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1
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Apr-24 13:24:29.226 [main] DEBUG nextflow.cli.Launcher - $> /opt/exp_soft/cbio/nextflow/nextflow -log /researchdata/fhgfs/katie/NGI-RNAseq-test/nextflow.log run uct-cbio/RNAseq -r dev --reads /researchdata/fhgfs/katie/NGI-RNAseq-test/*_R{1,2}.fastq.gz --genome GRCh37 -profile uct_hex -with-singularity /scratch/DB/bio/singularity-containers/uct-cbio-rnaseq.img --outdir /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-outdir -w /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir --email katie.viljoen@uct.ac.za
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Apr-24 13:24:29.424 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.28.0
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Apr-24 13:24:30.356 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/.git/config; branch: master; remote: origin; url: https://github.com/uct-cbio/RNAseq.git
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4
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Apr-24 13:24:30.565 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/.git/config; branch: master; remote: origin; url: https://github.com/uct-cbio/RNAseq.git
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Apr-24 13:24:31.702 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/.git/config; branch: master; remote: origin; url: https://github.com/uct-cbio/RNAseq.git
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Apr-24 13:24:31.703 [main] INFO nextflow.cli.CmdRun - Launching `uct-cbio/RNAseq` [mad_ptolemy] - revision: 718fb1aff1 [dev]
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Apr-24 13:24:33.369 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/nextflow.config
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Apr-24 13:24:33.372 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/nextflow.config
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Apr-24 13:24:33.388 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `uct_hex`
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Apr-24 13:24:34.244 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, hebbe, cfc, uppmax_devel, amazon_test, uppmax, none, docker, uct_hex, singularity, aws, uppmax_modules, binac]
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Apr-24 13:24:34.388 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by cli option `-with-singularity null`
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Apr-24 13:24:34.455 [main] DEBUG nextflow.Session - Session uuid: 623be393-8589-433d-8914-7a3b6390d0af
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Apr-24 13:24:34.456 [main] DEBUG nextflow.Session - Run name: mad_ptolemy
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Apr-24 13:24:34.459 [main] DEBUG nextflow.Session - Executor pool size: 64
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Apr-24 13:24:34.593 [main] DEBUG nextflow.cli.CmdRun -
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Version: 0.28.0 build 4779
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Modified: 10-03-2018 12:13 UTC (14:13 SAST)
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System: Linux 3.0.101-108.10-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: 47974@srvslshpc600.uct.ac.za [137.158.155.219]
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CPUs: 64 - Mem: 126 GB (82.5 GB) - Swap: 0 (0)
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Apr-24 13:24:34.628 [main] DEBUG nextflow.Session - Work-dir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir [UNKNOWN (0x19830326)]
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Apr-24 13:24:36.058 [main] DEBUG nextflow.Session - Session start invoked
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Apr-24 13:24:36.064 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
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Apr-24 13:24:36.066 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-outdir/pipeline_info/nfcore-RNAseq_trace.txt
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Apr-24 13:24:36.088 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
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Apr-24 13:24:37.508 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
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Apr-24 13:24:37.780 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: /researchdata/fhgfs/katie/NGI-RNAseq-test/; pattern: *_R{1,2}.fastq.gz; options: [:]
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Apr-24 13:24:37.831 [main] INFO nextflow.Nextflow - ===================================
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Apr-24 13:24:37.832 [main] INFO nextflow.Nextflow - nfcore/RNAseq ~ version 1.5dev
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Apr-24 13:24:37.833 [main] INFO nextflow.Nextflow - ===================================
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Apr-24 13:24:37.844 [main] INFO nextflow.Nextflow - Run Name : mad_ptolemy
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Reads : /researchdata/fhgfs/katie/NGI-RNAseq-test/*_R{1,2}.fastq.gz
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Data Type : Paired-End
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Genome : GRCh37
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Strandedness : None
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Trim R1 : 0
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Trim R2 : 0
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Trim 3' R1 : 0
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Trim 3' R2 : 0
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Aligner : STAR
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STAR Index : /scratch/DB/bio/rna-seq/references/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/
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GTF Annotation : /scratch/DB/bio/rna-seq/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf
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BED Annotation : /scratch/DB/bio/rna-seq/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed
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Save Reference : No
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Save Trimmed : No
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48
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Save Intermeds : No
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Max Memory : 256 GB
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Max CPUs : 64
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Max Time : 24d 20h 31m 24s
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Output dir : /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-outdir
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Working dir : /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir
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54
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Container : /scratch/DB/bio/singularity-containers/uct-cbio-rnaseq.img
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Pipeline Release: dev
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56
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Current home : /home/kviljoen
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57
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Current user : kviljoen
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58
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Current path : /researchdata/fhgfs/katie/NGI-RNAseq-test
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R libraries : false
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60
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Script dir : /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq
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Config Profile : uct_hex
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E-mail Address : katie.viljoen@uct.ac.za
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63
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Apr-24 13:24:37.845 [main] INFO nextflow.Nextflow - =========================================
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64
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Apr-24 13:24:37.987 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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65
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Apr-24 13:24:37.988 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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66
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Apr-24 13:24:38.006 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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67
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Apr-24 13:24:38.010 [main] INFO nextflow.executor.Executor - [warm up] executor > pbs
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68
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Apr-24 13:24:38.019 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbs' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
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69
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Apr-24 13:24:38.023 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor
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70
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Apr-24 13:24:38.024 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: pbs)
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71
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Apr-24 13:24:38.028 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: pbs
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72
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Apr-24 13:24:38.029 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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73
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Apr-24 13:24:38.080 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
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74
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Apr-24 13:24:38.084 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 64
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75
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Apr-24 13:24:38.124 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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Apr-24 13:24:38.125 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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77
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Apr-24 13:24:38.126 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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78
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Apr-24 13:24:38.127 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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79
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Apr-24 13:24:38.130 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_galore)
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80
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Apr-24 13:24:38.133 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 64
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81
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Apr-24 13:24:38.236 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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82
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Apr-24 13:24:38.237 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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83
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Apr-24 13:24:38.238 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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84
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Apr-24 13:24:38.240 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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85
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Apr-24 13:24:38.242 [main] DEBUG nextflow.Session - >>> barrier register (process: star)
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86
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Apr-24 13:24:38.243 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > star -- maxForks: 64
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87
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Apr-24 13:24:38.279 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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88
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Apr-24 13:24:38.279 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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89
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Apr-24 13:24:38.281 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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90
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Apr-24 13:24:38.282 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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91
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Apr-24 13:24:38.283 [main] DEBUG nextflow.Session - >>> barrier register (process: rseqc)
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92
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Apr-24 13:24:38.284 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > rseqc -- maxForks: 64
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93
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Apr-24 13:24:38.306 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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94
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Apr-24 13:24:38.306 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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95
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Apr-24 13:24:38.311 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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96
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Apr-24 13:24:38.312 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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97
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Apr-24 13:24:38.315 [main] DEBUG nextflow.Session - >>> barrier register (process: genebody_coverage)
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98
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Apr-24 13:24:38.316 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > genebody_coverage -- maxForks: 64
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99
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Apr-24 13:24:38.333 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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100
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Apr-24 13:24:38.334 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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101
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Apr-24 13:24:38.335 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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102
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Apr-24 13:24:38.336 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
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103
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Apr-24 13:24:38.338 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq)
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104
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Apr-24 13:24:38.346 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 64
|
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105
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Apr-24 13:24:38.372 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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106
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Apr-24 13:24:38.373 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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107
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Apr-24 13:24:38.378 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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108
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Apr-24 13:24:38.379 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
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109
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Apr-24 13:24:38.386 [main] DEBUG nextflow.Session - >>> barrier register (process: markDuplicates)
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110
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Apr-24 13:24:38.387 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDuplicates -- maxForks: 64
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111
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Apr-24 13:24:38.630 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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112
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Apr-24 13:24:38.631 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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113
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Apr-24 13:24:38.632 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
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114
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Apr-24 13:24:38.633 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
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115
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Apr-24 13:24:38.636 [main] DEBUG nextflow.Session - >>> barrier register (process: dupradar)
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116
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Apr-24 13:24:38.639 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dupradar -- maxForks: 64
|
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117
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Apr-24 13:24:38.662 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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118
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Apr-24 13:24:38.663 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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119
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Apr-24 13:24:38.663 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
|
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120
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Apr-24 13:24:38.665 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
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121
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Apr-24 13:24:38.670 [main] DEBUG nextflow.Session - >>> barrier register (process: featureCounts)
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122
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Apr-24 13:24:38.671 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 64
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123
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Apr-24 13:24:38.697 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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124
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Apr-24 13:24:38.698 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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125
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Apr-24 13:24:38.699 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
|
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126
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Apr-24 13:24:38.700 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
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127
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Apr-24 13:24:38.701 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_featureCounts)
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128
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Apr-24 13:24:38.702 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_featureCounts -- maxForks: 64
|
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129
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Apr-24 13:24:38.713 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
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130
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Apr-24 13:24:38.714 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
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131
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Apr-24 13:24:38.715 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
|
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132
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Apr-24 13:24:38.716 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
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133
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Apr-24 13:24:38.718 [main] DEBUG nextflow.Session - >>> barrier register (process: stringtieFPKM)
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134
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Apr-24 13:24:38.719 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringtieFPKM -- maxForks: 64
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135
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Apr-24 13:24:38.758 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
|
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136
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Apr-24 13:24:38.759 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
|
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137
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Apr-24 13:24:38.759 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
|
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138
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Apr-24 13:24:38.760 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
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139
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Apr-24 13:24:38.762 [main] DEBUG nextflow.Session - >>> barrier register (process: sample_correlation)
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140
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Apr-24 13:24:38.763 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sample_correlation -- maxForks: 64
|
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141
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Apr-24 13:24:38.776 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
|
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142
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Apr-24 13:24:38.777 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
|
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143
|
Apr-24 13:24:38.782 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
|
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144
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Apr-24 13:24:38.783 [main] INFO nextflow.executor.Executor - [warm up] executor > local
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145
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Apr-24 13:24:38.791 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=126 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
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146
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Apr-24 13:24:38.796 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
|
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147
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Apr-24 13:24:38.797 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
|
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148
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Apr-24 13:24:38.798 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
|
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149
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Apr-24 13:24:38.800 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions)
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150
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Apr-24 13:24:38.800 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 64
|
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151
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Apr-24 13:24:38.806 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local
|
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152
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Apr-24 13:24:38.807 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
|
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153
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Apr-24 13:24:38.808 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
|
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154
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Apr-24 13:24:38.809 [main] DEBUG nextflow.Session - >>> barrier register (process: workflow_summary_mqc)
|
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155
|
Apr-24 13:24:38.810 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > workflow_summary_mqc -- maxForks: 64
|
|
156
|
Apr-24 13:24:38.830 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.VersionNumber -- 0.28.0
|
|
157
|
Apr-24 13:24:38.838 [Task submitter] INFO nextflow.Session - [81/2834d4] Submitted process > workflow_summary_mqc
|
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158
|
Apr-24 13:24:38.855 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
|
|
159
|
Apr-24 13:24:38.856 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
|
|
160
|
Apr-24 13:24:38.859 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
|
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161
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Apr-24 13:24:38.860 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
|
162
|
Apr-24 13:24:38.863 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc)
|
|
163
|
Apr-24 13:24:38.864 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 64
|
|
164
|
Apr-24 13:24:38.878 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: workflow_summary_mqc; status: COMPLETED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/81/2834d4e8300f3297e1f2a959a297aa]
|
|
165
