.srvslshpc001; id: 11; name: ChimeraTaxonomy; status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/65/ed492478a7b7550a0a215378139afa started: 1528120108434; exited: -; ]
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Jun-04 15:51:48.448 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921178.srvslshpc001; id: 11; name: ChimeraTaxonomy; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/65/ed492478a7b7550a0a215378139afa started: 1528120108434; exited: 2018-06-04T13:51:43Z; ]
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Jun-04 15:51:48.456 [Actor Thread 35] DEBUG nextflow.Session - <<< barrier arrive (process: ChimeraTaxonomy)
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Jun-04 15:51:48.498 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process AlignAndGenerateTree > jobId: 1921209.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/99/fbc8396c812f939cbe1444bb6a4c10
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Jun-04 15:51:48.500 [Task submitter] INFO nextflow.Session - [99/fbc839] Submitted process > AlignAndGenerateTree
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Jun-04 15:51:48.534 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process ReadTracking > jobId: 1921210.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/ba/915864362710615797ba62c0720bca
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Jun-04 15:51:48.535 [Task submitter] INFO nextflow.Session - [ba/915864] Submitted process > ReadTracking
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Jun-04 15:51:48.567 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process BiomFile > jobId: 1921211.srvslshpc001; workDir: /researchdata/fhgfs/katie/dada2-test/work/82/216d88fef42454b9e25ec63e0d277d
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Jun-04 15:51:48.568 [Task submitter] INFO nextflow.Session - [82/216d88] Submitted process > BiomFile
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Jun-04 15:53:38.456 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below
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~> TaskHandler[jobId: 1921209.srvslshpc001; id: 13; name: AlignAndGenerateTree; status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/99/fbc8396c812f939cbe1444bb6a4c10 started: -; exited: -; ]
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~> TaskHandler[jobId: 1921210.srvslshpc001; id: 12; name: ReadTracking; status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/ba/915864362710615797ba62c0720bca started: -; exited: -; ]
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~> TaskHandler[jobId: 1921211.srvslshpc001; id: 14; name: BiomFile; status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/82/216d88fef42454b9e25ec63e0d277d started: -; exited: -; ]
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Jun-04 15:54:38.462 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921211.srvslshpc001; id: 14; name: BiomFile; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/82/216d88fef42454b9e25ec63e0d277d started: 1528120473485; exited: 2018-06-04T13:54:34Z; ]
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Jun-04 15:54:38.466 [Actor Thread 35] DEBUG nextflow.Session - <<< barrier arrive (process: BiomFile)
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163
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Jun-04 15:54:48.464 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921210.srvslshpc001; id: 12; name: ReadTracking; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/ba/915864362710615797ba62c0720bca started: 1528120473482; exited: 2018-06-04T13:54:46Z; ]
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164
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Jun-04 15:54:48.468 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: ReadTracking)
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165
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Jun-04 15:58:38.467 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
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166
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~> TaskHandler[jobId: 1921209.srvslshpc001; id: 13; name: AlignAndGenerateTree; status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/99/fbc8396c812f939cbe1444bb6a4c10 started: 1528120473459; exited: -; ]
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167
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Jun-04 16:03:38.475 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
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168
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~> TaskHandler[jobId: 1921209.srvslshpc001; id: 13; name: AlignAndGenerateTree; status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/99/fbc8396c812f939cbe1444bb6a4c10 started: 1528120473459; exited: -; ]
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169
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Jun-04 16:08:38.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
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170
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~> TaskHandler[jobId: 1921209.srvslshpc001; id: 13; name: AlignAndGenerateTree; status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/99/fbc8396c812f939cbe1444bb6a4c10 started: 1528120473459; exited: -; ]
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Jun-04 16:10:38.500 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1921209.srvslshpc001; id: 13; name: AlignAndGenerateTree; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/dada2-test/work/99/fbc8396c812f939cbe1444bb6a4c10 started: 1528120473459; exited: 2018-06-04T14:10:33Z; ]
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Jun-04 16:10:38.506 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: AlignAndGenerateTree)
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173
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Jun-04 16:10:38.507 [main] DEBUG nextflow.Session - Session await > all process finished