|
Apr-24 13:24:38.883 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs
|
|
166
|
Apr-24 13:24:38.885 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs'
|
|
167
|
Apr-24 13:24:38.887 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs
|
|
168
|
Apr-24 13:24:38.889 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
|
|
169
|
Apr-24 13:24:38.894 [main] DEBUG nextflow.Session - >>> barrier register (process: output_documentation)
|
|
170
|
Apr-24 13:24:38.895 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 64
|
|
171
|
Apr-24 13:24:38.897 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
|
|
172
|
Apr-24 13:24:38.902 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
|
|
173
|
Apr-24 13:24:38.902 [main] DEBUG nextflow.Session - Session await
|
|
174
|
Apr-24 13:24:38.906 [Task submitter] INFO nextflow.Session - [4a/6b391a] Submitted process > get_software_versions
|
|
175
|
Apr-24 13:24:38.965 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: workflow_summary_mqc)
|
|
176
|
Apr-24 13:24:43.876 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process fastqc (sample37) > jobId: 1842278.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8a/402e2e8ac1be60d94b6a48ec1ba569
|
|
177
|
Apr-24 13:24:43.885 [Task submitter] INFO nextflow.Session - [8a/402e2e] Submitted process > fastqc (sample37)
|
|
178
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Apr-24 13:24:44.656 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4a/6b391a279c781edf0f0c3c64c4802f]
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Apr-24 13:24:44.666 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: get_software_versions)
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Apr-24 13:24:47.121 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process fastqc (sample40) > jobId: 1842279.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/44/9020e4e5cabf230fd4f43624409906
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Apr-24 13:24:47.122 [Task submitter] INFO nextflow.Session - [44/9020e4] Submitted process > fastqc (sample40)
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Apr-24 13:24:47.159 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process trim_galore (sample41) > jobId: 1842280.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013
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Apr-24 13:24:47.160 [Task submitter] INFO nextflow.Session - [7f/3e00fc] Submitted process > trim_galore (sample41)
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Apr-24 13:24:47.190 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process trim_galore (sample40) > jobId: 1842281.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7
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Apr-24 13:24:47.191 [Task submitter] INFO nextflow.Session - [4d/c3b6f7] Submitted process > trim_galore (sample40)
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Apr-24 13:24:47.234 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process fastqc (sample38) > jobId: 1842282.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/0f/1550017dcb5b1f1231ff8b8f15b680
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Apr-24 13:24:47.235 [Task submitter] INFO nextflow.Session - [0f/155001] Submitted process > fastqc (sample38)
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Apr-24 13:24:47.305 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process fastqc (sample39) > jobId: 1842283.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cf/fd065a57282366a8867e013427fdcb
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Apr-24 13:24:47.305 [Task submitter] INFO nextflow.Session - [cf/fd065a] Submitted process > fastqc (sample39)
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Apr-24 13:24:47.343 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process trim_galore (sample38) > jobId: 1842284.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893
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Apr-24 13:24:47.344 [Task submitter] INFO nextflow.Session - [41/11c319] Submitted process > trim_galore (sample38)
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Apr-24 13:24:47.424 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process fastqc (sample41) > jobId: 1842285.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/71/fa68aa0b4372fdabc63c164e45d700
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Apr-24 13:24:47.425 [Task submitter] INFO nextflow.Session - [71/fa68aa] Submitted process > fastqc (sample41)
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Apr-24 13:24:47.510 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process trim_galore (sample39) > jobId: 1842286.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25
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Apr-24 13:24:47.511 [Task submitter] INFO nextflow.Session - [6f/55d00a] Submitted process > trim_galore (sample39)
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Apr-24 13:24:47.539 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process trim_galore (sample37) > jobId: 1842287.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ac/d8cf85904f9bfe0c89a0fb87af576d
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Apr-24 13:24:47.540 [Task submitter] INFO nextflow.Session - [ac/d8cf85] Submitted process > trim_galore (sample37)
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Apr-24 13:29:38.956 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
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[process] star
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status=ACTIVE
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port 0: (queue) OPEN; channel: reads
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port 1: (value) - ; channel: index
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203
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port 2: (value) - ; channel: gtf
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204
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port 3: (value) - ; channel: wherearemyfiles
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port 4: (cntrl) OPEN; channel: $
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[process] rseqc
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam_rseqc
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port 1: (value) - ; channel: bed12
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port 2: (cntrl) OPEN; channel: $
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[process] genebody_coverage
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam_geneBodyCoverage
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port 1: (value) - ; channel: bed12
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port 2: (cntrl) OPEN; channel: $
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[process] preseq
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam_preseq
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port 1: (cntrl) OPEN; channel: $
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[process] markDuplicates
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam
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port 1: (cntrl) OPEN; channel: $
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228
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[process] dupradar
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam_md
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port 1: (value) - ; channel: gtf
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port 2: (cntrl) OPEN; channel: $
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234
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[process] featureCounts
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam_featurecounts
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port 1: (value) - ; channel: gtf
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port 2: (value) - ; channel: biotypes_header
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port 3: (cntrl) OPEN; channel: $
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241
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[process] merge_featureCounts
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status=ACTIVE
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244
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port 0: (value) - ; channel: input_files
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port 1: (cntrl) OPEN; channel: $
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[process] stringtieFPKM
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status=ACTIVE
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port 0: (queue) OPEN; channel: bam_stringtieFPKM
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port 1: (value) - ; channel: gtf
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port 2: (cntrl) OPEN; channel: $
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[process] sample_correlation
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status=ACTIVE
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port 0: (value) - ; channel: input_files
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256
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port 1: (value) - ; channel: num_bams
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257
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port 2: (value) - ; channel: mdsplot_header
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port 3: (value) - ; channel: heatmap_header
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port 4: (cntrl) OPEN; channel: $
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[process] multiqc
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status=ACTIVE
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port 0: (value) - ; channel: multiqc_config
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port 1: (value) - ; channel: fastqc
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port 2: (value) - ; channel: trimgalore/*
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port 3: (value) - ; channel: alignment/*
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port 4: (value) - ; channel: rseqc/*
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port 5: (value) - ; channel: rseqc/*
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port 6: (value) - ; channel: preseq/*
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270
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port 7: (value) - ; channel: dupradar/*
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port 8: (value) - ; channel: featureCounts/*
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port 9: (value) - ; channel: featureCounts_biotype/*
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port 10: (value) - ; channel: stringtie/stringtie_log*
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port 11: (value) - ; channel: sample_correlation_results/*
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275
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port 12: (value) - ; channel: software_versions/*
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port 13: (value) - ; channel: workflow_summary/*
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port 14: (cntrl) OPEN; channel: $
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[process] output_documentation
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status=ACTIVE
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port 0: (value) - ; channel: output_docs
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port 1: (value) - ; channel: prefix
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port 2: (cntrl) OPEN; channel: $
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Apr-24 13:29:43.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below
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286
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~> TaskHandler[jobId: 1842278.srvslshpc001; id: 4; name: fastqc (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8a/402e2e8ac1be60d94b6a48ec1ba569 started: 1524569228039; exited: -; ]
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~> TaskHandler[jobId: 1842279.srvslshpc001; id: 2; name: fastqc (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/44/9020e4e5cabf230fd4f43624409906 started: 1524569228086; exited: -; ]
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~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
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~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
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~> TaskHandler[jobId: 1842282.srvslshpc001; id: 1; name: fastqc (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/0f/1550017dcb5b1f1231ff8b8f15b680 started: 1524569233043; exited: -; ]
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~> TaskHandler[jobId: 1842283.srvslshpc001; id: 5; name: fastqc (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cf/fd065a57282366a8867e013427fdcb started: 1524569233046; exited: -; ]
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~> TaskHandler[jobId: 1842284.srvslshpc001; id: 6; name: trim_galore (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893 started: 1524569233049; exited: -; ]
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~> TaskHandler[jobId: 1842285.srvslshpc001; id: 3; name: fastqc (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/71/fa68aa0b4372fdabc63c164e45d700 started: 1524569238037; exited: -; ]
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294
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~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
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~> TaskHandler[jobId: 1842287.srvslshpc001; id: 10; name: trim_galore (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ac/d8cf85904f9bfe0c89a0fb87af576d started: 1524569238044; exited: -; ]
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Apr-24 13:32:38.074 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842285.srvslshpc001; id: 3; name: fastqc (sample41); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/71/fa68aa0b4372fdabc63c164e45d700 started: 1524569238037; exited: 2018-04-24T11:32:36Z; ]
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Apr-24 13:33:28.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842278.srvslshpc001; id: 4; name: fastqc (sample37); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8a/402e2e8ac1be60d94b6a48ec1ba569 started: 1524569228039; exited: 2018-04-24T11:33:23Z; ]
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298
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Apr-24 13:33:53.066 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842282.srvslshpc001; id: 1; name: fastqc (sample38); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/0f/1550017dcb5b1f1231ff8b8f15b680 started: 1524569233043; exited: 2018-04-24T11:33:51Z; ]
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Apr-24 13:34:38.923 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
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300
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[process] star
|
|
301
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status=ACTIVE
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302
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port 0: (queue) OPEN; channel: reads
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303
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port 1: (value) - ; channel: index
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304
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port 2: (value) - ; channel: gtf
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305
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port 3: (value) - ; channel: wherearemyfiles
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306
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port 4: (cntrl) OPEN; channel: $
|
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307
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308
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[process] rseqc
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309
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status=ACTIVE
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310
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port 0: (queue) OPEN; channel: bam_rseqc
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311
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port 1: (value) - ; channel: bed12
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312
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port 2: (cntrl) OPEN; channel: $
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313
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314
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[process] genebody_coverage
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315
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status=ACTIVE
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316
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port 0: (queue) OPEN; channel: bam_geneBodyCoverage
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317
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port 1: (value) - ; channel: bed12
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318
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port 2: (cntrl) OPEN; channel: $
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319
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320
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[process] preseq
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321
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status=ACTIVE
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322
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port 0: (queue) OPEN; channel: bam_preseq
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323
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port 1: (cntrl) OPEN; channel: $
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324
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325
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[process] markDuplicates
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326
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status=ACTIVE
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327
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port 0: (queue) OPEN; channel: bam
|
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328
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port 1: (cntrl) OPEN; channel: $
|
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329
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330
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[process] dupradar
|
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331
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status=ACTIVE
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332
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port 0: (queue) OPEN; channel: bam_md
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333
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port 1: (value) - ; channel: gtf
|
|
334
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port 2: (cntrl) OPEN; channel: $
|
|
335
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|
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336
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[process] featureCounts
|
|
337
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status=ACTIVE
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338
|
port 0: (queue) OPEN; channel: bam_featurecounts
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339
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port 1: (value) - ; channel: gtf
|
|
340
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port 2: (value) - ; channel: biotypes_header
|
|
341
|
port 3: (cntrl) OPEN; channel: $
|
|
342
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|
|
343
|
[process] merge_featureCounts
|
|
344
|
status=ACTIVE
|
|
345
|
port 0: (value) - ; channel: input_files
|
|
346
|
port 1: (cntrl) OPEN; channel: $
|
|
347
|
|
|
348
|
[process] stringtieFPKM
|
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349
|
status=ACTIVE
|
|
350
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port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
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351
|
port 1: (value) - ; channel: gtf
|
|
352
|
port 2: (cntrl) OPEN; channel: $
|
|
353
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|
|
354
|
[process] sample_correlation
|
|
355
|
status=ACTIVE
|
|
356
|
port 0: (value) - ; channel: input_files
|
|
357
|
port 1: (value) - ; channel: num_bams
|
|
358
|
port 2: (value) - ; channel: mdsplot_header
|
|
359
|
port 3: (value) - ; channel: heatmap_header
|
|
360
|
port 4: (cntrl) OPEN; channel: $
|
|
361
|
|
|
362
|
[process] multiqc
|
|
363
|
status=ACTIVE
|
|
364
|
port 0: (value) - ; channel: multiqc_config
|
|
365
|
port 1: (value) - ; channel: fastqc
|
|
366
|
port 2: (value) - ; channel: trimgalore/*
|
|
367
|
port 3: (value) - ; channel: alignment/*
|
|
368
|
port 4: (value) - ; channel: rseqc/*
|
|
369
|
port 5: (value) - ; channel: rseqc/*
|
|
370
|
port 6: (value) - ; channel: preseq/*
|
|
371
|
port 7: (value) - ; channel: dupradar/*
|
|
372
|
port 8: (value) - ; channel: featureCounts/*
|
|
373
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
374
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
375
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
376
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port 12: (value) - ; channel: software_versions/*
|
|
377
|
port 13: (value) - ; channel: workflow_summary/*
|
|
378
|
port 14: (cntrl) OPEN; channel: $
|
|
379
|
|
|
380
|
[process] output_documentation
|
|
381
|
status=ACTIVE
|
|
382
|
port 0: (value) - ; channel: output_docs
|
|
383
|
port 1: (value) - ; channel: prefix
|
|
384
|
port 2: (cntrl) OPEN; channel: $
|
|
385
|
|
|
386
|
Apr-24 13:34:43.076 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 7 -- pending tasks are shown below
|
|
387
|
~> TaskHandler[jobId: 1842279.srvslshpc001; id: 2; name: fastqc (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/44/9020e4e5cabf230fd4f43624409906 started: 1524569228086; exited: -; ]
|
|
388
|
~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
|
|
389
|
~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
|
|
390
|
~> TaskHandler[jobId: 1842283.srvslshpc001; id: 5; name: fastqc (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cf/fd065a57282366a8867e013427fdcb started: 1524569233046; exited: -; ]
|
|
391
|
~> TaskHandler[jobId: 1842284.srvslshpc001; id: 6; name: trim_galore (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893 started: 1524569233049; exited: -; ]
|
|
392
|
~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
|
|
393
|
~> TaskHandler[jobId: 1842287.srvslshpc001; id: 10; name: trim_galore (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ac/d8cf85904f9bfe0c89a0fb87af576d started: 1524569238044; exited: -; ]
|
|
394
|
Apr-24 13:36:48.082 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842279.srvslshpc001; id: 2; name: fastqc (sample40); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/44/9020e4e5cabf230fd4f43624409906 started: 1524569228086; exited: 2018-04-24T11:36:46Z; ]
|
|
395
|
Apr-24 13:37:03.083 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842283.srvslshpc001; id: 5; name: fastqc (sample39); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cf/fd065a57282366a8867e013427fdcb started: 1524569233046; exited: 2018-04-24T11:36:58Z; ]
|
|
396
|
Apr-24 13:37:03.092 [Actor Thread 20] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
|
|
397
|
Apr-24 13:39:38.943 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
398
|
[process] star
|
|
399
|
status=ACTIVE
|
|
400
|
port 0: (queue) OPEN; channel: reads
|
|
401
|
port 1: (value) - ; channel: index
|
|
402
|
port 2: (value) - ; channel: gtf
|
|
403
|
port 3: (value) - ; channel: wherearemyfiles
|
|
404
|
port 4: (cntrl) OPEN; channel: $
|
|
405
|
|
|
406
|
[process] rseqc
|
|
407
|
status=ACTIVE
|
|
408
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
409
|
port 1: (value) - ; channel: bed12
|
|
410
|
port 2: (cntrl) OPEN; channel: $
|
|
411
|
|
|
412
|
[process] genebody_coverage
|
|
413
|
status=ACTIVE
|
|
414
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
415
|
port 1: (value) - ; channel: bed12
|
|
416
|
port 2: (cntrl) OPEN; channel: $
|
|
417
|
|
|
418
|
[process] preseq
|
|
419
|
status=ACTIVE
|
|
420
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
421
|
port 1: (cntrl) OPEN; channel: $
|
|
422
|
|
|
423
|
[process] markDuplicates
|
|
424
|
status=ACTIVE
|
|
425
|
port 0: (queue) OPEN; channel: bam
|
|
426
|
port 1: (cntrl) OPEN; channel: $
|
|
427
|
|
|
428
|
[process] dupradar
|
|
429
|
status=ACTIVE
|
|
430
|
port 0: (queue) OPEN; channel: bam_md
|
|
431
|
port 1: (value) - ; channel: gtf
|
|
432
|
port 2: (cntrl) OPEN; channel: $
|
|
433
|
|
|
434
|
[process] featureCounts
|
|
435
|
status=ACTIVE
|
|
436
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
437
|
port 1: (value) - ; channel: gtf
|
|
438
|
port 2: (value) - ; channel: biotypes_header
|
|
439
|
port 3: (cntrl) OPEN; channel: $
|
|
440
|
|
|
441
|
[process] merge_featureCounts
|
|
442
|
status=ACTIVE
|
|
443
|
port 0: (value) - ; channel: input_files
|
|
444
|
port 1: (cntrl) OPEN; channel: $
|
|
445
|
|
|
446
|
[process] stringtieFPKM
|
|
447
|
status=ACTIVE
|
|
448
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
449
|
port 1: (value) - ; channel: gtf
|
|
450
|
port 2: (cntrl) OPEN; channel: $
|
|
451
|
|
|
452
|
[process] sample_correlation
|
|
453
|
status=ACTIVE
|
|
454
|
port 0: (value) - ; channel: input_files
|
|
455
|
port 1: (value) - ; channel: num_bams
|
|
456
|
port 2: (value) - ; channel: mdsplot_header
|
|
457
|
port 3: (value) - ; channel: heatmap_header
|
|
458
|
port 4: (cntrl) OPEN; channel: $
|
|
459
|
|
|
460
|
[process] multiqc
|
|
461
|
status=ACTIVE
|
|
462
|
port 0: (value) - ; channel: multiqc_config
|
|
463
|
port 1: (value) - ; channel: fastqc
|
|
464
|
port 2: (value) - ; channel: trimgalore/*
|
|
465
|
port 3: (value) - ; channel: alignment/*
|
|
466
|
port 4: (value) - ; channel: rseqc/*
|
|
467
|
port 5: (value) - ; channel: rseqc/*
|
|
468
|
port 6: (value) - ; channel: preseq/*
|
|
469
|
port 7: (value) - ; channel: dupradar/*
|
|
470
|
port 8: (value) - ; channel: featureCounts/*
|
|
471
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
472
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
473
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
474
|
port 12: (value) - ; channel: software_versions/*
|
|
475
|
port 13: (value) - ; channel: workflow_summary/*
|
|
476
|
port 14: (cntrl) OPEN; channel: $
|
|
477
|
|
|
478
|
[process] output_documentation
|
|
479
|
status=ACTIVE
|
|
480
|
port 0: (value) - ; channel: output_docs
|
|
481
|
port 1: (value) - ; channel: prefix
|
|
482
|
port 2: (cntrl) OPEN; channel: $
|
|
483
|
|
|
484
|
Apr-24 13:39:43.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
485
|
~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
|
|
486
|
~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
|
|
487
|
~> TaskHandler[jobId: 1842284.srvslshpc001; id: 6; name: trim_galore (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893 started: 1524569233049; exited: -; ]
|
|
488
|
~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
|
|
489
|
~> TaskHandler[jobId: 1842287.srvslshpc001; id: 10; name: trim_galore (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ac/d8cf85904f9bfe0c89a0fb87af576d started: 1524569238044; exited: -; ]
|
|
490
|
Apr-24 13:44:38.960 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
491
|
[process] star
|
|
492
|
status=ACTIVE
|
|
493
|
port 0: (queue) OPEN; channel: reads
|
|
494
|
port 1: (value) - ; channel: index
|
|
495
|
port 2: (value) - ; channel: gtf
|
|
496
|
port 3: (value) - ; channel: wherearemyfiles
|
|
497
|
port 4: (cntrl) OPEN; channel: $
|
|
498
|
|
|
499
|
[process] rseqc
|
|
500
|
status=ACTIVE
|
|
501
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
502
|
port 1: (value) - ; channel: bed12
|
|
503
|
port 2: (cntrl) OPEN; channel: $
|
|
504
|
|
|
505
|
[process] genebody_coverage
|
|
506
|
status=ACTIVE
|
|
507
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
508
|
port 1: (value) - ; channel: bed12
|
|
509
|
port 2: (cntrl) OPEN; channel: $
|
|
510
|
|
|
511
|
[process] preseq
|
|
512
|
status=ACTIVE
|
|
513
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
514
|
port 1: (cntrl) OPEN; channel: $
|
|
515
|
|
|
516
|
[process] markDuplicates
|
|
517
|
status=ACTIVE
|
|
518
|
port 0: (queue) OPEN; channel: bam
|
|
519
|
port 1: (cntrl) OPEN; channel: $
|
|
520
|
|
|
521
|
[process] dupradar
|
|
522
|
status=ACTIVE
|
|
523
|
port 0: (queue) OPEN; channel: bam_md
|
|
524
|
port 1: (value) - ; channel: gtf
|
|
525
|
port 2: (cntrl) OPEN; channel: $
|
|
526
|
|
|
527
|
[process] featureCounts
|
|
528
|
status=ACTIVE
|
|
529
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
530
|
port 1: (value) - ; channel: gtf
|
|
531
|
port 2: (value) - ; channel: biotypes_header
|
|
532
|
port 3: (cntrl) OPEN; channel: $
|
|
533
|
|
|
534
|
[process] merge_featureCounts
|
|
535
|
status=ACTIVE
|
|
536
|
port 0: (value) - ; channel: input_files
|
|
537
|
port 1: (cntrl) OPEN; channel: $
|
|
538
|
|
|
539
|
[process] stringtieFPKM
|
|
540
|
status=ACTIVE
|
|
541
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
542
|
port 1: (value) - ; channel: gtf
|
|
543
|
port 2: (cntrl) OPEN; channel: $
|
|
544
|
|
|
545
|
[process] sample_correlation
|
|
546
|
status=ACTIVE
|
|
547
|
port 0: (value) - ; channel: input_files
|
|
548
|
port 1: (value) - ; channel: num_bams
|
|
549
|
port 2: (value) - ; channel: mdsplot_header
|
|
550
|
port 3: (value) - ; channel: heatmap_header
|
|
551
|
port 4: (cntrl) OPEN; channel: $
|
|
552
|
|
|
553
|
[process] multiqc
|
|
554
|
status=ACTIVE
|
|
555
|
port 0: (value) - ; channel: multiqc_config
|
|
556
|
port 1: (value) - ; channel: fastqc
|
|
557
|
port 2: (value) - ; channel: trimgalore/*
|
|
558
|
port 3: (value) - ; channel: alignment/*
|
|
559
|
port 4: (value) - ; channel: rseqc/*
|
|
560
|
port 5: (value) - ; channel: rseqc/*
|
|
561
|
port 6: (value) - ; channel: preseq/*
|
|
562
|
port 7: (value) - ; channel: dupradar/*
|
|
563
|
port 8: (value) - ; channel: featureCounts/*
|
|
564
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
565
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
566
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
567
|
port 12: (value) - ; channel: software_versions/*
|
|
568
|
port 13: (value) - ; channel: workflow_summary/*
|
|
569
|
port 14: (cntrl) OPEN; channel: $
|
|
570
|
|
|
571
|
[process] output_documentation
|
|
572
|
status=ACTIVE
|
|
573
|
port 0: (value) - ; channel: output_docs
|
|
574
|
port 1: (value) - ; channel: prefix
|
|
575
|
port 2: (cntrl) OPEN; channel: $
|
|
576
|
|
|
577
|
Apr-24 13:44:43.097 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
578
|
~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
|
|
579
|
~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
|
|
580
|
~> TaskHandler[jobId: 1842284.srvslshpc001; id: 6; name: trim_galore (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893 started: 1524569233049; exited: -; ]
|
|
581
|
~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
|
|
582
|
~> TaskHandler[jobId: 1842287.srvslshpc001; id: 10; name: trim_galore (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ac/d8cf85904f9bfe0c89a0fb87af576d started: 1524569238044; exited: -; ]
|
|
583
|
Apr-24 13:49:28.110 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842287.srvslshpc001; id: 10; name: trim_galore (sample37); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ac/d8cf85904f9bfe0c89a0fb87af576d started: 1524569238044; exited: 2018-04-24T11:49:25Z; ]
|
|
584
|
Apr-24 13:49:31.242 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process star (sample37) > jobId: 1842289.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade
|
|
585
|
Apr-24 13:49:31.243 [Task submitter] INFO nextflow.Session - [8f/480101] Submitted process > star (sample37)
|
|
586
|
Apr-24 13:49:38.989 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
587
|
[process] star
|
|
588
|
status=ACTIVE
|
|
589
|
port 0: (queue) OPEN; channel: reads
|
|
590
|
port 1: (value) - ; channel: index
|
|
591
|
port 2: (value) - ; channel: gtf
|
|
592
|
port 3: (value) - ; channel: wherearemyfiles
|
|
593
|
port 4: (cntrl) OPEN; channel: $
|
|
594
|
|
|
595
|
[process] rseqc
|
|
596
|
status=ACTIVE
|
|
597
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
598
|
port 1: (value) - ; channel: bed12
|
|
599
|
port 2: (cntrl) OPEN; channel: $
|
|
600
|
|
|
601
|
[process] genebody_coverage
|
|
602
|
status=ACTIVE
|
|
603
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
604
|
port 1: (value) - ; channel: bed12
|
|
605
|
port 2: (cntrl) OPEN; channel: $
|
|
606
|
|
|
607
|
[process] preseq
|
|
608
|
status=ACTIVE
|
|
609
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
610
|
port 1: (cntrl) OPEN; channel: $
|
|
611
|
|
|
612
|
[process] markDuplicates
|
|
613
|
status=ACTIVE
|
|
614
|
port 0: (queue) OPEN; channel: bam
|
|
615
|
port 1: (cntrl) OPEN; channel: $
|
|
616
|
|
|
617
|
[process] dupradar
|
|
618
|
status=ACTIVE
|
|
619
|
port 0: (queue) OPEN; channel: bam_md
|
|
620
|
port 1: (value) - ; channel: gtf
|
|
621
|
port 2: (cntrl) OPEN; channel: $
|
|
622
|
|
|
623
|
[process] featureCounts
|
|
624
|
status=ACTIVE
|
|
625
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
626
|
port 1: (value) - ; channel: gtf
|
|
627
|
port 2: (value) - ; channel: biotypes_header
|
|
628
|
port 3: (cntrl) OPEN; channel: $
|
|
629
|
|
|
630
|
[process] merge_featureCounts
|
|
631
|
status=ACTIVE
|
|
632
|
port 0: (value) - ; channel: input_files
|
|
633
|
port 1: (cntrl) OPEN; channel: $
|
|
634
|
|
|
635
|
[process] stringtieFPKM
|
|
636
|
status=ACTIVE
|
|
637
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
638
|
port 1: (value) - ; channel: gtf
|
|
639
|
port 2: (cntrl) OPEN; channel: $
|
|
640
|
|
|
641
|
[process] sample_correlation
|
|
642
|
status=ACTIVE
|
|
643
|
port 0: (value) - ; channel: input_files
|
|
644
|
port 1: (value) - ; channel: num_bams
|
|
645
|
port 2: (value) - ; channel: mdsplot_header
|
|
646
|
port 3: (value) - ; channel: heatmap_header
|
|
647
|
port 4: (cntrl) OPEN; channel: $
|
|
648
|
|
|
649
|
[process] multiqc
|
|
650
|
status=ACTIVE
|
|
651
|
port 0: (value) - ; channel: multiqc_config
|
|
652
|
port 1: (value) - ; channel: fastqc
|
|
653
|
port 2: (value) - ; channel: trimgalore/*
|
|
654
|
port 3: (value) - ; channel: alignment/*
|
|
655
|
port 4: (value) - ; channel: rseqc/*
|
|
656
|
port 5: (value) - ; channel: rseqc/*
|
|
657
|
port 6: (value) - ; channel: preseq/*
|
|
658
|
port 7: (value) - ; channel: dupradar/*
|
|
659
|
port 8: (value) - ; channel: featureCounts/*
|
|
660
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
661
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
662
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
663
|
port 12: (value) - ; channel: software_versions/*
|
|
664
|
port 13: (value) - ; channel: workflow_summary/*
|
|
665
|
port 14: (cntrl) OPEN; channel: $
|
|
666
|
|
|
667
|
[process] output_documentation
|
|
668
|
status=ACTIVE
|
|
669
|
port 0: (value) - ; channel: output_docs
|
|
670
|
port 1: (value) - ; channel: prefix
|
|
671
|
port 2: (cntrl) OPEN; channel: $
|
|
672
|
|
|
673
|
Apr-24 13:49:43.110 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
674
|
~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
|
|
675
|
~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
|
|
676
|
~> TaskHandler[jobId: 1842284.srvslshpc001; id: 6; name: trim_galore (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893 started: 1524569233049; exited: -; ]
|
|
677
|
~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
|
|
678
|
~> TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: -; exited: -; ]
|
|
679
|
Apr-24 13:50:28.115 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842284.srvslshpc001; id: 6; name: trim_galore (sample38); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/41/11c319a493ca16b21dbefc387cb893 started: 1524569233049; exited: 2018-04-24T11:50:25Z; ]
|
|
680
|
Apr-24 13:50:28.190 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process star (sample38) > jobId: 1842290.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf
|
|
681
|
Apr-24 13:50:28.191 [Task submitter] INFO nextflow.Session - [98/1630fc] Submitted process > star (sample38)
|
|
682
|
Apr-24 13:54:39.003 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
683
|
[process] star
|
|
684
|
status=ACTIVE
|
|
685
|
port 0: (queue) OPEN; channel: reads
|
|
686
|
port 1: (value) - ; channel: index
|
|
687
|
port 2: (value) - ; channel: gtf
|
|
688
|
port 3: (value) - ; channel: wherearemyfiles
|
|
689
|
port 4: (cntrl) OPEN; channel: $
|
|
690
|
|
|
691
|
[process] rseqc
|
|
692
|
status=ACTIVE
|
|
693
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
694
|
port 1: (value) - ; channel: bed12
|
|
695
|
port 2: (cntrl) OPEN; channel: $
|
|
696
|
|
|
697
|
[process] genebody_coverage
|
|
698
|
status=ACTIVE
|
|
699
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
700
|
port 1: (value) - ; channel: bed12
|
|
701
|
port 2: (cntrl) OPEN; channel: $
|
|
702
|
|
|
703
|
[process] preseq
|
|
704
|
status=ACTIVE
|
|
705
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
706
|
port 1: (cntrl) OPEN; channel: $
|
|
707
|
|
|
708
|
[process] markDuplicates
|
|
709
|
status=ACTIVE
|
|
710
|
port 0: (queue) OPEN; channel: bam
|
|
711
|
port 1: (cntrl) OPEN; channel: $
|
|
712
|
|
|
713
|
[process] dupradar
|
|
714
|
status=ACTIVE
|
|
715
|
port 0: (queue) OPEN; channel: bam_md
|
|
716
|
port 1: (value) - ; channel: gtf
|
|
717
|
port 2: (cntrl) OPEN; channel: $
|
|
718
|
|
|
719
|
[process] featureCounts
|
|
720
|
status=ACTIVE
|
|
721
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
722
|
port 1: (value) - ; channel: gtf
|
|
723
|
port 2: (value) - ; channel: biotypes_header
|
|
724
|
port 3: (cntrl) OPEN; channel: $
|
|
725
|
|
|
726
|
[process] merge_featureCounts
|
|
727
|
status=ACTIVE
|
|
728
|
port 0: (value) - ; channel: input_files
|
|
729
|
port 1: (cntrl) OPEN; channel: $
|
|
730
|
|
|
731
|
[process] stringtieFPKM
|
|
732
|
status=ACTIVE
|
|
733
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
734
|
port 1: (value) - ; channel: gtf
|
|
735
|
port 2: (cntrl) OPEN; channel: $
|
|
736
|
|
|
737
|
[process] sample_correlation
|
|
738
|
status=ACTIVE
|
|
739
|
port 0: (value) - ; channel: input_files
|
|
740
|
port 1: (value) - ; channel: num_bams
|
|
741
|
port 2: (value) - ; channel: mdsplot_header
|
|
742
|
port 3: (value) - ; channel: heatmap_header
|
|
743
|
port 4: (cntrl) OPEN; channel: $
|
|
744
|
|
|
745
|
[process] multiqc
|
|
746
|
status=ACTIVE
|
|
747
|
port 0: (value) - ; channel: multiqc_config
|
|
748
|
port 1: (value) - ; channel: fastqc
|
|
749
|
port 2: (value) - ; channel: trimgalore/*
|
|
750
|
port 3: (value) - ; channel: alignment/*
|
|
751
|
port 4: (value) - ; channel: rseqc/*
|
|
752
|
port 5: (value) - ; channel: rseqc/*
|
|
753
|
port 6: (value) - ; channel: preseq/*
|
|
754
|
port 7: (value) - ; channel: dupradar/*
|
|
755
|
port 8: (value) - ; channel: featureCounts/*
|
|
756
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
757
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
758
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
759
|
port 12: (value) - ; channel: software_versions/*
|
|
760
|
port 13: (value) - ; channel: workflow_summary/*
|
|
761
|
port 14: (cntrl) OPEN; channel: $
|
|
762
|
|
|
763
|
[process] output_documentation
|
|
764
|
status=ACTIVE
|
|
765
|
port 0: (value) - ; channel: output_docs
|
|
766
|
port 1: (value) - ; channel: prefix
|
|
767
|
port 2: (cntrl) OPEN; channel: $
|
|
768
|
|
|
769
|
Apr-24 13:54:43.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
770
|
~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
|
|
771
|
~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
|
|
772
|
~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
|
|
773
|
~> TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: 1524570668114; exited: -; ]
|
|
774
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: -; exited: -; ]
|
|
775
|
Apr-24 13:59:39.007 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
776
|
[process] star
|
|
777
|
status=ACTIVE
|
|
778
|
port 0: (queue) OPEN; channel: reads
|
|
779
|
port 1: (value) - ; channel: index
|
|
780
|
port 2: (value) - ; channel: gtf
|
|
781
|
port 3: (value) - ; channel: wherearemyfiles
|
|
782
|
port 4: (cntrl) OPEN; channel: $
|
|
783
|
|
|
784
|
[process] rseqc
|
|
785
|
status=ACTIVE
|
|
786
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
787
|
port 1: (value) - ; channel: bed12
|
|
788
|
port 2: (cntrl) OPEN; channel: $
|
|
789
|
|
|
790
|
[process] genebody_coverage
|
|
791
|
status=ACTIVE
|
|
792
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
793
|
port 1: (value) - ; channel: bed12
|
|
794
|
port 2: (cntrl) OPEN; channel: $
|
|
795
|
|
|
796
|
[process] preseq
|
|
797
|
status=ACTIVE
|
|
798
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
799
|
port 1: (cntrl) OPEN; channel: $
|
|
800
|
|
|
801
|
[process] markDuplicates
|
|
802
|
status=ACTIVE
|
|
803
|
port 0: (queue) OPEN; channel: bam
|
|
804
|
port 1: (cntrl) OPEN; channel: $
|
|
805
|
|
|
806
|
[process] dupradar
|
|
807
|
status=ACTIVE
|
|
808
|
port 0: (queue) OPEN; channel: bam_md
|
|
809
|
port 1: (value) - ; channel: gtf
|
|
810
|
port 2: (cntrl) OPEN; channel: $
|
|
811
|
|
|
812
|
[process] featureCounts
|
|
813
|
status=ACTIVE
|
|
814
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
815
|
port 1: (value) - ; channel: gtf
|
|
816
|
port 2: (value) - ; channel: biotypes_header
|
|
817
|
port 3: (cntrl) OPEN; channel: $
|
|
818
|
|
|
819
|
[process] merge_featureCounts
|
|
820
|
status=ACTIVE
|
|
821
|
port 0: (value) - ; channel: input_files
|
|
822
|
port 1: (cntrl) OPEN; channel: $
|
|
823
|
|
|
824
|
[process] stringtieFPKM
|
|
825
|
status=ACTIVE
|
|
826
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
827
|
port 1: (value) - ; channel: gtf
|
|
828
|
port 2: (cntrl) OPEN; channel: $
|
|
829
|
|
|
830
|
[process] sample_correlation
|
|
831
|
status=ACTIVE
|
|
832
|
port 0: (value) - ; channel: input_files
|
|
833
|
port 1: (value) - ; channel: num_bams
|
|
834
|
port 2: (value) - ; channel: mdsplot_header
|
|
835
|
port 3: (value) - ; channel: heatmap_header
|
|
836
|
port 4: (cntrl) OPEN; channel: $
|
|
837
|
|
|
838
|
[process] multiqc
|
|
839
|
status=ACTIVE
|
|
840
|
port 0: (value) - ; channel: multiqc_config
|
|
841
|
port 1: (value) - ; channel: fastqc
|
|
842
|
port 2: (value) - ; channel: trimgalore/*
|
|
843
|
port 3: (value) - ; channel: alignment/*
|
|
844
|
port 4: (value) - ; channel: rseqc/*
|
|
845
|
port 5: (value) - ; channel: rseqc/*
|
|
846
|
port 6: (value) - ; channel: preseq/*
|
|
847
|
port 7: (value) - ; channel: dupradar/*
|
|
848
|
port 8: (value) - ; channel: featureCounts/*
|
|
849
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
850
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
851
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
852
|
port 12: (value) - ; channel: software_versions/*
|
|
853
|
port 13: (value) - ; channel: workflow_summary/*
|
|
854
|
port 14: (cntrl) OPEN; channel: $
|
|
855
|
|
|
856
|
[process] output_documentation
|
|
857
|
status=ACTIVE
|
|
858
|
port 0: (value) - ; channel: output_docs
|
|
859
|
port 1: (value) - ; channel: prefix
|
|
860
|
port 2: (cntrl) OPEN; channel: $
|
|
861
|
|
|
862
|
Apr-24 13:59:43.127 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
863
|
~> TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: -; ]
|
|
864
|
~> TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: -; ]
|
|
865
|
~> TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: -; ]
|
|
866
|
~> TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: 1524570668114; exited: -; ]
|
|
867
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: -; exited: -; ]
|
|
868
|
Apr-24 14:01:18.131 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842281.srvslshpc001; id: 8; name: trim_galore (sample40); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4d/c3b6f72cecda025cca9a6301fc95b7 started: 1524569233039; exited: 2018-04-24T12:01:17Z; ]
|
|
869
|
Apr-24 14:01:18.224 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process star (sample40) > jobId: 1842291.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922
|
|
870
|
Apr-24 14:01:18.225 [Task submitter] INFO nextflow.Session - [31/a2fe86] Submitted process > star (sample40)
|
|
871
|
Apr-24 14:02:28.132 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842280.srvslshpc001; id: 9; name: trim_galore (sample41); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/7f/3e00fc893a29a94641a9473c25c013 started: 1524569233034; exited: 2018-04-24T12:02:25Z; ]
|
|
872
|
Apr-24 14:02:28.275 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process star (sample41) > jobId: 1842292.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967
|
|
873
|
Apr-24 14:02:28.277 [Task submitter] INFO nextflow.Session - [25/113d9b] Submitted process > star (sample41)
|
|
874
|
Apr-24 14:03:53.131 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842286.srvslshpc001; id: 7; name: trim_galore (sample39); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/6f/55d00a650e474aa0e66fd5b6f11e25 started: 1524569238040; exited: 2018-04-24T12:03:51Z; ]
|
|
875
|
Apr-24 14:03:53.151 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: trim_galore)
|
|
876
|
Apr-24 14:03:53.212 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process star (sample39) > jobId: 1842293.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317
|
|
877
|
Apr-24 14:03:53.213 [Task submitter] INFO nextflow.Session - [a7/97254c] Submitted process > star (sample39)
|
|
878
|
Apr-24 14:04:39.102 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
879
|
[process] rseqc
|
|
880
|
status=ACTIVE
|
|
881
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
882
|
port 1: (value) - ; channel: bed12
|
|
883
|
port 2: (cntrl) OPEN; channel: $
|
|
884
|
|
|
885
|
[process] genebody_coverage
|
|
886
|
status=ACTIVE
|
|
887
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
888
|
port 1: (value) - ; channel: bed12
|
|
889
|
port 2: (cntrl) OPEN; channel: $
|
|
890
|
|
|
891
|
[process] preseq
|
|
892
|
status=ACTIVE
|
|
893
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
894
|
port 1: (cntrl) OPEN; channel: $
|
|
895
|
|
|
896
|
[process] markDuplicates
|
|
897
|
status=ACTIVE
|
|
898
|
port 0: (queue) OPEN; channel: bam
|
|
899
|
port 1: (cntrl) OPEN; channel: $
|
|
900
|
|
|
901
|
[process] dupradar
|
|
902
|
status=ACTIVE
|
|
903
|
port 0: (queue) OPEN; channel: bam_md
|
|
904
|
port 1: (value) - ; channel: gtf
|
|
905
|
port 2: (cntrl) OPEN; channel: $
|
|
906
|
|
|
907
|
[process] featureCounts
|
|
908
|
status=ACTIVE
|
|
909
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
910
|
port 1: (value) - ; channel: gtf
|
|
911
|
port 2: (value) - ; channel: biotypes_header
|
|
912
|
port 3: (cntrl) OPEN; channel: $
|
|
913
|
|
|
914
|
[process] merge_featureCounts
|
|
915
|
status=ACTIVE
|
|
916
|
port 0: (value) - ; channel: input_files
|
|
917
|
port 1: (cntrl) OPEN; channel: $
|
|
918
|
|
|
919
|
[process] stringtieFPKM
|
|
920
|
status=ACTIVE
|
|
921
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
922
|
port 1: (value) - ; channel: gtf
|
|
923
|
port 2: (cntrl) OPEN; channel: $
|
|
924
|
|
|
925
|
[process] sample_correlation
|
|
926
|
status=ACTIVE
|
|
927
|
port 0: (value) - ; channel: input_files
|
|
928
|
port 1: (value) - ; channel: num_bams
|
|
929
|
port 2: (value) - ; channel: mdsplot_header
|
|
930
|
port 3: (value) - ; channel: heatmap_header
|
|
931
|
port 4: (cntrl) OPEN; channel: $
|
|
932
|
|
|
933
|
[process] multiqc
|
|
934
|
status=ACTIVE
|
|
935
|
port 0: (value) - ; channel: multiqc_config
|
|
936
|
port 1: (value) - ; channel: fastqc
|
|
937
|
port 2: (value) - ; channel: trimgalore/*
|
|
938
|
port 3: (value) - ; channel: alignment/*
|
|
939
|
port 4: (value) - ; channel: rseqc/*
|
|
940
|
port 5: (value) - ; channel: rseqc/*
|
|
941
|
port 6: (value) - ; channel: preseq/*
|
|
942
|
port 7: (value) - ; channel: dupradar/*
|
|
943
|
port 8: (value) - ; channel: featureCounts/*
|
|
944
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
945
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
946
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
947
|
port 12: (value) - ; channel: software_versions/*
|
|
948
|
port 13: (value) - ; channel: workflow_summary/*
|
|
949
|
port 14: (cntrl) OPEN; channel: $
|
|
950
|
|
|
951
|
[process] output_documentation
|
|
952
|
status=ACTIVE
|
|
953
|
port 0: (value) - ; channel: output_docs
|
|
954
|
port 1: (value) - ; channel: prefix
|
|
955
|
port 2: (cntrl) OPEN; channel: $
|
|
956
|
|
|
957
|
Apr-24 14:04:43.136 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
958
|
~> TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: 1524570668114; exited: -; ]
|
|
959
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: -; exited: -; ]
|
|
960
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: -; exited: -; ]
|
|
961
|
~> TaskHandler[jobId: 1842292.srvslshpc001; id: 16; name: star (sample41); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967 started: -; exited: -; ]
|
|
962
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: -; exited: -; ]
|
|
963
|
Apr-24 14:09:39.190 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
964
|
[process] rseqc
|
|
965
|
status=ACTIVE
|
|
966
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
967
|
port 1: (value) - ; channel: bed12
|
|
968
|
port 2: (cntrl) OPEN; channel: $
|
|
969
|
|
|
970
|
[process] genebody_coverage
|
|
971
|
status=ACTIVE
|
|
972
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
973
|
port 1: (value) - ; channel: bed12
|
|
974
|
port 2: (cntrl) OPEN; channel: $
|
|
975
|
|
|
976
|
[process] preseq
|
|
977
|
status=ACTIVE
|
|
978
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
979
|
port 1: (cntrl) OPEN; channel: $
|
|
980
|
|
|
981
|
[process] markDuplicates
|
|
982
|
status=ACTIVE
|
|
983
|
port 0: (queue) OPEN; channel: bam
|
|
984
|
port 1: (cntrl) OPEN; channel: $
|
|
985
|
|
|
986
|
[process] dupradar
|
|
987
|
status=ACTIVE
|
|
988
|
port 0: (queue) OPEN; channel: bam_md
|
|
989
|
port 1: (value) - ; channel: gtf
|
|
990
|
port 2: (cntrl) OPEN; channel: $
|
|
991
|
|
|
992
|
[process] featureCounts
|
|
993
|
status=ACTIVE
|
|
994
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
995
|
port 1: (value) - ; channel: gtf
|
|
996
|
port 2: (value) - ; channel: biotypes_header
|
|
997
|
port 3: (cntrl) OPEN; channel: $
|
|
998
|
|
|
999
|
[process] merge_featureCounts
|
|
1000
|
status=ACTIVE
|
|
1001
|
port 0: (value) - ; channel: input_files
|
|
1002
|
port 1: (cntrl) OPEN; channel: $
|
|
1003
|
|
|
1004
|
[process] stringtieFPKM
|
|
1005
|
status=ACTIVE
|
|
1006
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1007
|
port 1: (value) - ; channel: gtf
|
|
1008
|
port 2: (cntrl) OPEN; channel: $
|
|
1009
|
|
|
1010
|
[process] sample_correlation
|
|
1011
|
status=ACTIVE
|
|
1012
|
port 0: (value) - ; channel: input_files
|
|
1013
|
port 1: (value) - ; channel: num_bams
|
|
1014
|
port 2: (value) - ; channel: mdsplot_header
|
|
1015
|
port 3: (value) - ; channel: heatmap_header
|
|
1016
|
port 4: (cntrl) OPEN; channel: $
|
|
1017
|
|
|
1018
|
[process] multiqc
|
|
1019
|
status=ACTIVE
|
|
1020
|
port 0: (value) - ; channel: multiqc_config
|
|
1021
|
port 1: (value) - ; channel: fastqc
|
|
1022
|
port 2: (value) - ; channel: trimgalore/*
|
|
1023
|
port 3: (value) - ; channel: alignment/*
|
|
1024
|
port 4: (value) - ; channel: rseqc/*
|
|
1025
|
port 5: (value) - ; channel: rseqc/*
|
|
1026
|
port 6: (value) - ; channel: preseq/*
|
|
1027
|
port 7: (value) - ; channel: dupradar/*
|
|
1028
|
port 8: (value) - ; channel: featureCounts/*
|
|
1029
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1030
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1031
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1032
|
port 12: (value) - ; channel: software_versions/*
|
|
1033
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1034
|
port 14: (cntrl) OPEN; channel: $
|
|
1035
|
|
|
1036
|
[process] output_documentation
|
|
1037
|
status=ACTIVE
|
|
1038
|
port 0: (value) - ; channel: output_docs
|
|
1039
|
port 1: (value) - ; channel: prefix
|
|
1040
|
port 2: (cntrl) OPEN; channel: $
|
|
1041
|
|
|
1042
|
Apr-24 14:09:43.142 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
1043
|
~> TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: 1524570668114; exited: -; ]
|
|
1044
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: -; exited: -; ]
|
|
1045