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174
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Jun-04 16:10:43.497 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: pbs)
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175
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Jun-04 16:10:43.498 [main] DEBUG nextflow.Session - Session await > all barriers passed
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176
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Jun-04 16:10:43.531 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=10; failedCount=0; ignoredCount=0; cachedCount=4; succeedDuration=30m 10s; failedDuration=0ms; cachedDuration=2m]
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177
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Jun-04 16:10:43.532 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
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178
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Jun-04 16:10:43.538 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
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179
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Jun-04 16:10:43.645 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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180
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{"mergeDadaRDS":{"cpu":null,"mem":null,"time":{"mean":14998,"min":14998,"q1":14998,"q2":14998,"q3":14998,"max":14998,"minLabel":"mergeDadaRDS","maxLabel":"mergeDadaRDS","q1Label":"mergeDadaRDS","q2Label":"mergeDadaRDS","q3Label":"mergeDadaRDS"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"mergeTrimmedTable":{"cpu":null,"mem":null,"time":{"mean":5,"min":5,"q1":5,"q2":5,"q3":5,"max":5,"minLabel":"mergeTrimmedTable (dada2-nextflow-pipeline.mergTrimmedTable)","maxLabel":"mergeTrimmedTable (dada2-nextflow-pipeline.mergTrimmedTable)","q1Label":"mergeTrimmedTable (dada2-nextflow-pipeline.mergTrimmedTable)","q2Label":"mergeTrimmedTable (dada2-nextflow-pipeline.mergTrimmedTable)","q3Label":"mergeTrimmedTable (dada2-nextflow-pipeline.mergTrimmedTable)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"ChimeraTaxonomy":{"cpu":null,"mem":null,"time":{"mean":200013,"min":200013,"q1":200013,"q2":200013,"q3":200013,"max":200013,"minLabel":"ChimeraTaxonomy","maxLabel":"ChimeraTaxonomy","q1Label":"ChimeraTaxonomy","q2Label":"ChimeraTaxonomy","q3Label":"ChimeraTaxonomy"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"BiomFile":{"cpu":null,"mem":null,"time":{"mean":4976,"min":4976,"q1":4976,"q2":4976,"q3":4976,"max":4976,"minLabel":"BiomFile","maxLabel":"BiomFile","q1Label":"BiomFile","q2Label":"BiomFile","q3Label":"BiomFile"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"plotQual":{"cpu":null,"mem":null,"time":{"mean":34974,"min":34974,"q1":34974,"q2":34974,"q3":34974,"max":34974,"minLabel":"plotQual (plotQ)","maxLabel":"plotQual (plotQ)","q1Label":"plotQual (plotQ)","q2Label":"plotQual (plotQ)","q3Label":"plotQual (plotQ)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"LearnErrorsRev":{"cpu":null,"mem":null,"time":{"mean":320035,"min":320035,"q1":320035,"q2":320035,"q3":320035,"max":320035,"minLabel":"LearnErrorsRev","maxLabel":"LearnErrorsRev","q1Label":"LearnErrorsRev","q2Label":"LearnErrorsRev","q3Label":"LearnErrorsRev"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"SequenceTable":{"cpu":null,"mem":null,"time":{"mean":15002,"min":15002,"q1":15002,"q2":15002,"q3":15002,"max":15002,"minLabel":"SequenceTable","maxLabel":"SequenceTable","q1Label":"SequenceTable","q2Label":"SequenceTable","q3Label":"SequenceTable"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"ReadTracking":{"cpu":null,"mem":null,"time":{"mean":14980,"min":14980,"q1":14980,"q2":14980,"q3":14980,"max":14980,"minLabel":"ReadTracking","maxLabel":"ReadTracking","q1Label":"ReadTracking","q2Label":"ReadTracking","q3Label":"ReadTracking"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"LearnErrorsFor":{"cpu":null,"mem":null,"time":{"mean":125026,"min":125026,"q1":125026,"q2":125026,"q3":125026,"max":125026,"minLabel":"LearnErrorsFor","maxLabel":"LearnErrorsFor","q1Label":"LearnErrorsFor","q2Label":"LearnErrorsFor","q3Label":"LearnErrorsFor"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"SampleInferDerepAndMerge":{"cpu":null,"mem":null,"time":{"mean":75007,"min":45002,"q1":60004.5,"q2":75007,"q3":90009.5,"max":105012,"minLabel":"SampleInferDerepAndMerge (1)","maxLabel":"SampleInferDerepAndMerge (2)","q1Label":"SampleInferDerepAndMerge (1)","q2Label":"SampleInferDerepAndMerge (1)","q3Label":"SampleInferDerepAndMerge (1)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"AlignAndGenerateTree":{"cpu":null,"mem":null,"time":{"mean":965040,"min":965040,"q1":965040,"q2":965040,"q3":965040,"max":965040,"minLabel":"AlignAndGenerateTree","maxLabel":"AlignAndGenerateTree","q1Label":"AlignAndGenerateTree","q2Label":"AlignAndGenerateTree","q3Label":"AlignAndGenerateTree"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"filterAndTrim":{"cpu":null,"mem":null,"time":{"mean":42500,"min":39998,"q1":41249,"q2":42500,"q3":43751,"max":45002,"minLabel":"filterAndTrim (filterAndTrim)","maxLabel":"filterAndTrim (filterAndTrim)","q1Label":"filterAndTrim (filterAndTrim)","q2Label":"filterAndTrim (filterAndTrim)","q3Label":"filterAndTrim (filterAndTrim)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null}}
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181
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Jun-04 16:10:45.025 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
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182
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Jun-04 16:10:45.141 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
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183
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Jun-04 16:10:45.171 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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