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: -; exited: -; ]
|
|
1046
|
~> TaskHandler[jobId: 1842292.srvslshpc001; id: 16; name: star (sample41); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967 started: -; exited: -; ]
|
|
1047
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: -; exited: -; ]
|
|
1048
|
Apr-24 14:14:39.197 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1049
|
[process] rseqc
|
|
1050
|
status=ACTIVE
|
|
1051
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1052
|
port 1: (value) - ; channel: bed12
|
|
1053
|
port 2: (cntrl) OPEN; channel: $
|
|
1054
|
|
|
1055
|
[process] genebody_coverage
|
|
1056
|
status=ACTIVE
|
|
1057
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1058
|
port 1: (value) - ; channel: bed12
|
|
1059
|
port 2: (cntrl) OPEN; channel: $
|
|
1060
|
|
|
1061
|
[process] preseq
|
|
1062
|
status=ACTIVE
|
|
1063
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1064
|
port 1: (cntrl) OPEN; channel: $
|
|
1065
|
|
|
1066
|
[process] markDuplicates
|
|
1067
|
status=ACTIVE
|
|
1068
|
port 0: (queue) OPEN; channel: bam
|
|
1069
|
port 1: (cntrl) OPEN; channel: $
|
|
1070
|
|
|
1071
|
[process] dupradar
|
|
1072
|
status=ACTIVE
|
|
1073
|
port 0: (queue) OPEN; channel: bam_md
|
|
1074
|
port 1: (value) - ; channel: gtf
|
|
1075
|
port 2: (cntrl) OPEN; channel: $
|
|
1076
|
|
|
1077
|
[process] featureCounts
|
|
1078
|
status=ACTIVE
|
|
1079
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1080
|
port 1: (value) - ; channel: gtf
|
|
1081
|
port 2: (value) - ; channel: biotypes_header
|
|
1082
|
port 3: (cntrl) OPEN; channel: $
|
|
1083
|
|
|
1084
|
[process] merge_featureCounts
|
|
1085
|
status=ACTIVE
|
|
1086
|
port 0: (value) - ; channel: input_files
|
|
1087
|
port 1: (cntrl) OPEN; channel: $
|
|
1088
|
|
|
1089
|
[process] stringtieFPKM
|
|
1090
|
status=ACTIVE
|
|
1091
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1092
|
port 1: (value) - ; channel: gtf
|
|
1093
|
port 2: (cntrl) OPEN; channel: $
|
|
1094
|
|
|
1095
|
[process] sample_correlation
|
|
1096
|
status=ACTIVE
|
|
1097
|
port 0: (value) - ; channel: input_files
|
|
1098
|
port 1: (value) - ; channel: num_bams
|
|
1099
|
port 2: (value) - ; channel: mdsplot_header
|
|
1100
|
port 3: (value) - ; channel: heatmap_header
|
|
1101
|
port 4: (cntrl) OPEN; channel: $
|
|
1102
|
|
|
1103
|
[process] multiqc
|
|
1104
|
status=ACTIVE
|
|
1105
|
port 0: (value) - ; channel: multiqc_config
|
|
1106
|
port 1: (value) - ; channel: fastqc
|
|
1107
|
port 2: (value) - ; channel: trimgalore/*
|
|
1108
|
port 3: (value) - ; channel: alignment/*
|
|
1109
|
port 4: (value) - ; channel: rseqc/*
|
|
1110
|
port 5: (value) - ; channel: rseqc/*
|
|
1111
|
port 6: (value) - ; channel: preseq/*
|
|
1112
|
port 7: (value) - ; channel: dupradar/*
|
|
1113
|
port 8: (value) - ; channel: featureCounts/*
|
|
1114
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1115
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1116
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1117
|
port 12: (value) - ; channel: software_versions/*
|
|
1118
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1119
|
port 14: (cntrl) OPEN; channel: $
|
|
1120
|
|
|
1121
|
[process] output_documentation
|
|
1122
|
status=ACTIVE
|
|
1123
|
port 0: (value) - ; channel: output_docs
|
|
1124
|
port 1: (value) - ; channel: prefix
|
|
1125
|
port 2: (cntrl) OPEN; channel: $
|
|
1126
|
|
|
1127
|
Apr-24 14:14:43.150 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below
|
|
1128
|
~> TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: 1524570668114; exited: -; ]
|
|
1129
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: -; exited: -; ]
|
|
1130
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: -; exited: -; ]
|
|
1131
|
~> TaskHandler[jobId: 1842292.srvslshpc001; id: 16; name: star (sample41); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967 started: -; exited: -; ]
|
|
1132
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: -; exited: -; ]
|
|
1133
|
Apr-24 14:16:48.154 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842289.srvslshpc001; id: 13; name: star (sample37); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8f/4801019271bdf8895608ecc324bade started: 1524570668114; exited: 2018-04-24T12:16:48Z; ]
|
|
1134
|
Apr-24 14:16:48.686 [Actor Thread 38] INFO nextflow.Nextflow - Passed alignment > star (sample37) >> 95.88% <<
|
|
1135
|
Apr-24 14:16:51.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process preseq (sample37AlignedByCoord.out) > jobId: 1842295.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7
|
|
1136
|
Apr-24 14:16:51.776 [Task submitter] INFO nextflow.Session - [48/f5722e] Submitted process > preseq (sample37AlignedByCoord.out)
|
|
1137
|
Apr-24 14:16:51.820 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process markDuplicates (sample37AlignedByCoord.out) > jobId: 1842296.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51
|
|
1138
|
Apr-24 14:16:51.821 [Task submitter] INFO nextflow.Session - [86/089c84] Submitted process > markDuplicates (sample37AlignedByCoord.out)
|
|
1139
|
Apr-24 14:16:51.868 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process stringtieFPKM (sample37AlignedByCoord.out) > jobId: 1842297.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/5e/8884c765ab32c26942f59716c607b0
|
|
1140
|
Apr-24 14:16:51.869 [Task submitter] INFO nextflow.Session - [5e/8884c7] Submitted process > stringtieFPKM (sample37AlignedByCoord.out)
|
|
1141
|
Apr-24 14:16:51.904 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process featureCounts (sample37AlignedByCoord.out) > jobId: 1842298.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee
|
|
1142
|
Apr-24 14:16:51.905 [Task submitter] INFO nextflow.Session - [4e/0b1fbd] Submitted process > featureCounts (sample37AlignedByCoord.out)
|
|
1143
|
Apr-24 14:16:51.971 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process genebody_coverage (sample37AlignedByCoord.out) > jobId: 1842299.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3
|
|
1144
|
Apr-24 14:16:51.972 [Task submitter] INFO nextflow.Session - [df/c16f93] Submitted process > genebody_coverage (sample37AlignedByCoord.out)
|
|
1145
|
Apr-24 14:16:52.023 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process rseqc (sample37AlignedByCoord.out) > jobId: 1842300.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797
|
|
1146
|
Apr-24 14:16:52.023 [Task submitter] INFO nextflow.Session - [1d/848400] Submitted process > rseqc (sample37AlignedByCoord.out)
|
|
1147
|
Apr-24 14:19:39.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1148
|
[process] rseqc
|
|
1149
|
status=ACTIVE
|
|
1150
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1151
|
port 1: (value) - ; channel: bed12
|
|
1152
|
port 2: (cntrl) OPEN; channel: $
|
|
1153
|
|
|
1154
|
[process] genebody_coverage
|
|
1155
|
status=ACTIVE
|
|
1156
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1157
|
port 1: (value) - ; channel: bed12
|
|
1158
|
port 2: (cntrl) OPEN; channel: $
|
|
1159
|
|
|
1160
|
[process] preseq
|
|
1161
|
status=ACTIVE
|
|
1162
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1163
|
port 1: (cntrl) OPEN; channel: $
|
|
1164
|
|
|
1165
|
[process] markDuplicates
|
|
1166
|
status=ACTIVE
|
|
1167
|
port 0: (queue) OPEN; channel: bam
|
|
1168
|
port 1: (cntrl) OPEN; channel: $
|
|
1169
|
|
|
1170
|
[process] dupradar
|
|
1171
|
status=ACTIVE
|
|
1172
|
port 0: (queue) OPEN; channel: bam_md
|
|
1173
|
port 1: (value) - ; channel: gtf
|
|
1174
|
port 2: (cntrl) OPEN; channel: $
|
|
1175
|
|
|
1176
|
[process] featureCounts
|
|
1177
|
status=ACTIVE
|
|
1178
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1179
|
port 1: (value) - ; channel: gtf
|
|
1180
|
port 2: (value) - ; channel: biotypes_header
|
|
1181
|
port 3: (cntrl) OPEN; channel: $
|
|
1182
|
|
|
1183
|
[process] merge_featureCounts
|
|
1184
|
status=ACTIVE
|
|
1185
|
port 0: (value) - ; channel: input_files
|
|
1186
|
port 1: (cntrl) OPEN; channel: $
|
|
1187
|
|
|
1188
|
[process] stringtieFPKM
|
|
1189
|
status=ACTIVE
|
|
1190
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1191
|
port 1: (value) - ; channel: gtf
|
|
1192
|
port 2: (cntrl) OPEN; channel: $
|
|
1193
|
|
|
1194
|
[process] sample_correlation
|
|
1195
|
status=ACTIVE
|
|
1196
|
port 0: (value) - ; channel: input_files
|
|
1197
|
port 1: (value) - ; channel: num_bams
|
|
1198
|
port 2: (value) - ; channel: mdsplot_header
|
|
1199
|
port 3: (value) - ; channel: heatmap_header
|
|
1200
|
port 4: (cntrl) OPEN; channel: $
|
|
1201
|
|
|
1202
|
[process] multiqc
|
|
1203
|
status=ACTIVE
|
|
1204
|
port 0: (value) - ; channel: multiqc_config
|
|
1205
|
port 1: (value) - ; channel: fastqc
|
|
1206
|
port 2: (value) - ; channel: trimgalore/*
|
|
1207
|
port 3: (value) - ; channel: alignment/*
|
|
1208
|
port 4: (value) - ; channel: rseqc/*
|
|
1209
|
port 5: (value) - ; channel: rseqc/*
|
|
1210
|
port 6: (value) - ; channel: preseq/*
|
|
1211
|
port 7: (value) - ; channel: dupradar/*
|
|
1212
|
port 8: (value) - ; channel: featureCounts/*
|
|
1213
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1214
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1215
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1216
|
port 12: (value) - ; channel: software_versions/*
|
|
1217
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1218
|
port 14: (cntrl) OPEN; channel: $
|
|
1219
|
|
|
1220
|
[process] output_documentation
|
|
1221
|
status=ACTIVE
|
|
1222
|
port 0: (value) - ; channel: output_docs
|
|
1223
|
port 1: (value) - ; channel: prefix
|
|
1224
|
port 2: (cntrl) OPEN; channel: $
|
|
1225
|
|
|
1226
|
Apr-24 14:19:43.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below
|
|
1227
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: -; ]
|
|
1228
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: 1524572088172; exited: -; ]
|
|
1229
|
~> TaskHandler[jobId: 1842292.srvslshpc001; id: 16; name: star (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967 started: 1524572108154; exited: -; ]
|
|
1230
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: -; ]
|
|
1231
|
~> TaskHandler[jobId: 1842295.srvslshpc001; id: 22; name: preseq (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7 started: -; exited: -; ]
|
|
1232
|
~> TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: -; exited: -; ]
|
|
1233
|
~> TaskHandler[jobId: 1842297.srvslshpc001; id: 20; name: stringtieFPKM (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/5e/8884c765ab32c26942f59716c607b0 started: -; exited: -; ]
|
|
1234
|
~> TaskHandler[jobId: 1842298.srvslshpc001; id: 18; name: featureCounts (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee started: -; exited: -; ]
|
|
1235
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: -; exited: -; ]
|
|
1236
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: -; exited: -; ]
|
|
1237
|
Apr-24 14:24:39.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1238
|
[process] rseqc
|
|
1239
|
status=ACTIVE
|
|
1240
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1241
|
port 1: (value) - ; channel: bed12
|
|
1242
|
port 2: (cntrl) OPEN; channel: $
|
|
1243
|
|
|
1244
|
[process] genebody_coverage
|
|
1245
|
status=ACTIVE
|
|
1246
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1247
|
port 1: (value) - ; channel: bed12
|
|
1248
|
port 2: (cntrl) OPEN; channel: $
|
|
1249
|
|
|
1250
|
[process] preseq
|
|
1251
|
status=ACTIVE
|
|
1252
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1253
|
port 1: (cntrl) OPEN; channel: $
|
|
1254
|
|
|
1255
|
[process] markDuplicates
|
|
1256
|
status=ACTIVE
|
|
1257
|
port 0: (queue) OPEN; channel: bam
|
|
1258
|
port 1: (cntrl) OPEN; channel: $
|
|
1259
|
|
|
1260
|
[process] dupradar
|
|
1261
|
status=ACTIVE
|
|
1262
|
port 0: (queue) OPEN; channel: bam_md
|
|
1263
|
port 1: (value) - ; channel: gtf
|
|
1264
|
port 2: (cntrl) OPEN; channel: $
|
|
1265
|
|
|
1266
|
[process] featureCounts
|
|
1267
|
status=ACTIVE
|
|
1268
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1269
|
port 1: (value) - ; channel: gtf
|
|
1270
|
port 2: (value) - ; channel: biotypes_header
|
|
1271
|
port 3: (cntrl) OPEN; channel: $
|
|
1272
|
|
|
1273
|
[process] merge_featureCounts
|
|
1274
|
status=ACTIVE
|
|
1275
|
port 0: (value) - ; channel: input_files
|
|
1276
|
port 1: (cntrl) OPEN; channel: $
|
|
1277
|
|
|
1278
|
[process] stringtieFPKM
|
|
1279
|
status=ACTIVE
|
|
1280
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1281
|
port 1: (value) - ; channel: gtf
|
|
1282
|
port 2: (cntrl) OPEN; channel: $
|
|
1283
|
|
|
1284
|
[process] sample_correlation
|
|
1285
|
status=ACTIVE
|
|
1286
|
port 0: (value) - ; channel: input_files
|
|
1287
|
port 1: (value) - ; channel: num_bams
|
|
1288
|
port 2: (value) - ; channel: mdsplot_header
|
|
1289
|
port 3: (value) - ; channel: heatmap_header
|
|
1290
|
port 4: (cntrl) OPEN; channel: $
|
|
1291
|
|
|
1292
|
[process] multiqc
|
|
1293
|
status=ACTIVE
|
|
1294
|
port 0: (value) - ; channel: multiqc_config
|
|
1295
|
port 1: (value) - ; channel: fastqc
|
|
1296
|
port 2: (value) - ; channel: trimgalore/*
|
|
1297
|
port 3: (value) - ; channel: alignment/*
|
|
1298
|
port 4: (value) - ; channel: rseqc/*
|
|
1299
|
port 5: (value) - ; channel: rseqc/*
|
|
1300
|
port 6: (value) - ; channel: preseq/*
|
|
1301
|
port 7: (value) - ; channel: dupradar/*
|
|
1302
|
port 8: (value) - ; channel: featureCounts/*
|
|
1303
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1304
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1305
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1306
|
port 12: (value) - ; channel: software_versions/*
|
|
1307
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1308
|
port 14: (cntrl) OPEN; channel: $
|
|
1309
|
|
|
1310
|
[process] output_documentation
|
|
1311
|
status=ACTIVE
|
|
1312
|
port 0: (value) - ; channel: output_docs
|
|
1313
|
port 1: (value) - ; channel: prefix
|
|
1314
|
port 2: (cntrl) OPEN; channel: $
|
|
1315
|
|
|
1316
|
Apr-24 14:24:43.176 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below
|
|
1317
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: -; ]
|
|
1318
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: 1524572088172; exited: -; ]
|
|
1319
|
~> TaskHandler[jobId: 1842292.srvslshpc001; id: 16; name: star (sample41); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967 started: 1524572108154; exited: -; ]
|
|
1320
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: -; ]
|
|
1321
|
~> TaskHandler[jobId: 1842295.srvslshpc001; id: 22; name: preseq (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7 started: -; exited: -; ]
|
|
1322
|
~> TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: -; exited: -; ]
|
|
1323
|
~> TaskHandler[jobId: 1842297.srvslshpc001; id: 20; name: stringtieFPKM (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/5e/8884c765ab32c26942f59716c607b0 started: -; exited: -; ]
|
|
1324
|
~> TaskHandler[jobId: 1842298.srvslshpc001; id: 18; name: featureCounts (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee started: -; exited: -; ]
|
|
1325
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: -; exited: -; ]
|
|
1326
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: -; exited: -; ]
|
|
1327
|
Apr-24 14:29:38.183 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842292.srvslshpc001; id: 16; name: star (sample41); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/25/113d9b4c9788b3bb713df0eff4f967 started: 1524572108154; exited: 2018-04-24T12:29:35Z; ]
|
|
1328
|
Apr-24 14:29:38.722 [Actor Thread 38] INFO nextflow.Nextflow - Passed alignment > star (sample41) >> 97.27% <<
|
|
1329
|
Apr-24 14:29:38.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process markDuplicates (sample41AlignedByCoord.out) > jobId: 1842301.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44
|
|
1330
|
Apr-24 14:29:38.774 [Task submitter] INFO nextflow.Session - [61/b53bbb] Submitted process > markDuplicates (sample41AlignedByCoord.out)
|
|
1331
|
Apr-24 14:29:38.807 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process featureCounts (sample41AlignedByCoord.out) > jobId: 1842302.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b4/fa71eee10b925bb98d1eb73c9710d0
|
|
1332
|
Apr-24 14:29:38.807 [Task submitter] INFO nextflow.Session - [b4/fa71ee] Submitted process > featureCounts (sample41AlignedByCoord.out)
|
|
1333
|
Apr-24 14:29:38.842 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process preseq (sample41AlignedByCoord.out) > jobId: 1842303.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/87/5d9fb641d21df20b01c20e9ccf7ce7
|
|
1334
|
Apr-24 14:29:38.843 [Task submitter] INFO nextflow.Session - [87/5d9fb6] Submitted process > preseq (sample41AlignedByCoord.out)
|
|
1335
|
Apr-24 14:29:38.900 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process stringtieFPKM (sample41AlignedByCoord.out) > jobId: 1842304.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bd/783d842857da1ebbcc7d312829632d
|
|
1336
|
Apr-24 14:29:38.901 [Task submitter] INFO nextflow.Session - [bd/783d84] Submitted process > stringtieFPKM (sample41AlignedByCoord.out)
|
|
1337
|
Apr-24 14:29:38.940 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process rseqc (sample41AlignedByCoord.out) > jobId: 1842305.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a
|
|
1338
|
Apr-24 14:29:38.942 [Task submitter] INFO nextflow.Session - [b0/7aa70c] Submitted process > rseqc (sample41AlignedByCoord.out)
|
|
1339
|
Apr-24 14:29:38.973 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process genebody_coverage (sample41AlignedByCoord.out) > jobId: 1842306.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e
|
|
1340
|
Apr-24 14:29:38.974 [Task submitter] INFO nextflow.Session - [59/f12334] Submitted process > genebody_coverage (sample41AlignedByCoord.out)
|
|
1341
|
Apr-24 14:29:39.307 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1342
|
[process] rseqc
|
|
1343
|
status=ACTIVE
|
|
1344
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1345
|
port 1: (value) - ; channel: bed12
|
|
1346
|
port 2: (cntrl) OPEN; channel: $
|
|
1347
|
|
|
1348
|
[process] genebody_coverage
|
|
1349
|
status=ACTIVE
|
|
1350
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1351
|
port 1: (value) - ; channel: bed12
|
|
1352
|
port 2: (cntrl) OPEN; channel: $
|
|
1353
|
|
|
1354
|
[process] preseq
|
|
1355
|
status=ACTIVE
|
|
1356
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1357
|
port 1: (cntrl) OPEN; channel: $
|
|
1358
|
|
|
1359
|
[process] markDuplicates
|
|
1360
|
status=ACTIVE
|
|
1361
|
port 0: (queue) OPEN; channel: bam
|
|
1362
|
port 1: (cntrl) OPEN; channel: $
|
|
1363
|
|
|
1364
|
[process] dupradar
|
|
1365
|
status=ACTIVE
|
|
1366
|
port 0: (queue) OPEN; channel: bam_md
|
|
1367
|
port 1: (value) - ; channel: gtf
|
|
1368
|
port 2: (cntrl) OPEN; channel: $
|
|
1369
|
|
|
1370
|
[process] featureCounts
|
|
1371
|
status=ACTIVE
|
|
1372
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1373
|
port 1: (value) - ; channel: gtf
|
|
1374
|
port 2: (value) - ; channel: biotypes_header
|
|
1375
|
port 3: (cntrl) OPEN; channel: $
|
|
1376
|
|
|
1377
|
[process] merge_featureCounts
|
|
1378
|
status=ACTIVE
|
|
1379
|
port 0: (value) - ; channel: input_files
|
|
1380
|
port 1: (cntrl) OPEN; channel: $
|
|
1381
|
|
|
1382
|
[process] stringtieFPKM
|
|
1383
|
status=ACTIVE
|
|
1384
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1385
|
port 1: (value) - ; channel: gtf
|
|
1386
|
port 2: (cntrl) OPEN; channel: $
|
|
1387
|
|
|
1388
|
[process] sample_correlation
|
|
1389
|
status=ACTIVE
|
|
1390
|
port 0: (value) - ; channel: input_files
|
|
1391
|
port 1: (value) - ; channel: num_bams
|
|
1392
|
port 2: (value) - ; channel: mdsplot_header
|
|
1393
|
port 3: (value) - ; channel: heatmap_header
|
|
1394
|
port 4: (cntrl) OPEN; channel: $
|
|
1395
|
|
|
1396
|
[process] multiqc
|
|
1397
|
status=ACTIVE
|
|
1398
|
port 0: (value) - ; channel: multiqc_config
|
|
1399
|
port 1: (value) - ; channel: fastqc
|
|
1400
|
port 2: (value) - ; channel: trimgalore/*
|
|
1401
|
port 3: (value) - ; channel: alignment/*
|
|
1402
|
port 4: (value) - ; channel: rseqc/*
|
|
1403
|
port 5: (value) - ; channel: rseqc/*
|
|
1404
|
port 6: (value) - ; channel: preseq/*
|
|
1405
|
port 7: (value) - ; channel: dupradar/*
|
|
1406
|
port 8: (value) - ; channel: featureCounts/*
|
|
1407
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1408
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1409
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1410
|
port 12: (value) - ; channel: software_versions/*
|
|
1411
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1412
|
port 14: (cntrl) OPEN; channel: $
|
|
1413
|
|
|
1414
|
[process] output_documentation
|
|
1415
|
status=ACTIVE
|
|
1416
|
port 0: (value) - ; channel: output_docs
|
|
1417
|
port 1: (value) - ; channel: prefix
|
|
1418
|
port 2: (cntrl) OPEN; channel: $
|
|
1419
|
|
|
1420
|
Apr-24 14:29:43.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 15 -- pending tasks are shown below
|
|
1421
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: -; ]
|
|
1422
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: 1524572088172; exited: -; ]
|
|
1423
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: -; ]
|
|
1424
|
~> TaskHandler[jobId: 1842295.srvslshpc001; id: 22; name: preseq (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7 started: -; exited: -; ]
|
|
1425
|
~> TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: -; exited: -; ]
|
|
1426
|
~> TaskHandler[jobId: 1842297.srvslshpc001; id: 20; name: stringtieFPKM (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/5e/8884c765ab32c26942f59716c607b0 started: -; exited: -; ]
|
|
1427
|
~> TaskHandler[jobId: 1842298.srvslshpc001; id: 18; name: featureCounts (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee started: -; exited: -; ]
|
|
1428
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: -; exited: -; ]
|
|
1429
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: -; exited: -; ]
|
|
1430
|
~> TaskHandler[jobId: 1842301.srvslshpc001; id: 28; name: markDuplicates (sample41AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44 started: -; exited: -; ]
|
|
1431
|
.. remaining tasks omitted.
|
|
1432
|
Apr-24 14:34:39.404 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1433
|
[process] rseqc
|
|
1434
|
status=ACTIVE
|
|
1435
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1436
|
port 1: (value) - ; channel: bed12
|
|
1437
|
port 2: (cntrl) OPEN; channel: $
|
|
1438
|
|
|
1439
|
[process] genebody_coverage
|
|
1440
|
status=ACTIVE
|
|
1441
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1442
|
port 1: (value) - ; channel: bed12
|
|
1443
|
port 2: (cntrl) OPEN; channel: $
|
|
1444
|
|
|
1445
|
[process] preseq
|
|
1446
|
status=ACTIVE
|
|
1447
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1448
|
port 1: (cntrl) OPEN; channel: $
|
|
1449
|
|
|
1450
|
[process] markDuplicates
|
|
1451
|
status=ACTIVE
|
|
1452
|
port 0: (queue) OPEN; channel: bam
|
|
1453
|
port 1: (cntrl) OPEN; channel: $
|
|
1454
|
|
|
1455
|
[process] dupradar
|
|
1456
|
status=ACTIVE
|
|
1457
|
port 0: (queue) OPEN; channel: bam_md
|
|
1458
|
port 1: (value) - ; channel: gtf
|
|
1459
|
port 2: (cntrl) OPEN; channel: $
|
|
1460
|
|
|
1461
|
[process] featureCounts
|
|
1462
|
status=ACTIVE
|
|
1463
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1464
|
port 1: (value) - ; channel: gtf
|
|
1465
|
port 2: (value) - ; channel: biotypes_header
|
|
1466
|
port 3: (cntrl) OPEN; channel: $
|
|
1467
|
|
|
1468
|
[process] merge_featureCounts
|
|
1469
|
status=ACTIVE
|
|
1470
|
port 0: (value) - ; channel: input_files
|
|
1471
|
port 1: (cntrl) OPEN; channel: $
|
|
1472
|
|
|
1473
|
[process] stringtieFPKM
|
|
1474
|
status=ACTIVE
|
|
1475
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1476
|
port 1: (value) - ; channel: gtf
|
|
1477
|
port 2: (cntrl) OPEN; channel: $
|
|
1478
|
|
|
1479
|
[process] sample_correlation
|
|
1480
|
status=ACTIVE
|
|
1481
|
port 0: (value) - ; channel: input_files
|
|
1482
|
port 1: (value) - ; channel: num_bams
|
|
1483
|
port 2: (value) - ; channel: mdsplot_header
|
|
1484
|
port 3: (value) - ; channel: heatmap_header
|
|
1485
|
port 4: (cntrl) OPEN; channel: $
|
|
1486
|
|
|
1487
|
[process] multiqc
|
|
1488
|
status=ACTIVE
|
|
1489
|
port 0: (value) - ; channel: multiqc_config
|
|
1490
|
port 1: (value) - ; channel: fastqc
|
|
1491
|
port 2: (value) - ; channel: trimgalore/*
|
|
1492
|
port 3: (value) - ; channel: alignment/*
|
|
1493
|
port 4: (value) - ; channel: rseqc/*
|
|
1494
|
port 5: (value) - ; channel: rseqc/*
|
|
1495
|
port 6: (value) - ; channel: preseq/*
|
|
1496
|
port 7: (value) - ; channel: dupradar/*
|
|
1497
|
port 8: (value) - ; channel: featureCounts/*
|
|
1498
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1499
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1500
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1501
|
port 12: (value) - ; channel: software_versions/*
|
|
1502
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1503
|
port 14: (cntrl) OPEN; channel: $
|
|
1504
|
|
|
1505
|
[process] output_documentation
|
|
1506
|
status=ACTIVE
|
|
1507
|
port 0: (value) - ; channel: output_docs
|
|
1508
|
port 1: (value) - ; channel: prefix
|
|
1509
|
port 2: (cntrl) OPEN; channel: $
|
|
1510
|
|
|
1511
|
Apr-24 14:34:43.207 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 15 -- pending tasks are shown below
|
|
1512
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: -; ]
|
|
1513
|
~> TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: 1524572088172; exited: -; ]
|
|
1514
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: -; ]
|
|
1515
|
~> TaskHandler[jobId: 1842295.srvslshpc001; id: 22; name: preseq (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7 started: 1524573043191; exited: -; ]
|
|
1516
|
~> TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: 1524573058238; exited: -; ]
|
|
1517
|
~> TaskHandler[jobId: 1842297.srvslshpc001; id: 20; name: stringtieFPKM (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/5e/8884c765ab32c26942f59716c607b0 started: 1524573058240; exited: -; ]
|
|
1518
|
~> TaskHandler[jobId: 1842298.srvslshpc001; id: 18; name: featureCounts (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee started: 1524573058242; exited: -; ]
|
|
1519
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1520
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1521
|
~> TaskHandler[jobId: 1842301.srvslshpc001; id: 28; name: markDuplicates (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44 started: 1524573058249; exited: -; ]
|
|
1522
|
.. remaining tasks omitted.
|
|
1523
|
Apr-24 14:34:58.230 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842291.srvslshpc001; id: 15; name: star (sample40); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/31/a2fe8640d0f8391bc463848ba84922 started: 1524572088172; exited: 2018-04-24T12:34:57Z; ]
|
|
1524
|
Apr-24 14:34:58.271 [Actor Thread 55] INFO nextflow.Nextflow - Passed alignment > star (sample40) >> 97.30% <<
|
|
1525
|
Apr-24 14:35:03.310 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process preseq (sample40AlignedByCoord.out) > jobId: 1842307.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/4046a296be31368e5b1c7996ba140a
|
|
1526
|
Apr-24 14:35:03.311 [Task submitter] INFO nextflow.Session - [b8/4046a2] Submitted process > preseq (sample40AlignedByCoord.out)
|
|
1527
|
Apr-24 14:35:03.337 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process markDuplicates (sample40AlignedByCoord.out) > jobId: 1842308.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a5/d4109cf20280d3aba30aa337921e84
|
|
1528
|
Apr-24 14:35:03.338 [Task submitter] INFO nextflow.Session - [a5/d4109c] Submitted process > markDuplicates (sample40AlignedByCoord.out)
|
|
1529
|
Apr-24 14:35:03.362 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process genebody_coverage (sample40AlignedByCoord.out) > jobId: 1842309.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36
|
|
1530
|
Apr-24 14:35:03.363 [Task submitter] INFO nextflow.Session - [b8/05430f] Submitted process > genebody_coverage (sample40AlignedByCoord.out)
|
|
1531
|
Apr-24 14:35:03.386 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process rseqc (sample40AlignedByCoord.out) > jobId: 1842310.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a
|
|
1532
|
Apr-24 14:35:03.387 [Task submitter] INFO nextflow.Session - [a8/79b168] Submitted process > rseqc (sample40AlignedByCoord.out)
|
|
1533
|
Apr-24 14:35:03.439 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process stringtieFPKM (sample40AlignedByCoord.out) > jobId: 1842311.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/06/9dc499f29b1e9f51e9c6d1988b74e4
|
|
1534
|
Apr-24 14:35:03.440 [Task submitter] INFO nextflow.Session - [06/9dc499] Submitted process > stringtieFPKM (sample40AlignedByCoord.out)
|
|
1535
|
Apr-24 14:35:03.466 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process featureCounts (sample40AlignedByCoord.out) > jobId: 1842312.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/49/d847cba9c32af97ec6720c3fe65818
|
|
1536
|
Apr-24 14:35:03.468 [Task submitter] INFO nextflow.Session - [49/d847cb] Submitted process > featureCounts (sample40AlignedByCoord.out)
|
|
1537
|
Apr-24 14:36:48.215 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842304.srvslshpc001; id: 27; name: stringtieFPKM (sample41AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bd/783d842857da1ebbcc7d312829632d started: 1524573058256; exited: 2018-04-24T12:36:46Z; ]
|
|
1538
|
Apr-24 14:38:08.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842297.srvslshpc001; id: 20; name: stringtieFPKM (sample37AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/5e/8884c765ab32c26942f59716c607b0 started: 1524573058240; exited: 2018-04-24T12:38:03Z; ]
|
|
1539
|
Apr-24 14:39:39.463 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1540
|
[process] rseqc
|
|
1541
|
status=ACTIVE
|
|
1542
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1543
|
port 1: (value) - ; channel: bed12
|
|
1544
|
port 2: (cntrl) OPEN; channel: $
|
|
1545
|
|
|
1546
|
[process] genebody_coverage
|
|
1547
|
status=ACTIVE
|
|
1548
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1549
|
port 1: (value) - ; channel: bed12
|
|
1550
|
port 2: (cntrl) OPEN; channel: $
|
|
1551
|
|
|
1552
|
[process] preseq
|
|
1553
|
status=ACTIVE
|
|
1554
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1555
|
port 1: (cntrl) OPEN; channel: $
|
|
1556
|
|
|
1557
|
[process] markDuplicates
|
|
1558
|
status=ACTIVE
|
|
1559
|
port 0: (queue) OPEN; channel: bam
|
|
1560
|
port 1: (cntrl) OPEN; channel: $
|
|
1561
|
|
|
1562
|
[process] dupradar
|
|
1563
|
status=ACTIVE
|
|
1564
|
port 0: (queue) OPEN; channel: bam_md
|
|
1565
|
port 1: (value) - ; channel: gtf
|
|
1566
|
port 2: (cntrl) OPEN; channel: $
|
|
1567
|
|
|
1568
|
[process] featureCounts
|
|
1569
|
status=ACTIVE
|
|
1570
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1571
|
port 1: (value) - ; channel: gtf
|
|
1572
|
port 2: (value) - ; channel: biotypes_header
|
|
1573
|
port 3: (cntrl) OPEN; channel: $
|
|
1574
|
|
|
1575
|
[process] merge_featureCounts
|
|
1576
|
status=ACTIVE
|
|
1577
|
port 0: (value) - ; channel: input_files
|
|
1578
|
port 1: (cntrl) OPEN; channel: $
|
|
1579
|
|
|
1580
|
[process] stringtieFPKM
|
|
1581
|
status=ACTIVE
|
|
1582
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1583
|
port 1: (value) - ; channel: gtf
|
|
1584
|
port 2: (cntrl) OPEN; channel: $
|
|
1585
|
|
|
1586
|
[process] sample_correlation
|
|
1587
|
status=ACTIVE
|
|
1588
|
port 0: (value) - ; channel: input_files
|
|
1589
|
port 1: (value) - ; channel: num_bams
|
|
1590
|
port 2: (value) - ; channel: mdsplot_header
|
|
1591
|
port 3: (value) - ; channel: heatmap_header
|
|
1592
|
port 4: (cntrl) OPEN; channel: $
|
|
1593
|
|
|
1594
|
[process] multiqc
|
|
1595
|
status=ACTIVE
|
|
1596
|
port 0: (value) - ; channel: multiqc_config
|
|
1597
|
port 1: (value) - ; channel: fastqc
|
|
1598
|
port 2: (value) - ; channel: trimgalore/*
|
|
1599
|
port 3: (value) - ; channel: alignment/*
|
|
1600
|
port 4: (value) - ; channel: rseqc/*
|
|
1601
|
port 5: (value) - ; channel: rseqc/*
|
|
1602
|
port 6: (value) - ; channel: preseq/*
|
|
1603
|
port 7: (value) - ; channel: dupradar/*
|
|
1604
|
port 8: (value) - ; channel: featureCounts/*
|
|
1605
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1606
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1607
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1608
|
port 12: (value) - ; channel: software_versions/*
|
|
1609
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1610
|
port 14: (cntrl) OPEN; channel: $
|
|
1611
|
|
|
1612
|
[process] output_documentation
|
|
1613
|
status=ACTIVE
|
|
1614
|
port 0: (value) - ; channel: output_docs
|
|
1615
|
port 1: (value) - ; channel: prefix
|
|
1616
|
port 2: (cntrl) OPEN; channel: $
|
|
1617
|
|
|
1618
|
Apr-24 14:39:43.227 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 18 -- pending tasks are shown below
|
|
1619
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: -; ]
|
|
1620
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: -; ]
|
|
1621
|
~> TaskHandler[jobId: 1842295.srvslshpc001; id: 22; name: preseq (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7 started: 1524573043191; exited: -; ]
|
|
1622
|
~> TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: 1524573058238; exited: -; ]
|
|
1623
|
~> TaskHandler[jobId: 1842298.srvslshpc001; id: 18; name: featureCounts (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee started: 1524573058242; exited: -; ]
|
|
1624
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1625
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1626
|
~> TaskHandler[jobId: 1842301.srvslshpc001; id: 28; name: markDuplicates (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44 started: 1524573058249; exited: -; ]
|
|
1627
|
~> TaskHandler[jobId: 1842302.srvslshpc001; id: 25; name: featureCounts (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b4/fa71eee10b925bb98d1eb73c9710d0 started: 1524573058251; exited: -; ]
|
|
1628
|
~> TaskHandler[jobId: 1842303.srvslshpc001; id: 26; name: preseq (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/87/5d9fb641d21df20b01c20e9ccf7ce7 started: 1524573058252; exited: -; ]
|
|
1629
|
.. remaining tasks omitted.
|
|
1630
|
Apr-24 14:41:13.238 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842302.srvslshpc001; id: 25; name: featureCounts (sample41AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b4/fa71eee10b925bb98d1eb73c9710d0 started: 1524573058251; exited: 2018-04-24T12:41:08Z; ]
|
|
1631
|
Apr-24 14:42:08.237 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842298.srvslshpc001; id: 18; name: featureCounts (sample37AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/4e/0b1fbdf1ea290e5eb433985da34dee started: 1524573058242; exited: 2018-04-24T12:42:03Z; ]
|
|
1632
|
Apr-24 14:43:38.239 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842303.srvslshpc001; id: 26; name: preseq (sample41AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/87/5d9fb641d21df20b01c20e9ccf7ce7 started: 1524573058252; exited: 2018-04-24T12:43:36Z; ]
|
|
1633
|
Apr-24 14:44:23.240 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842295.srvslshpc001; id: 22; name: preseq (sample37AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/48/f5722eef03ae43001bf579ea9783f7 started: 1524573043191; exited: 2018-04-24T12:44:21Z; ]
|
|
1634
|
Apr-24 14:44:39.557 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1635
|
[process] rseqc
|
|
1636
|
status=ACTIVE
|
|
1637
|
port 0: (queue) OPEN; channel: bam_rseqc
|
|
1638
|
port 1: (value) - ; channel: bed12
|
|
1639
|
port 2: (cntrl) OPEN; channel: $
|
|
1640
|
|
|
1641
|
[process] genebody_coverage
|
|
1642
|
status=ACTIVE
|
|
1643
|
port 0: (queue) OPEN; channel: bam_geneBodyCoverage
|
|
1644
|
port 1: (value) - ; channel: bed12
|
|
1645
|
port 2: (cntrl) OPEN; channel: $
|
|
1646
|
|
|
1647
|
[process] preseq
|
|
1648
|
status=ACTIVE
|
|
1649
|
port 0: (queue) OPEN; channel: bam_preseq
|
|
1650
|
port 1: (cntrl) OPEN; channel: $
|
|
1651
|
|
|
1652
|
[process] markDuplicates
|
|
1653
|
status=ACTIVE
|
|
1654
|
port 0: (queue) OPEN; channel: bam
|
|
1655
|
port 1: (cntrl) OPEN; channel: $
|
|
1656
|
|
|
1657
|
[process] dupradar
|
|
1658
|
status=ACTIVE
|
|
1659
|
port 0: (queue) OPEN; channel: bam_md
|
|
1660
|
port 1: (value) - ; channel: gtf
|
|
1661
|
port 2: (cntrl) OPEN; channel: $
|
|
1662
|
|
|
1663
|
[process] featureCounts
|
|
1664
|
status=ACTIVE
|
|
1665
|
port 0: (queue) OPEN; channel: bam_featurecounts
|
|
1666
|
port 1: (value) - ; channel: gtf
|
|
1667
|
port 2: (value) - ; channel: biotypes_header
|
|
1668
|
port 3: (cntrl) OPEN; channel: $
|
|
1669
|
|
|
1670
|
[process] merge_featureCounts
|
|
1671
|
status=ACTIVE
|
|
1672
|
port 0: (value) - ; channel: input_files
|
|
1673
|
port 1: (cntrl) OPEN; channel: $
|
|
1674
|
|
|
1675
|
[process] stringtieFPKM
|
|
1676
|
status=ACTIVE
|
|
1677
|
port 0: (queue) OPEN; channel: bam_stringtieFPKM
|
|
1678
|
port 1: (value) - ; channel: gtf
|
|
1679
|
port 2: (cntrl) OPEN; channel: $
|
|
1680
|
|
|
1681
|
[process] sample_correlation
|
|
1682
|
status=ACTIVE
|
|
1683
|
port 0: (value) - ; channel: input_files
|
|
1684
|
port 1: (value) - ; channel: num_bams
|
|
1685
|
port 2: (value) - ; channel: mdsplot_header
|
|
1686
|
port 3: (value) - ; channel: heatmap_header
|
|
1687
|
port 4: (cntrl) OPEN; channel: $
|
|
1688
|
|
|
1689
|
[process] multiqc
|
|
1690
|
status=ACTIVE
|
|
1691
|
port 0: (value) - ; channel: multiqc_config
|
|
1692
|
port 1: (value) - ; channel: fastqc
|
|
1693
|
port 2: (value) - ; channel: trimgalore/*
|
|
1694
|
port 3: (value) - ; channel: alignment/*
|
|
1695
|
port 4: (value) - ; channel: rseqc/*
|
|
1696
|
port 5: (value) - ; channel: rseqc/*
|
|
1697
|
port 6: (value) - ; channel: preseq/*
|
|
1698
|
port 7: (value) - ; channel: dupradar/*
|
|
1699
|
port 8: (value) - ; channel: featureCounts/*
|
|
1700
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1701
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1702
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1703
|
port 12: (value) - ; channel: software_versions/*
|
|
1704
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1705
|
port 14: (cntrl) OPEN; channel: $
|
|
1706
|
|
|
1707
|
[process] output_documentation
|
|
1708
|
status=ACTIVE
|
|
1709
|
port 0: (value) - ; channel: output_docs
|
|
1710
|
port 1: (value) - ; channel: prefix
|
|
1711
|
port 2: (cntrl) OPEN; channel: $
|
|
1712
|
|
|
1713
|
Apr-24 14:44:43.246 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 14 -- pending tasks are shown below
|
|
1714
|
~> TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: -; ]
|
|
1715
|
~> TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: -; ]
|
|
1716
|
~> TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: 1524573058238; exited: -; ]
|
|
1717
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1718
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1719
|
~> TaskHandler[jobId: 1842301.srvslshpc001; id: 28; name: markDuplicates (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44 started: 1524573058249; exited: -; ]
|
|
1720
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
1721
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
1722
|
~> TaskHandler[jobId: 1842307.srvslshpc001; id: 31; name: preseq (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/4046a296be31368e5b1c7996ba140a started: 1524573463216; exited: -; ]
|
|
1723
|
~> TaskHandler[jobId: 1842308.srvslshpc001; id: 32; name: markDuplicates (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a5/d4109cf20280d3aba30aa337921e84 started: 1524573463218; exited: -; ]
|
|
1724
|
.. remaining tasks omitted.
|
|
1725
|
Apr-24 14:45:13.254 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842311.srvslshpc001; id: 34; name: stringtieFPKM (sample40AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/06/9dc499f29b1e9f51e9c6d1988b74e4 started: 1524573463223; exited: 2018-04-24T12:45:10Z; ]
|
|
1726
|
Apr-24 14:45:18.252 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842308.srvslshpc001; id: 32; name: markDuplicates (sample40AlignedByCoord.out); status: COMPLETED; exit: 143; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a5/d4109cf20280d3aba30aa337921e84 started: 1524573463218; exited: 2018-04-24T12:45:17Z; ]
|
|
1727
|
Apr-24 14:45:18.269 [Task monitor] INFO nextflow.processor.TaskProcessor - [a5/d4109c] NOTE: Process `markDuplicates (sample40AlignedByCoord.out)` terminated with an error exit status (143) -- Execution is retried (1)
|
|
1728
|
Apr-24 14:45:21.323 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process markDuplicates (sample40AlignedByCoord.out) > jobId: 1842313.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5
|
|
1729
|
Apr-24 14:45:21.324 [Task submitter] INFO nextflow.Session - [b1/cac4bc] Re-submitted process > markDuplicates (sample40AlignedByCoord.out)
|
|
1730
|
Apr-24 14:46:58.282 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842293.srvslshpc001; id: 17; name: star (sample39); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a7/97254c743ef7bddae7eeca43a8c317 started: 1524572108157; exited: 2018-04-24T12:46:54Z; ]
|
|
1731
|
Apr-24 14:46:58.323 [Actor Thread 79] INFO nextflow.Nextflow - Passed alignment > star (sample39) >> 97.57% <<
|
|
1732
|
Apr-24 14:46:58.449 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process stringtieFPKM (sample39AlignedByCoord.out) > jobId: 1842314.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cc/c538b46689497359caf8261fb61dee
|
|
1733
|
Apr-24 14:46:58.450 [Task submitter] INFO nextflow.Session - [cc/c538b4] Submitted process > stringtieFPKM (sample39AlignedByCoord.out)
|
|
1734
|
Apr-24 14:46:58.593 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process markDuplicates (sample39AlignedByCoord.out) > jobId: 1842315.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3
|
|
1735
|
Apr-24 14:46:58.593 [Task submitter] INFO nextflow.Session - [a1/4544b7] Submitted process > markDuplicates (sample39AlignedByCoord.out)
|
|
1736
|
Apr-24 14:46:58.758 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process preseq (sample39AlignedByCoord.out) > jobId: 1842316.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/a48c0c068a40b2a80328ab5eddead4
|
|
1737
|
Apr-24 14:46:58.759 [Task submitter] INFO nextflow.Session - [3b/a48c0c] Submitted process > preseq (sample39AlignedByCoord.out)
|
|
1738
|
Apr-24 14:46:58.813 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process featureCounts (sample39AlignedByCoord.out) > jobId: 1842317.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/34/91dbe046475450d8e70ee0f2d71a1a
|
|
1739
|
Apr-24 14:46:58.814 [Task submitter] INFO nextflow.Session - [34/91dbe0] Submitted process > featureCounts (sample39AlignedByCoord.out)
|
|
1740
|
Apr-24 14:46:58.841 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process rseqc (sample39AlignedByCoord.out) > jobId: 1842318.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a
|
|
1741
|
Apr-24 14:46:58.842 [Task submitter] INFO nextflow.Session - [50/a9d819] Submitted process > rseqc (sample39AlignedByCoord.out)
|
|
1742
|
Apr-24 14:46:58.864 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process genebody_coverage (sample39AlignedByCoord.out) > jobId: 1842319.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed
|
|
1743
|
Apr-24 14:46:58.864 [Task submitter] INFO nextflow.Session - [89/4b5c51] Submitted process > genebody_coverage (sample39AlignedByCoord.out)
|
|
1744
|
Apr-24 14:48:33.257 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842290.srvslshpc001; id: 14; name: star (sample38); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/98/1630fc5a2c21182f9619736d3e9fdf started: 1524572088170; exited: 2018-04-24T12:48:28Z; ]
|
|
1745
|
Apr-24 14:48:33.298 [Actor Thread 90] INFO nextflow.Nextflow - Passed alignment > star (sample38) >> 97.36% <<
|
|
1746
|
Apr-24 14:48:33.298 [Actor Thread 83] DEBUG nextflow.Session - <<< barrier arrive (process: star)
|
|
1747
|
Apr-24 14:48:33.335 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process genebody_coverage (sample38AlignedByCoord.out) > jobId: 1842320.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1
|
|
1748
|
Apr-24 14:48:33.335 [Task submitter] INFO nextflow.Session - [f5/975056] Submitted process > genebody_coverage (sample38AlignedByCoord.out)
|
|
1749
|
Apr-24 14:48:33.439 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process rseqc (sample38AlignedByCoord.out) > jobId: 1842321.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd
|
|
1750
|
Apr-24 14:48:33.439 [Task submitter] INFO nextflow.Session - [bb/d8291f] Submitted process > rseqc (sample38AlignedByCoord.out)
|
|
1751
|
Apr-24 14:48:33.497 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process preseq (sample38AlignedByCoord.out) > jobId: 1842322.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/3b36e2c56c60e6903c2a838bd70819
|
|
1752
|
Apr-24 14:48:33.498 [Task submitter] INFO nextflow.Session - [3b/3b36e2] Submitted process > preseq (sample38AlignedByCoord.out)
|
|
1753
|
Apr-24 14:48:33.534 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process stringtieFPKM (sample38AlignedByCoord.out) > jobId: 1842323.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/de/7484a47dcfd9d4f5a6ce740182dd6d
|
|
1754
|
Apr-24 14:48:33.535 [Task submitter] INFO nextflow.Session - [de/7484a4] Submitted process > stringtieFPKM (sample38AlignedByCoord.out)
|
|
1755
|
Apr-24 14:48:33.559 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process markDuplicates (sample38AlignedByCoord.out) > jobId: 1842324.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a3/d55720e4e3b67b31941a29101bc00d
|
|
1756
|
Apr-24 14:48:33.559 [Task submitter] INFO nextflow.Session - [a3/d55720] Submitted process > markDuplicates (sample38AlignedByCoord.out)
|
|
1757
|
Apr-24 14:48:33.612 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process featureCounts (sample38AlignedByCoord.out) > jobId: 1842325.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/1d7f16db978e30e80db23a19ea188a
|
|
1758
|
Apr-24 14:48:33.613 [Task submitter] INFO nextflow.Session - [a8/1d7f16] Submitted process > featureCounts (sample38AlignedByCoord.out)
|
|
1759
|
Apr-24 14:49:33.259 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842296.srvslshpc001; id: 21; name: markDuplicates (sample37AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/86/089c84b1f0c3846e37e664b0bf5c51 started: 1524573058238; exited: 2018-04-24T12:49:32Z; ]
|
|
1760
|
Apr-24 14:49:33.540 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process dupradar (sample37Aligned.sortedByCoord.out.markDups) > jobId: 1842326.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/fc/c14f95a3a40e606c1c57023f0c1124
|
|
1761
|
Apr-24 14:49:33.540 [Task submitter] INFO nextflow.Session - [fc/c14f95] Submitted process > dupradar (sample37Aligned.sortedByCoord.out.markDups)
|
|
1762
|
Apr-24 14:49:39.649 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1763
|
[process] dupradar
|
|
1764
|
status=ACTIVE
|
|
1765
|
port 0: (queue) OPEN; channel: bam_md
|
|
1766
|
port 1: (value) - ; channel: gtf
|
|
1767
|
port 2: (cntrl) OPEN; channel: $
|
|
1768
|
|
|
1769
|
[process] merge_featureCounts
|
|
1770
|
status=ACTIVE
|
|
1771
|
port 0: (value) - ; channel: input_files
|
|
1772
|
port 1: (cntrl) OPEN; channel: $
|
|
1773
|
|
|
1774
|
[process] sample_correlation
|
|
1775
|
status=ACTIVE
|
|
1776
|
port 0: (value) - ; channel: input_files
|
|
1777
|
port 1: (value) - ; channel: num_bams
|
|
1778
|
port 2: (value) - ; channel: mdsplot_header
|
|
1779
|
port 3: (value) - ; channel: heatmap_header
|
|
1780
|
port 4: (cntrl) OPEN; channel: $
|
|
1781
|
|
|
1782
|
[process] multiqc
|
|
1783
|
status=ACTIVE
|
|
1784
|
port 0: (value) - ; channel: multiqc_config
|
|
1785
|
port 1: (value) - ; channel: fastqc
|
|
1786
|
port 2: (value) - ; channel: trimgalore/*
|
|
1787
|
port 3: (value) - ; channel: alignment/*
|
|
1788
|
port 4: (value) - ; channel: rseqc/*
|
|
1789
|
port 5: (value) - ; channel: rseqc/*
|
|
1790
|
port 6: (value) - ; channel: preseq/*
|
|
1791
|
port 7: (value) - ; channel: dupradar/*
|
|
1792
|
port 8: (value) - ; channel: featureCounts/*
|
|
1793
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1794
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1795
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1796
|
port 12: (value) - ; channel: software_versions/*
|
|
1797
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1798
|
port 14: (cntrl) OPEN; channel: $
|
|
1799
|
|
|
1800
|
[process] output_documentation
|
|
1801
|
status=ACTIVE
|
|
1802
|
port 0: (value) - ; channel: output_docs
|
|
1803
|
port 1: (value) - ; channel: prefix
|
|
1804
|
port 2: (cntrl) OPEN; channel: $
|
|
1805
|
|
|
1806
|
Apr-24 14:49:43.265 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 23 -- pending tasks are shown below
|
|
1807
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1808
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1809
|
~> TaskHandler[jobId: 1842301.srvslshpc001; id: 28; name: markDuplicates (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44 started: 1524573058249; exited: -; ]
|
|
1810
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
1811
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
1812
|
~> TaskHandler[jobId: 1842307.srvslshpc001; id: 31; name: preseq (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/4046a296be31368e5b1c7996ba140a started: 1524573463216; exited: -; ]
|
|
1813
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
1814
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
1815
|
~> TaskHandler[jobId: 1842312.srvslshpc001; id: 35; name: featureCounts (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/49/d847cba9c32af97ec6720c3fe65818 started: 1524573463225; exited: -; ]
|
|
1816
|
~> TaskHandler[jobId: 1842313.srvslshpc001; id: 36; name: markDuplicates (sample40AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5 started: -; exited: -; ]
|
|
1817
|
.. remaining tasks omitted.
|
|
1818
|
Apr-24 14:49:48.269 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842301.srvslshpc001; id: 28; name: markDuplicates (sample41AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/61/b53bbb8eefb5b89222adc975cc9a44 started: 1524573058249; exited: 2018-04-24T12:49:44Z; ]
|
|
1819
|
Apr-24 14:49:48.323 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process dupradar (sample41Aligned.sortedByCoord.out.markDups) > jobId: 1842327.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/24/7338efd21c4542b010e4d409274e73
|
|
1820
|
Apr-24 14:49:48.324 [Task submitter] INFO nextflow.Session - [24/7338ef] Submitted process > dupradar (sample41Aligned.sortedByCoord.out.markDups)
|
|
1821
|
Apr-24 14:50:18.270 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842312.srvslshpc001; id: 35; name: featureCounts (sample40AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/49/d847cba9c32af97ec6720c3fe65818 started: 1524573463225; exited: 2018-04-24T12:50:14Z; ]
|
|
1822
|
Apr-24 14:53:48.274 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842307.srvslshpc001; id: 31; name: preseq (sample40AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/4046a296be31368e5b1c7996ba140a started: 1524573463216; exited: 2018-04-24T12:53:44Z; ]
|
|
1823
|
Apr-24 14:54:39.656 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1824
|
[process] dupradar
|
|
1825
|
status=ACTIVE
|
|
1826
|
port 0: (queue) OPEN; channel: bam_md
|
|
1827
|
port 1: (value) - ; channel: gtf
|
|
1828
|
port 2: (cntrl) OPEN; channel: $
|
|
1829
|
|
|
1830
|
[process] merge_featureCounts
|
|
1831
|
status=ACTIVE
|
|
1832
|
port 0: (value) - ; channel: input_files
|
|
1833
|
port 1: (cntrl) OPEN; channel: $
|
|
1834
|
|
|
1835
|
[process] sample_correlation
|
|
1836
|
status=ACTIVE
|
|
1837
|
port 0: (value) - ; channel: input_files
|
|
1838
|
port 1: (value) - ; channel: num_bams
|
|
1839
|
port 2: (value) - ; channel: mdsplot_header
|
|
1840
|
port 3: (value) - ; channel: heatmap_header
|
|
1841
|
port 4: (cntrl) OPEN; channel: $
|
|
1842
|
|
|
1843
|
[process] multiqc
|
|
1844
|
status=ACTIVE
|
|
1845
|
port 0: (value) - ; channel: multiqc_config
|
|
1846
|
port 1: (value) - ; channel: fastqc
|
|
1847
|
port 2: (value) - ; channel: trimgalore/*
|
|
1848
|
port 3: (value) - ; channel: alignment/*
|
|
1849
|
port 4: (value) - ; channel: rseqc/*
|
|
1850
|
port 5: (value) - ; channel: rseqc/*
|
|
1851
|
port 6: (value) - ; channel: preseq/*
|
|
1852
|
port 7: (value) - ; channel: dupradar/*
|
|
1853
|
port 8: (value) - ; channel: featureCounts/*
|
|
1854
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1855
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1856
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1857
|
port 12: (value) - ; channel: software_versions/*
|
|
1858
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1859
|
port 14: (cntrl) OPEN; channel: $
|
|
1860
|
|
|
1861
|
[process] output_documentation
|
|
1862
|
status=ACTIVE
|
|
1863
|
port 0: (value) - ; channel: output_docs
|
|
1864
|
port 1: (value) - ; channel: prefix
|
|
1865
|
port 2: (cntrl) OPEN; channel: $
|
|
1866
|
|
|
1867
|
Apr-24 14:54:43.283 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 21 -- pending tasks are shown below
|
|
1868
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1869
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1870
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
1871
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
1872
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
1873
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
1874
|
~> TaskHandler[jobId: 1842313.srvslshpc001; id: 36; name: markDuplicates (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5 started: 1524574268271; exited: -; ]
|
|
1875
|
~> TaskHandler[jobId: 1842314.srvslshpc001; id: 40; name: stringtieFPKM (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cc/c538b46689497359caf8261fb61dee started: 1524574273271; exited: -; ]
|
|
1876
|
~> TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: -; ]
|
|
1877
|
~> TaskHandler[jobId: 1842316.srvslshpc001; id: 38; name: preseq (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/a48c0c068a40b2a80328ab5eddead4 started: 1524574273274; exited: -; ]
|
|
1878
|
.. remaining tasks omitted.
|
|
1879
|
Apr-24 14:59:39.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1880
|
[process] dupradar
|
|
1881
|
status=ACTIVE
|
|
1882
|
port 0: (queue) OPEN; channel: bam_md
|
|
1883
|
port 1: (value) - ; channel: gtf
|
|
1884
|
port 2: (cntrl) OPEN; channel: $
|
|
1885
|
|
|
1886
|
[process] merge_featureCounts
|
|
1887
|
status=ACTIVE
|
|
1888
|
port 0: (value) - ; channel: input_files
|
|
1889
|
port 1: (cntrl) OPEN; channel: $
|
|
1890
|
|
|
1891
|
[process] sample_correlation
|
|
1892
|
status=ACTIVE
|
|
1893
|
port 0: (value) - ; channel: input_files
|
|
1894
|
port 1: (value) - ; channel: num_bams
|
|
1895
|
port 2: (value) - ; channel: mdsplot_header
|
|
1896
|
port 3: (value) - ; channel: heatmap_header
|
|
1897
|
port 4: (cntrl) OPEN; channel: $
|
|
1898
|
|
|
1899
|
[process] multiqc
|
|
1900
|
status=ACTIVE
|
|
1901
|
port 0: (value) - ; channel: multiqc_config
|
|
1902
|
port 1: (value) - ; channel: fastqc
|
|
1903
|
port 2: (value) - ; channel: trimgalore/*
|
|
1904
|
port 3: (value) - ; channel: alignment/*
|
|
1905
|
port 4: (value) - ; channel: rseqc/*
|
|
1906
|
port 5: (value) - ; channel: rseqc/*
|
|
1907
|
port 6: (value) - ; channel: preseq/*
|
|
1908
|
port 7: (value) - ; channel: dupradar/*
|
|
1909
|
port 8: (value) - ; channel: featureCounts/*
|
|
1910
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1911
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1912
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1913
|
port 12: (value) - ; channel: software_versions/*
|
|
1914
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1915
|
port 14: (cntrl) OPEN; channel: $
|
|
1916
|
|
|
1917
|
[process] output_documentation
|
|
1918
|
status=ACTIVE
|
|
1919
|
port 0: (value) - ; channel: output_docs
|
|
1920
|
port 1: (value) - ; channel: prefix
|
|
1921
|
port 2: (cntrl) OPEN; channel: $
|
|
1922
|
|
|
1923
|
Apr-24 14:59:43.302 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 21 -- pending tasks are shown below
|
|
1924
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1925
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1926
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
1927
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
1928
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
1929
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
1930
|
~> TaskHandler[jobId: 1842313.srvslshpc001; id: 36; name: markDuplicates (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5 started: 1524574268271; exited: -; ]
|
|
1931
|
~> TaskHandler[jobId: 1842314.srvslshpc001; id: 40; name: stringtieFPKM (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cc/c538b46689497359caf8261fb61dee started: 1524574273271; exited: -; ]
|
|
1932
|
~> TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: -; ]
|
|
1933
|
~> TaskHandler[jobId: 1842316.srvslshpc001; id: 38; name: preseq (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/a48c0c068a40b2a80328ab5eddead4 started: 1524574273274; exited: -; ]
|
|
1934
|
.. remaining tasks omitted.
|
|
1935
|
Apr-24 15:00:38.310 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842314.srvslshpc001; id: 40; name: stringtieFPKM (sample39AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/cc/c538b46689497359caf8261fb61dee started: 1524574273271; exited: 2018-04-24T13:00:34Z; ]
|
|
1936
|
Apr-24 15:04:39.747 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1937
|
[process] dupradar
|
|
1938
|
status=ACTIVE
|
|
1939
|
port 0: (queue) OPEN; channel: bam_md
|
|
1940
|
port 1: (value) - ; channel: gtf
|
|
1941
|
port 2: (cntrl) OPEN; channel: $
|
|
1942
|
|
|
1943
|
[process] merge_featureCounts
|
|
1944
|
status=ACTIVE
|
|
1945
|
port 0: (value) - ; channel: input_files
|
|
1946
|
port 1: (cntrl) OPEN; channel: $
|
|
1947
|
|
|
1948
|
[process] sample_correlation
|
|
1949
|
status=ACTIVE
|
|
1950
|
port 0: (value) - ; channel: input_files
|
|
1951
|
port 1: (value) - ; channel: num_bams
|
|
1952
|
port 2: (value) - ; channel: mdsplot_header
|
|
1953
|
port 3: (value) - ; channel: heatmap_header
|
|
1954
|
port 4: (cntrl) OPEN; channel: $
|
|
1955
|
|
|
1956
|
[process] multiqc
|
|
1957
|
status=ACTIVE
|
|
1958
|
port 0: (value) - ; channel: multiqc_config
|
|
1959
|
port 1: (value) - ; channel: fastqc
|
|
1960
|
port 2: (value) - ; channel: trimgalore/*
|
|
1961
|
port 3: (value) - ; channel: alignment/*
|
|
1962
|
port 4: (value) - ; channel: rseqc/*
|
|
1963
|
port 5: (value) - ; channel: rseqc/*
|
|
1964
|
port 6: (value) - ; channel: preseq/*
|
|
1965
|
port 7: (value) - ; channel: dupradar/*
|
|
1966
|
port 8: (value) - ; channel: featureCounts/*
|
|
1967
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
1968
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
1969
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
1970
|
port 12: (value) - ; channel: software_versions/*
|
|
1971
|
port 13: (value) - ; channel: workflow_summary/*
|
|
1972
|
port 14: (cntrl) OPEN; channel: $
|
|
1973
|
|
|
1974
|
[process] output_documentation
|
|
1975
|
status=ACTIVE
|
|
1976
|
port 0: (value) - ; channel: output_docs
|
|
1977
|
port 1: (value) - ; channel: prefix
|
|
1978
|
port 2: (cntrl) OPEN; channel: $
|
|
1979
|
|
|
1980
|
Apr-24 15:04:43.323 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 20 -- pending tasks are shown below
|
|
1981
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
1982
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
1983
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
1984
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
1985
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
1986
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
1987
|
~> TaskHandler[jobId: 1842313.srvslshpc001; id: 36; name: markDuplicates (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5 started: 1524574268271; exited: -; ]
|
|
1988
|
~> TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: -; ]
|
|
1989
|
~> TaskHandler[jobId: 1842316.srvslshpc001; id: 38; name: preseq (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/a48c0c068a40b2a80328ab5eddead4 started: 1524574273274; exited: -; ]
|
|
1990
|
~> TaskHandler[jobId: 1842317.srvslshpc001; id: 39; name: featureCounts (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/34/91dbe046475450d8e70ee0f2d71a1a started: 1524574273275; exited: -; ]
|
|
1991
|
.. remaining tasks omitted.
|
|
1992
|
Apr-24 15:08:38.332 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842317.srvslshpc001; id: 39; name: featureCounts (sample39AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/34/91dbe046475450d8e70ee0f2d71a1a started: 1524574273275; exited: 2018-04-24T13:08:35Z; ]
|
|
1993
|
Apr-24 15:09:39.772 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
1994
|
[process] dupradar
|
|
1995
|
status=ACTIVE
|
|
1996
|
port 0: (queue) OPEN; channel: bam_md
|
|
1997
|
port 1: (value) - ; channel: gtf
|
|
1998
|
port 2: (cntrl) OPEN; channel: $
|
|
1999
|
|
|
2000
|
[process] merge_featureCounts
|
|
2001
|
status=ACTIVE
|
|
2002
|
port 0: (value) - ; channel: input_files
|
|
2003
|
port 1: (cntrl) OPEN; channel: $
|
|
2004
|
|
|
2005
|
[process] sample_correlation
|
|
2006
|
status=ACTIVE
|
|
2007
|
port 0: (value) - ; channel: input_files
|
|
2008
|
port 1: (value) - ; channel: num_bams
|
|
2009
|
port 2: (value) - ; channel: mdsplot_header
|
|
2010
|
port 3: (value) - ; channel: heatmap_header
|
|
2011
|
port 4: (cntrl) OPEN; channel: $
|
|
2012
|
|
|
2013
|
[process] multiqc
|
|
2014
|
status=ACTIVE
|
|
2015
|
port 0: (value) - ; channel: multiqc_config
|
|
2016
|
port 1: (value) - ; channel: fastqc
|
|
2017
|
port 2: (value) - ; channel: trimgalore/*
|
|
2018
|
port 3: (value) - ; channel: alignment/*
|
|
2019
|
port 4: (value) - ; channel: rseqc/*
|
|
2020
|
port 5: (value) - ; channel: rseqc/*
|
|
2021
|
port 6: (value) - ; channel: preseq/*
|
|
2022
|
port 7: (value) - ; channel: dupradar/*
|
|
2023
|
port 8: (value) - ; channel: featureCounts/*
|
|
2024
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2025
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2026
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2027
|
port 12: (value) - ; channel: software_versions/*
|
|
2028
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2029
|
port 14: (cntrl) OPEN; channel: $
|
|
2030
|
|
|
2031
|
[process] output_documentation
|
|
2032
|
status=ACTIVE
|
|
2033
|
port 0: (value) - ; channel: output_docs
|
|
2034
|
port 1: (value) - ; channel: prefix
|
|
2035
|
port 2: (cntrl) OPEN; channel: $
|
|
2036
|
|
|
2037
|
Apr-24 15:09:43.340 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 19 -- pending tasks are shown below
|
|
2038
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2039
|
~> TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: -; ]
|
|
2040
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
2041
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2042
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2043
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2044
|
~> TaskHandler[jobId: 1842313.srvslshpc001; id: 36; name: markDuplicates (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5 started: 1524574268271; exited: -; ]
|
|
2045
|
~> TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: -; ]
|
|
2046
|
~> TaskHandler[jobId: 1842316.srvslshpc001; id: 38; name: preseq (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/a48c0c068a40b2a80328ab5eddead4 started: 1524574273274; exited: -; ]
|
|
2047
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2048
|
.. remaining tasks omitted.
|
|
2049
|
Apr-24 15:12:38.346 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842300.srvslshpc001; id: 19; name: rseqc (sample37AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1d/8484008b08243efa0126fb6dd72797 started: 1524573058247; exited: 2018-04-24T13:12:35Z; ]
|
|
2050
|
Apr-24 15:14:33.349 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842313.srvslshpc001; id: 36; name: markDuplicates (sample40AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b1/cac4bc2e6c58071869bd65ab2f16c5 started: 1524574268271; exited: 2018-04-24T13:14:33Z; ]
|
|
2051
|
Apr-24 15:14:33.387 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process dupradar (sample40Aligned.sortedByCoord.out.markDups) > jobId: 1842329.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ff/cec1123d29d43098a87de2f5998888
|
|
2052
|
Apr-24 15:14:33.388 [Task submitter] INFO nextflow.Session - [ff/cec112] Submitted process > dupradar (sample40Aligned.sortedByCoord.out.markDups)
|
|
2053
|
Apr-24 15:14:38.350 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842316.srvslshpc001; id: 38; name: preseq (sample39AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/a48c0c068a40b2a80328ab5eddead4 started: 1524574273274; exited: 2018-04-24T13:14:35Z; ]
|
|
2054
|
Apr-24 15:14:39.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2055
|
[process] dupradar
|
|
2056
|
status=ACTIVE
|
|
2057
|
port 0: (queue) OPEN; channel: bam_md
|
|
2058
|
port 1: (value) - ; channel: gtf
|
|
2059
|
port 2: (cntrl) OPEN; channel: $
|
|
2060
|
|
|
2061
|
[process] merge_featureCounts
|
|
2062
|
status=ACTIVE
|
|
2063
|
port 0: (value) - ; channel: input_files
|
|
2064
|
port 1: (cntrl) OPEN; channel: $
|
|
2065
|
|
|
2066
|
[process] sample_correlation
|
|
2067
|
status=ACTIVE
|
|
2068
|
port 0: (value) - ; channel: input_files
|
|
2069
|
port 1: (value) - ; channel: num_bams
|
|
2070
|
port 2: (value) - ; channel: mdsplot_header
|
|
2071
|
port 3: (value) - ; channel: heatmap_header
|
|
2072
|
port 4: (cntrl) OPEN; channel: $
|
|
2073
|
|
|
2074
|
[process] multiqc
|
|
2075
|
status=ACTIVE
|
|
2076
|
port 0: (value) - ; channel: multiqc_config
|
|
2077
|
port 1: (value) - ; channel: fastqc
|
|
2078
|
port 2: (value) - ; channel: trimgalore/*
|
|
2079
|
port 3: (value) - ; channel: alignment/*
|
|
2080
|
port 4: (value) - ; channel: rseqc/*
|
|
2081
|
port 5: (value) - ; channel: rseqc/*
|
|
2082
|
port 6: (value) - ; channel: preseq/*
|
|
2083
|
port 7: (value) - ; channel: dupradar/*
|
|
2084
|
port 8: (value) - ; channel: featureCounts/*
|
|
2085
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2086
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2087
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2088
|
port 12: (value) - ; channel: software_versions/*
|
|
2089
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2090
|
port 14: (cntrl) OPEN; channel: $
|
|
2091
|
|
|
2092
|
[process] output_documentation
|
|
2093
|
status=ACTIVE
|
|
2094
|
port 0: (value) - ; channel: output_docs
|
|
2095
|
port 1: (value) - ; channel: prefix
|
|
2096
|
port 2: (cntrl) OPEN; channel: $
|
|
2097
|
|
|
2098
|
Apr-24 15:14:43.354 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 17 -- pending tasks are shown below
|
|
2099
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2100
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
2101
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2102
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2103
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2104
|
~> TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: -; ]
|
|
2105
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2106
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2107
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2108
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: SUBMITTED; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: -; exited: -; ]
|
|
2109
|
.. remaining tasks omitted.
|
|
2110
|
Apr-24 15:19:39.953 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2111
|
[process] dupradar
|
|
2112
|
status=ACTIVE
|
|
2113
|
port 0: (queue) OPEN; channel: bam_md
|
|
2114
|
port 1: (value) - ; channel: gtf
|
|
2115
|
port 2: (cntrl) OPEN; channel: $
|
|
2116
|
|
|
2117
|
[process] merge_featureCounts
|
|
2118
|
status=ACTIVE
|
|
2119
|
port 0: (value) - ; channel: input_files
|
|
2120
|
port 1: (cntrl) OPEN; channel: $
|
|
2121
|
|
|
2122
|
[process] sample_correlation
|
|
2123
|
status=ACTIVE
|
|
2124
|
port 0: (value) - ; channel: input_files
|
|
2125
|
port 1: (value) - ; channel: num_bams
|
|
2126
|
port 2: (value) - ; channel: mdsplot_header
|
|
2127
|
port 3: (value) - ; channel: heatmap_header
|
|
2128
|
port 4: (cntrl) OPEN; channel: $
|
|
2129
|
|
|
2130
|
[process] multiqc
|
|
2131
|
status=ACTIVE
|
|
2132
|
port 0: (value) - ; channel: multiqc_config
|
|
2133
|
port 1: (value) - ; channel: fastqc
|
|
2134
|
port 2: (value) - ; channel: trimgalore/*
|
|
2135
|
port 3: (value) - ; channel: alignment/*
|
|
2136
|
port 4: (value) - ; channel: rseqc/*
|
|
2137
|
port 5: (value) - ; channel: rseqc/*
|
|
2138
|
port 6: (value) - ; channel: preseq/*
|
|
2139
|
port 7: (value) - ; channel: dupradar/*
|
|
2140
|
port 8: (value) - ; channel: featureCounts/*
|
|
2141
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2142
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2143
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2144
|
port 12: (value) - ; channel: software_versions/*
|
|
2145
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2146
|
port 14: (cntrl) OPEN; channel: $
|
|
2147
|
|
|
2148
|
[process] output_documentation
|
|
2149
|
status=ACTIVE
|
|
2150
|
port 0: (value) - ; channel: output_docs
|
|
2151
|
port 1: (value) - ; channel: prefix
|
|
2152
|
port 2: (cntrl) OPEN; channel: $
|
|
2153
|
|
|
2154
|
Apr-24 15:19:43.379 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 17 -- pending tasks are shown below
|
|
2155
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2156
|
~> TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: -; ]
|
|
2157
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2158
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2159
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2160
|
~> TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: -; ]
|
|
2161
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2162
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2163
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2164
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2165
|
.. remaining tasks omitted.
|
|
2166
|
Apr-24 15:21:03.385 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842305.srvslshpc001; id: 24; name: rseqc (sample41AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b0/7aa70c09bd883b584b9af6a492d71a started: 1524573058257; exited: 2018-04-24T13:21:00Z; ]
|
|
2167
|
Apr-24 15:21:23.387 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842323.srvslshpc001; id: 47; name: stringtieFPKM (sample38AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/de/7484a47dcfd9d4f5a6ce740182dd6d started: 1524575708361; exited: 2018-04-24T13:21:19Z; ]
|
|
2168
|
Apr-24 15:21:23.391 [Actor Thread 125] DEBUG nextflow.Session - <<< barrier arrive (process: stringtieFPKM)
|
|
2169
|
Apr-24 15:21:58.407 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842315.srvslshpc001; id: 37; name: markDuplicates (sample39AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a1/4544b721b1c600608cbb578f3e9aa3 started: 1524574273272; exited: 2018-04-24T13:21:56Z; ]
|
|
2170
|
Apr-24 15:21:58.445 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process dupradar (sample39Aligned.sortedByCoord.out.markDups) > jobId: 1842331.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9
|
|
2171
|
Apr-24 15:21:58.446 [Task submitter] INFO nextflow.Session - [8d/e72fbf] Submitted process > dupradar (sample39Aligned.sortedByCoord.out.markDups)
|
|
2172
|
Apr-24 15:23:18.390 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842322.srvslshpc001; id: 46; name: preseq (sample38AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/3b/3b36e2c56c60e6903c2a838bd70819 started: 1524575348332; exited: 2018-04-24T13:23:16Z; ]
|
|
2173
|
Apr-24 15:23:18.393 [Actor Thread 129] DEBUG nextflow.Session - <<< barrier arrive (process: preseq)
|
|
2174
|
Apr-24 15:24:18.391 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842325.srvslshpc001; id: 43; name: featureCounts (sample38AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/1d7f16db978e30e80db23a19ea188a started: 1524575713362; exited: 2018-04-24T13:24:14Z; ]
|
|
2175
|
Apr-24 15:24:18.395 [Actor Thread 129] DEBUG nextflow.Session - <<< barrier arrive (process: featureCounts)
|
|
2176
|
Apr-24 15:24:18.438 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts) > jobId: 1842332.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/9b/84b3f476717268e540961960e252f2
|
|
2177
|
Apr-24 15:24:18.439 [Task submitter] INFO nextflow.Session - [9b/84b3f4] Submitted process > merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)
|
|
2178
|
Apr-24 15:24:18.470 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process sample_correlation (sample41.sortedByCoord.out_gene.featureCounts.txt) > jobId: 1842333.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1a/cf18a42ddc06c60d60b5f22761286a
|
|
2179
|
Apr-24 15:24:18.471 [Task submitter] INFO nextflow.Session - [1a/cf18a4] Submitted process > sample_correlation (sample41.sortedByCoord.out_gene.featureCounts.txt)
|
|
2180
|
Apr-24 15:24:40.040 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2181
|
[process] dupradar
|
|
2182
|
status=ACTIVE
|
|
2183
|
port 0: (queue) OPEN; channel: bam_md
|
|
2184
|
port 1: (value) - ; channel: gtf
|
|
2185
|
port 2: (cntrl) OPEN; channel: $
|
|
2186
|
|
|
2187
|
[process] multiqc
|
|
2188
|
status=ACTIVE
|
|
2189
|
port 0: (value) - ; channel: multiqc_config
|
|
2190
|
port 1: (value) - ; channel: fastqc
|
|
2191
|
port 2: (value) - ; channel: trimgalore/*
|
|
2192
|
port 3: (value) - ; channel: alignment/*
|
|
2193
|
port 4: (value) - ; channel: rseqc/*
|
|
2194
|
port 5: (value) - ; channel: rseqc/*
|
|
2195
|
port 6: (value) - ; channel: preseq/*
|
|
2196
|
port 7: (value) - ; channel: dupradar/*
|
|
2197
|
port 8: (value) - ; channel: featureCounts/*
|
|
2198
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2199
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2200
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2201
|
port 12: (value) - ; channel: software_versions/*
|
|
2202
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2203
|
port 14: (cntrl) OPEN; channel: $
|
|
2204
|
|
|
2205
|
[process] output_documentation
|
|
2206
|
status=ACTIVE
|
|
2207
|
port 0: (value) - ; channel: output_docs
|
|
2208
|
port 1: (value) - ; channel: prefix
|
|
2209
|
port 2: (cntrl) OPEN; channel: $
|
|
2210
|
|
|
2211
|
Apr-24 15:24:43.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 15 -- pending tasks are shown below
|
|
2212
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2213
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2214
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2215
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2216
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2217
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2218
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2219
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2220
|
~> TaskHandler[jobId: 1842324.srvslshpc001; id: 48; name: markDuplicates (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a3/d55720e4e3b67b31941a29101bc00d started: 1524575713360; exited: -; ]
|
|
2221
|
~> TaskHandler[jobId: 1842326.srvslshpc001; id: 49; name: dupradar (sample37Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/fc/c14f95a3a40e606c1c57023f0c1124 started: 1524575713363; exited: -; ]
|
|
2222
|
.. remaining tasks omitted.
|
|
2223
|
Apr-24 15:27:13.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842332.srvslshpc001; id: 53; name: merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/9b/84b3f476717268e540961960e252f2 started: 1524576428401; exited: 2018-04-24T13:27:10Z; ]
|
|
2224
|
Apr-24 15:27:13.406 [Actor Thread 136] DEBUG nextflow.Session - <<< barrier arrive (process: merge_featureCounts)
|
|
2225
|
Apr-24 15:27:18.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842333.srvslshpc001; id: 54; name: sample_correlation (sample41.sortedByCoord.out_gene.featureCounts.txt); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/1a/cf18a42ddc06c60d60b5f22761286a started: 1524576428402; exited: 2018-04-24T13:27:17Z; ]
|
|
2226
|
Apr-24 15:27:18.438 [Actor Thread 136] DEBUG nextflow.Session - <<< barrier arrive (process: sample_correlation)
|
|
2227
|
Apr-24 15:29:40.130 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2228
|
[process] dupradar
|
|
2229
|
status=ACTIVE
|
|
2230
|
port 0: (queue) OPEN; channel: bam_md
|
|
2231
|
port 1: (value) - ; channel: gtf
|
|
2232
|
port 2: (cntrl) OPEN; channel: $
|
|
2233
|
|
|
2234
|
[process] multiqc
|
|
2235
|
status=ACTIVE
|
|
2236
|
port 0: (value) - ; channel: multiqc_config
|
|
2237
|
port 1: (value) - ; channel: fastqc
|
|
2238
|
port 2: (value) - ; channel: trimgalore/*
|
|
2239
|
port 3: (value) - ; channel: alignment/*
|
|
2240
|
port 4: (value) - ; channel: rseqc/*
|
|
2241
|
port 5: (value) - ; channel: rseqc/*
|
|
2242
|
port 6: (value) - ; channel: preseq/*
|
|
2243
|
port 7: (value) - ; channel: dupradar/*
|
|
2244
|
port 8: (value) - ; channel: featureCounts/*
|
|
2245
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2246
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2247
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2248
|
port 12: (value) - ; channel: software_versions/*
|
|
2249
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2250
|
port 14: (cntrl) OPEN; channel: $
|
|
2251
|
|
|
2252
|
[process] output_documentation
|
|
2253
|
status=ACTIVE
|
|
2254
|
port 0: (value) - ; channel: output_docs
|
|
2255
|
port 1: (value) - ; channel: prefix
|
|
2256
|
port 2: (cntrl) OPEN; channel: $
|
|
2257
|
|
|
2258
|
Apr-24 15:29:43.409 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 13 -- pending tasks are shown below
|
|
2259
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2260
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2261
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2262
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2263
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2264
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2265
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2266
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2267
|
~> TaskHandler[jobId: 1842324.srvslshpc001; id: 48; name: markDuplicates (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a3/d55720e4e3b67b31941a29101bc00d started: 1524575713360; exited: -; ]
|
|
2268
|
~> TaskHandler[jobId: 1842326.srvslshpc001; id: 49; name: dupradar (sample37Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/fc/c14f95a3a40e606c1c57023f0c1124 started: 1524575713363; exited: -; ]
|
|
2269
|
.. remaining tasks omitted.
|
|
2270
|
Apr-24 15:32:03.416 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842324.srvslshpc001; id: 48; name: markDuplicates (sample38AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a3/d55720e4e3b67b31941a29101bc00d started: 1524575713360; exited: 2018-04-24T13:32:00Z; ]
|
|
2271
|
Apr-24 15:32:03.420 [Actor Thread 139] DEBUG nextflow.Session - <<< barrier arrive (process: markDuplicates)
|
|
2272
|
Apr-24 15:32:03.530 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process dupradar (sample38Aligned.sortedByCoord.out.markDups) > jobId: 1842334.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/af/842ef026bbf6d874ba8056af228875
|
|
2273
|
Apr-24 15:32:03.531 [Task submitter] INFO nextflow.Session - [af/842ef0] Submitted process > dupradar (sample38Aligned.sortedByCoord.out.markDups)
|
|
2274
|
Apr-24 15:34:40.215 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2275
|
[process] multiqc
|
|
2276
|
status=ACTIVE
|
|
2277
|
port 0: (value) - ; channel: multiqc_config
|
|
2278
|
port 1: (value) - ; channel: fastqc
|
|
2279
|
port 2: (value) - ; channel: trimgalore/*
|
|
2280
|
port 3: (value) - ; channel: alignment/*
|
|
2281
|
port 4: (value) - ; channel: rseqc/*
|
|
2282
|
port 5: (value) - ; channel: rseqc/*
|
|
2283
|
port 6: (value) - ; channel: preseq/*
|
|
2284
|
port 7: (value) - ; channel: dupradar/*
|
|
2285
|
port 8: (value) - ; channel: featureCounts/*
|
|
2286
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2287
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2288
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2289
|
port 12: (value) - ; channel: software_versions/*
|
|
2290
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2291
|
port 14: (cntrl) OPEN; channel: $
|
|
2292
|
|
|
2293
|
[process] output_documentation
|
|
2294
|
status=ACTIVE
|
|
2295
|
port 0: (value) - ; channel: output_docs
|
|
2296
|
port 1: (value) - ; channel: prefix
|
|
2297
|
port 2: (cntrl) OPEN; channel: $
|
|
2298
|
|
|
2299
|
Apr-24 15:34:43.420 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 13 -- pending tasks are shown below
|
|
2300
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2301
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2302
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2303
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2304
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2305
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2306
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2307
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2308
|
~> TaskHandler[jobId: 1842326.srvslshpc001; id: 49; name: dupradar (sample37Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/fc/c14f95a3a40e606c1c57023f0c1124 started: 1524575713363; exited: -; ]
|
|
2309
|
~> TaskHandler[jobId: 1842327.srvslshpc001; id: 50; name: dupradar (sample41Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/24/7338efd21c4542b010e4d409274e73 started: 1524575713365; exited: -; ]
|
|
2310
|
.. remaining tasks omitted.
|
|
2311
|
Apr-24 15:36:03.429 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842326.srvslshpc001; id: 49; name: dupradar (sample37Aligned.sortedByCoord.out.markDups); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/fc/c14f95a3a40e606c1c57023f0c1124 started: 1524575713363; exited: 2018-04-24T13:36:01Z; ]
|
|
2312
|
Apr-24 15:37:08.427 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842327.srvslshpc001; id: 50; name: dupradar (sample41Aligned.sortedByCoord.out.markDups); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/24/7338efd21c4542b010e4d409274e73 started: 1524575713365; exited: 2018-04-24T13:37:04Z; ]
|
|
2313
|
Apr-24 15:39:40.298 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2314
|
[process] multiqc
|
|
2315
|
status=ACTIVE
|
|
2316
|
port 0: (value) - ; channel: multiqc_config
|
|
2317
|
port 1: (value) - ; channel: fastqc
|
|
2318
|
port 2: (value) - ; channel: trimgalore/*
|
|
2319
|
port 3: (value) - ; channel: alignment/*
|
|
2320
|
port 4: (value) - ; channel: rseqc/*
|
|
2321
|
port 5: (value) - ; channel: rseqc/*
|
|
2322
|
port 6: (value) - ; channel: preseq/*
|
|
2323
|
port 7: (value) - ; channel: dupradar/*
|
|
2324
|
port 8: (value) - ; channel: featureCounts/*
|
|
2325
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2326
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2327
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2328
|
port 12: (value) - ; channel: software_versions/*
|
|
2329
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2330
|
port 14: (cntrl) OPEN; channel: $
|
|
2331
|
|
|
2332
|
[process] output_documentation
|
|
2333
|
status=ACTIVE
|
|
2334
|
port 0: (value) - ; channel: output_docs
|
|
2335
|
port 1: (value) - ; channel: prefix
|
|
2336
|
port 2: (cntrl) OPEN; channel: $
|
|
2337
|
|
|
2338
|
Apr-24 15:39:43.433 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 11 -- pending tasks are shown below
|
|
2339
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2340
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2341
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2342
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2343
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2344
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2345
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2346
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2347
|
~> TaskHandler[jobId: 1842329.srvslshpc001; id: 51; name: dupradar (sample40Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ff/cec1123d29d43098a87de2f5998888 started: 1524575718361; exited: -; ]
|
|
2348
|
~> TaskHandler[jobId: 1842331.srvslshpc001; id: 52; name: dupradar (sample39Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9 started: 1524576248390; exited: -; ]
|
|
2349
|
Apr-24 15:43:38.442 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842329.srvslshpc001; id: 51; name: dupradar (sample40Aligned.sortedByCoord.out.markDups); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/ff/cec1123d29d43098a87de2f5998888 started: 1524575718361; exited: 2018-04-24T13:43:36Z; ]
|
|
2350
|
Apr-24 15:44:40.386 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2351
|
[process] multiqc
|
|
2352
|
status=ACTIVE
|
|
2353
|
port 0: (value) - ; channel: multiqc_config
|
|
2354
|
port 1: (value) - ; channel: fastqc
|
|
2355
|
port 2: (value) - ; channel: trimgalore/*
|
|
2356
|
port 3: (value) - ; channel: alignment/*
|
|
2357
|
port 4: (value) - ; channel: rseqc/*
|
|
2358
|
port 5: (value) - ; channel: rseqc/*
|
|
2359
|
port 6: (value) - ; channel: preseq/*
|
|
2360
|
port 7: (value) - ; channel: dupradar/*
|
|
2361
|
port 8: (value) - ; channel: featureCounts/*
|
|
2362
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2363
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2364
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2365
|
port 12: (value) - ; channel: software_versions/*
|
|
2366
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2367
|
port 14: (cntrl) OPEN; channel: $
|
|
2368
|
|
|
2369
|
[process] output_documentation
|
|
2370
|
status=ACTIVE
|
|
2371
|
port 0: (value) - ; channel: output_docs
|
|
2372
|
port 1: (value) - ; channel: prefix
|
|
2373
|
port 2: (cntrl) OPEN; channel: $
|
|
2374
|
|
|
2375
|
Apr-24 15:44:43.446 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below
|
|
2376
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2377
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2378
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2379
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2380
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2381
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2382
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2383
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2384
|
~> TaskHandler[jobId: 1842331.srvslshpc001; id: 52; name: dupradar (sample39Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9 started: 1524576248390; exited: -; ]
|
|
2385
|
~> TaskHandler[jobId: 1842334.srvslshpc001; id: 55; name: dupradar (sample38Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/af/842ef026bbf6d874ba8056af228875 started: 1524576788416; exited: -; ]
|
|
2386
|
Apr-24 15:49:40.470 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2387
|
[process] multiqc
|
|
2388
|
status=ACTIVE
|
|
2389
|
port 0: (value) - ; channel: multiqc_config
|
|
2390
|
port 1: (value) - ; channel: fastqc
|
|
2391
|
port 2: (value) - ; channel: trimgalore/*
|
|
2392
|
port 3: (value) - ; channel: alignment/*
|
|
2393
|
port 4: (value) - ; channel: rseqc/*
|
|
2394
|
port 5: (value) - ; channel: rseqc/*
|
|
2395
|
port 6: (value) - ; channel: preseq/*
|
|
2396
|
port 7: (value) - ; channel: dupradar/*
|
|
2397
|
port 8: (value) - ; channel: featureCounts/*
|
|
2398
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2399
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2400
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2401
|
port 12: (value) - ; channel: software_versions/*
|
|
2402
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2403
|
port 14: (cntrl) OPEN; channel: $
|
|
2404
|
|
|
2405
|
[process] output_documentation
|
|
2406
|
status=ACTIVE
|
|
2407
|
port 0: (value) - ; channel: output_docs
|
|
2408
|
port 1: (value) - ; channel: prefix
|
|
2409
|
port 2: (cntrl) OPEN; channel: $
|
|
2410
|
|
|
2411
|
Apr-24 15:49:43.464 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below
|
|
2412
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2413
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2414
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2415
|
~> TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: -; ]
|
|
2416
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2417
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2418
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2419
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2420
|
~> TaskHandler[jobId: 1842331.srvslshpc001; id: 52; name: dupradar (sample39Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9 started: 1524576248390; exited: -; ]
|
|
2421
|
~> TaskHandler[jobId: 1842334.srvslshpc001; id: 55; name: dupradar (sample38Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/af/842ef026bbf6d874ba8056af228875 started: 1524576788416; exited: -; ]
|
|
2422
|
Apr-24 15:51:03.471 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842310.srvslshpc001; id: 30; name: rseqc (sample40AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/a8/79b1686b191caf20051787c082bc2a started: 1524573463221; exited: 2018-04-24T13:50:59Z; ]
|
|
2423
|
Apr-24 15:54:40.553 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2424
|
[process] multiqc
|
|
2425
|
status=ACTIVE
|
|
2426
|
port 0: (value) - ; channel: multiqc_config
|
|
2427
|
port 1: (value) - ; channel: fastqc
|
|
2428
|
port 2: (value) - ; channel: trimgalore/*
|
|
2429
|
port 3: (value) - ; channel: alignment/*
|
|
2430
|
port 4: (value) - ; channel: rseqc/*
|
|
2431
|
port 5: (value) - ; channel: rseqc/*
|
|
2432
|
port 6: (value) - ; channel: preseq/*
|
|
2433
|
port 7: (value) - ; channel: dupradar/*
|
|
2434
|
port 8: (value) - ; channel: featureCounts/*
|
|
2435
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2436
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2437
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2438
|
port 12: (value) - ; channel: software_versions/*
|
|
2439
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2440
|
port 14: (cntrl) OPEN; channel: $
|
|
2441
|
|
|
2442
|
[process] output_documentation
|
|
2443
|
status=ACTIVE
|
|
2444
|
port 0: (value) - ; channel: output_docs
|
|
2445
|
port 1: (value) - ; channel: prefix
|
|
2446
|
port 2: (cntrl) OPEN; channel: $
|
|
2447
|
|
|
2448
|
Apr-24 15:54:43.478 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 9 -- pending tasks are shown below
|
|
2449
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2450
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2451
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2452
|
~> TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: -; ]
|
|
2453
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2454
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2455
|
~> TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: -; ]
|
|
2456
|
~> TaskHandler[jobId: 1842331.srvslshpc001; id: 52; name: dupradar (sample39Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9 started: 1524576248390; exited: -; ]
|
|
2457
|
~> TaskHandler[jobId: 1842334.srvslshpc001; id: 55; name: dupradar (sample38Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/af/842ef026bbf6d874ba8056af228875 started: 1524576788416; exited: -; ]
|
|
2458
|
Apr-24 15:56:18.483 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842318.srvslshpc001; id: 41; name: rseqc (sample39AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/50/a9d819dbae8b159cc20ca722e7a03a started: 1524574273277; exited: 2018-04-24T13:56:13Z; ]
|
|
2459
|
Apr-24 15:57:43.485 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842321.srvslshpc001; id: 45; name: rseqc (sample38AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/bb/d8291ff0798f831622919ec00e10cd started: 1524575708360; exited: 2018-04-24T13:57:41Z; ]
|
|
2460
|
Apr-24 15:57:43.500 [Actor Thread 147] DEBUG nextflow.Session - <<< barrier arrive (process: rseqc)
|
|
2461
|
Apr-24 15:59:08.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842334.srvslshpc001; id: 55; name: dupradar (sample38Aligned.sortedByCoord.out.markDups); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/af/842ef026bbf6d874ba8056af228875 started: 1524576788416; exited: 2018-04-24T13:59:05Z; ]
|
|
2462
|
Apr-24 15:59:40.651 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2463
|
[process] multiqc
|
|
2464
|
status=ACTIVE
|
|
2465
|
port 0: (value) - ; channel: multiqc_config
|
|
2466
|
port 1: (value) - ; channel: fastqc
|
|
2467
|
port 2: (value) - ; channel: trimgalore/*
|
|
2468
|
port 3: (value) - ; channel: alignment/*
|
|
2469
|
port 4: (value) - ; channel: rseqc/*
|
|
2470
|
port 5: (value) - ; channel: rseqc/*
|
|
2471
|
port 6: (value) - ; channel: preseq/*
|
|
2472
|
port 7: (value) - ; channel: dupradar/*
|
|
2473
|
port 8: (value) - ; channel: featureCounts/*
|
|
2474
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2475
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2476
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2477
|
port 12: (value) - ; channel: software_versions/*
|
|
2478
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2479
|
port 14: (cntrl) OPEN; channel: $
|
|
2480
|
|
|
2481
|
[process] output_documentation
|
|
2482
|
status=ACTIVE
|
|
2483
|
port 0: (value) - ; channel: output_docs
|
|
2484
|
port 1: (value) - ; channel: prefix
|
|
2485
|
port 2: (cntrl) OPEN; channel: $
|
|
2486
|
|
|
2487
|
Apr-24 15:59:43.490 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 6 -- pending tasks are shown below
|
|
2488
|
~> TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: -; ]
|
|
2489
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2490
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2491
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2492
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2493
|
~> TaskHandler[jobId: 1842331.srvslshpc001; id: 52; name: dupradar (sample39Aligned.sortedByCoord.out.markDups); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9 started: 1524576248390; exited: -; ]
|
|
2494
|
Apr-24 16:03:03.495 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842299.srvslshpc001; id: 23; name: genebody_coverage (sample37AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/df/c16f93dd251058d09485a3f7b9c8b3 started: 1524573058245; exited: 2018-04-24T14:03:03Z; ]
|
|
2495
|
Apr-24 16:04:13.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842331.srvslshpc001; id: 52; name: dupradar (sample39Aligned.sortedByCoord.out.markDups); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/8d/e72fbfe00983dec1d90e31aca7a1a9 started: 1524576248390; exited: 2018-04-24T14:04:08Z; ]
|
|
2496
|
Apr-24 16:04:13.506 [Actor Thread 151] DEBUG nextflow.Session - <<< barrier arrive (process: dupradar)
|
|
2497
|
Apr-24 16:04:40.732 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2498
|
[process] multiqc
|
|
2499
|
status=ACTIVE
|
|
2500
|
port 0: (value) - ; channel: multiqc_config
|
|
2501
|
port 1: (value) - ; channel: fastqc
|
|
2502
|
port 2: (value) - ; channel: trimgalore/*
|
|
2503
|
port 3: (value) - ; channel: alignment/*
|
|
2504
|
port 4: (value) - ; channel: rseqc/*
|
|
2505
|
port 5: (value) - ; channel: rseqc/*
|
|
2506
|
port 6: (value) - ; channel: preseq/*
|
|
2507
|
port 7: (value) - ; channel: dupradar/*
|
|
2508
|
port 8: (value) - ; channel: featureCounts/*
|
|
2509
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2510
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2511
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2512
|
port 12: (value) - ; channel: software_versions/*
|
|
2513
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2514
|
port 14: (cntrl) OPEN; channel: $
|
|
2515
|
|
|
2516
|
[process] output_documentation
|
|
2517
|
status=ACTIVE
|
|
2518
|
port 0: (value) - ; channel: output_docs
|
|
2519
|
port 1: (value) - ; channel: prefix
|
|
2520
|
port 2: (cntrl) OPEN; channel: $
|
|
2521
|
|
|
2522
|
Apr-24 16:04:43.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2523
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2524
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2525
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2526
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2527
|
Apr-24 16:09:40.810 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2528
|
[process] multiqc
|
|
2529
|
status=ACTIVE
|
|
2530
|
port 0: (value) - ; channel: multiqc_config
|
|
2531
|
port 1: (value) - ; channel: fastqc
|
|
2532
|
port 2: (value) - ; channel: trimgalore/*
|
|
2533
|
port 3: (value) - ; channel: alignment/*
|
|
2534
|
port 4: (value) - ; channel: rseqc/*
|
|
2535
|
port 5: (value) - ; channel: rseqc/*
|
|
2536
|
port 6: (value) - ; channel: preseq/*
|
|
2537
|
port 7: (value) - ; channel: dupradar/*
|
|
2538
|
port 8: (value) - ; channel: featureCounts/*
|
|
2539
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2540
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2541
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2542
|
port 12: (value) - ; channel: software_versions/*
|
|
2543
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2544
|
port 14: (cntrl) OPEN; channel: $
|
|
2545
|
|
|
2546
|
[process] output_documentation
|
|
2547
|
status=ACTIVE
|
|
2548
|
port 0: (value) - ; channel: output_docs
|
|
2549
|
port 1: (value) - ; channel: prefix
|
|
2550
|
port 2: (cntrl) OPEN; channel: $
|
|
2551
|
|
|
2552
|
Apr-24 16:09:43.511 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2553
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2554
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2555
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2556
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2557
|
Apr-24 16:14:40.893 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2558
|
[process] multiqc
|
|
2559
|
status=ACTIVE
|
|
2560
|
port 0: (value) - ; channel: multiqc_config
|
|
2561
|
port 1: (value) - ; channel: fastqc
|
|
2562
|
port 2: (value) - ; channel: trimgalore/*
|
|
2563
|
port 3: (value) - ; channel: alignment/*
|
|
2564
|
port 4: (value) - ; channel: rseqc/*
|
|
2565
|
port 5: (value) - ; channel: rseqc/*
|
|
2566
|
port 6: (value) - ; channel: preseq/*
|
|
2567
|
port 7: (value) - ; channel: dupradar/*
|
|
2568
|
port 8: (value) - ; channel: featureCounts/*
|
|
2569
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2570
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2571
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2572
|
port 12: (value) - ; channel: software_versions/*
|
|
2573
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2574
|
port 14: (cntrl) OPEN; channel: $
|
|
2575
|
|
|
2576
|
[process] output_documentation
|
|
2577
|
status=ACTIVE
|
|
2578
|
port 0: (value) - ; channel: output_docs
|
|
2579
|
port 1: (value) - ; channel: prefix
|
|
2580
|
port 2: (cntrl) OPEN; channel: $
|
|
2581
|
|
|
2582
|
Apr-24 16:14:43.519 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2583
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2584
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2585
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2586
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2587
|
Apr-24 16:19:40.971 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2588
|
[process] multiqc
|
|
2589
|
status=ACTIVE
|
|
2590
|
port 0: (value) - ; channel: multiqc_config
|
|
2591
|
port 1: (value) - ; channel: fastqc
|
|
2592
|
port 2: (value) - ; channel: trimgalore/*
|
|
2593
|
port 3: (value) - ; channel: alignment/*
|
|
2594
|
port 4: (value) - ; channel: rseqc/*
|
|
2595
|
port 5: (value) - ; channel: rseqc/*
|
|
2596
|
port 6: (value) - ; channel: preseq/*
|
|
2597
|
port 7: (value) - ; channel: dupradar/*
|
|
2598
|
port 8: (value) - ; channel: featureCounts/*
|
|
2599
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2600
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2601
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2602
|
port 12: (value) - ; channel: software_versions/*
|
|
2603
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2604
|
port 14: (cntrl) OPEN; channel: $
|
|
2605
|
|
|
2606
|
[process] output_documentation
|
|
2607
|
status=ACTIVE
|
|
2608
|
port 0: (value) - ; channel: output_docs
|
|
2609
|
port 1: (value) - ; channel: prefix
|
|
2610
|
port 2: (cntrl) OPEN; channel: $
|
|
2611
|
|
|
2612
|
Apr-24 16:19:43.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2613
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2614
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2615
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2616
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2617
|
Apr-24 16:24:41.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2618
|
[process] multiqc
|
|
2619
|
status=ACTIVE
|
|
2620
|
port 0: (value) - ; channel: multiqc_config
|
|
2621
|
port 1: (value) - ; channel: fastqc
|
|
2622
|
port 2: (value) - ; channel: trimgalore/*
|
|
2623
|
port 3: (value) - ; channel: alignment/*
|
|
2624
|
port 4: (value) - ; channel: rseqc/*
|
|
2625
|
port 5: (value) - ; channel: rseqc/*
|
|
2626
|
port 6: (value) - ; channel: preseq/*
|
|
2627
|
port 7: (value) - ; channel: dupradar/*
|
|
2628
|
port 8: (value) - ; channel: featureCounts/*
|
|
2629
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2630
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2631
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2632
|
port 12: (value) - ; channel: software_versions/*
|
|
2633
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2634
|
port 14: (cntrl) OPEN; channel: $
|
|
2635
|
|
|
2636
|
[process] output_documentation
|
|
2637
|
status=ACTIVE
|
|
2638
|
port 0: (value) - ; channel: output_docs
|
|
2639
|
port 1: (value) - ; channel: prefix
|
|
2640
|
port 2: (cntrl) OPEN; channel: $
|
|
2641
|
|
|
2642
|
Apr-24 16:24:43.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2643
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2644
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2645
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2646
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2647
|
Apr-24 16:29:41.134 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2648
|
[process] multiqc
|
|
2649
|
status=ACTIVE
|
|
2650
|
port 0: (value) - ; channel: multiqc_config
|
|
2651
|
port 1: (value) - ; channel: fastqc
|
|
2652
|
port 2: (value) - ; channel: trimgalore/*
|
|
2653
|
port 3: (value) - ; channel: alignment/*
|
|
2654
|
port 4: (value) - ; channel: rseqc/*
|
|
2655
|
port 5: (value) - ; channel: rseqc/*
|
|
2656
|
port 6: (value) - ; channel: preseq/*
|
|
2657
|
port 7: (value) - ; channel: dupradar/*
|
|
2658
|
port 8: (value) - ; channel: featureCounts/*
|
|
2659
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2660
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2661
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2662
|
port 12: (value) - ; channel: software_versions/*
|
|
2663
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2664
|
port 14: (cntrl) OPEN; channel: $
|
|
2665
|
|
|
2666
|
[process] output_documentation
|
|
2667
|
status=ACTIVE
|
|
2668
|
port 0: (value) - ; channel: output_docs
|
|
2669
|
port 1: (value) - ; channel: prefix
|
|
2670
|
port 2: (cntrl) OPEN; channel: $
|
|
2671
|
|
|
2672
|
Apr-24 16:29:43.554 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2673
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2674
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2675
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2676
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2677
|
Apr-24 16:34:41.221 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2678
|
[process] multiqc
|
|
2679
|
status=ACTIVE
|
|
2680
|
port 0: (value) - ; channel: multiqc_config
|
|
2681
|
port 1: (value) - ; channel: fastqc
|
|
2682
|
port 2: (value) - ; channel: trimgalore/*
|
|
2683
|
port 3: (value) - ; channel: alignment/*
|
|
2684
|
port 4: (value) - ; channel: rseqc/*
|
|
2685
|
port 5: (value) - ; channel: rseqc/*
|
|
2686
|
port 6: (value) - ; channel: preseq/*
|
|
2687
|
port 7: (value) - ; channel: dupradar/*
|
|
2688
|
port 8: (value) - ; channel: featureCounts/*
|
|
2689
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2690
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2691
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2692
|
port 12: (value) - ; channel: software_versions/*
|
|
2693
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2694
|
port 14: (cntrl) OPEN; channel: $
|
|
2695
|
|
|
2696
|
[process] output_documentation
|
|
2697
|
status=ACTIVE
|
|
2698
|
port 0: (value) - ; channel: output_docs
|
|
2699
|
port 1: (value) - ; channel: prefix
|
|
2700
|
port 2: (cntrl) OPEN; channel: $
|
|
2701
|
|
|
2702
|
Apr-24 16:34:43.565 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2703
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2704
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2705
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2706
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2707
|
Apr-24 16:39:41.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2708
|
[process] multiqc
|
|
2709
|
status=ACTIVE
|
|
2710
|
port 0: (value) - ; channel: multiqc_config
|
|
2711
|
port 1: (value) - ; channel: fastqc
|
|
2712
|
port 2: (value) - ; channel: trimgalore/*
|
|
2713
|
port 3: (value) - ; channel: alignment/*
|
|
2714
|
port 4: (value) - ; channel: rseqc/*
|
|
2715
|
port 5: (value) - ; channel: rseqc/*
|
|
2716
|
port 6: (value) - ; channel: preseq/*
|
|
2717
|
port 7: (value) - ; channel: dupradar/*
|
|
2718
|
port 8: (value) - ; channel: featureCounts/*
|
|
2719
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2720
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2721
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2722
|
port 12: (value) - ; channel: software_versions/*
|
|
2723
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2724
|
port 14: (cntrl) OPEN; channel: $
|
|
2725
|
|
|
2726
|
[process] output_documentation
|
|
2727
|
status=ACTIVE
|
|
2728
|
port 0: (value) - ; channel: output_docs
|
|
2729
|
port 1: (value) - ; channel: prefix
|
|
2730
|
port 2: (cntrl) OPEN; channel: $
|
|
2731
|
|
|
2732
|
Apr-24 16:39:43.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2733
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2734
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2735
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2736
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2737
|
Apr-24 16:44:41.397 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2738
|
[process] multiqc
|
|
2739
|
status=ACTIVE
|
|
2740
|
port 0: (value) - ; channel: multiqc_config
|
|
2741
|
port 1: (value) - ; channel: fastqc
|
|
2742
|
port 2: (value) - ; channel: trimgalore/*
|
|
2743
|
port 3: (value) - ; channel: alignment/*
|
|
2744
|
port 4: (value) - ; channel: rseqc/*
|
|
2745
|
port 5: (value) - ; channel: rseqc/*
|
|
2746
|
port 6: (value) - ; channel: preseq/*
|
|
2747
|
port 7: (value) - ; channel: dupradar/*
|
|
2748
|
port 8: (value) - ; channel: featureCounts/*
|
|
2749
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2750
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2751
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2752
|
port 12: (value) - ; channel: software_versions/*
|
|
2753
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2754
|
port 14: (cntrl) OPEN; channel: $
|
|
2755
|
|
|
2756
|
[process] output_documentation
|
|
2757
|
status=ACTIVE
|
|
2758
|
port 0: (value) - ; channel: output_docs
|
|
2759
|
port 1: (value) - ; channel: prefix
|
|
2760
|
port 2: (cntrl) OPEN; channel: $
|
|
2761
|
|
|
2762
|
Apr-24 16:44:43.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2763
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2764
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2765
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2766
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2767
|
Apr-24 16:49:41.496 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2768
|
[process] multiqc
|
|
2769
|
status=ACTIVE
|
|
2770
|
port 0: (value) - ; channel: multiqc_config
|
|
2771
|
port 1: (value) - ; channel: fastqc
|
|
2772
|
port 2: (value) - ; channel: trimgalore/*
|
|
2773
|
port 3: (value) - ; channel: alignment/*
|
|
2774
|
port 4: (value) - ; channel: rseqc/*
|
|
2775
|
port 5: (value) - ; channel: rseqc/*
|
|
2776
|
port 6: (value) - ; channel: preseq/*
|
|
2777
|
port 7: (value) - ; channel: dupradar/*
|
|
2778
|
port 8: (value) - ; channel: featureCounts/*
|
|
2779
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2780
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2781
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2782
|
port 12: (value) - ; channel: software_versions/*
|
|
2783
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2784
|
port 14: (cntrl) OPEN; channel: $
|
|
2785
|
|
|
2786
|
[process] output_documentation
|
|
2787
|
status=ACTIVE
|
|
2788
|
port 0: (value) - ; channel: output_docs
|
|
2789
|
port 1: (value) - ; channel: prefix
|
|
2790
|
port 2: (cntrl) OPEN; channel: $
|
|
2791
|
|
|
2792
|
Apr-24 16:49:43.598 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2793
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2794
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2795
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2796
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2797
|
Apr-24 16:54:41.585 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2798
|
[process] multiqc
|
|
2799
|
status=ACTIVE
|
|
2800
|
port 0: (value) - ; channel: multiqc_config
|
|
2801
|
port 1: (value) - ; channel: fastqc
|
|
2802
|
port 2: (value) - ; channel: trimgalore/*
|
|
2803
|
port 3: (value) - ; channel: alignment/*
|
|
2804
|
port 4: (value) - ; channel: rseqc/*
|
|
2805
|
port 5: (value) - ; channel: rseqc/*
|
|
2806
|
port 6: (value) - ; channel: preseq/*
|
|
2807
|
port 7: (value) - ; channel: dupradar/*
|
|
2808
|
port 8: (value) - ; channel: featureCounts/*
|
|
2809
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2810
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2811
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2812
|
port 12: (value) - ; channel: software_versions/*
|
|
2813
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2814
|
port 14: (cntrl) OPEN; channel: $
|
|
2815
|
|
|
2816
|
[process] output_documentation
|
|
2817
|
status=ACTIVE
|
|
2818
|
port 0: (value) - ; channel: output_docs
|
|
2819
|
port 1: (value) - ; channel: prefix
|
|
2820
|
port 2: (cntrl) OPEN; channel: $
|
|
2821
|
|
|
2822
|
Apr-24 16:54:43.606 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2823
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2824
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2825
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2826
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2827
|
Apr-24 16:59:41.679 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2828
|
[process] multiqc
|
|
2829
|
status=ACTIVE
|
|
2830
|
port 0: (value) - ; channel: multiqc_config
|
|
2831
|
port 1: (value) - ; channel: fastqc
|
|
2832
|
port 2: (value) - ; channel: trimgalore/*
|
|
2833
|
port 3: (value) - ; channel: alignment/*
|
|
2834
|
port 4: (value) - ; channel: rseqc/*
|
|
2835
|
port 5: (value) - ; channel: rseqc/*
|
|
2836
|
port 6: (value) - ; channel: preseq/*
|
|
2837
|
port 7: (value) - ; channel: dupradar/*
|
|
2838
|
port 8: (value) - ; channel: featureCounts/*
|
|
2839
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2840
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2841
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2842
|
port 12: (value) - ; channel: software_versions/*
|
|
2843
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2844
|
port 14: (cntrl) OPEN; channel: $
|
|
2845
|
|
|
2846
|
[process] output_documentation
|
|
2847
|
status=ACTIVE
|
|
2848
|
port 0: (value) - ; channel: output_docs
|
|
2849
|
port 1: (value) - ; channel: prefix
|
|
2850
|
port 2: (cntrl) OPEN; channel: $
|
|
2851
|
|
|
2852
|
Apr-24 16:59:43.612 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2853
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2854
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2855
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2856
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2857
|
Apr-24 17:04:41.769 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2858
|
[process] multiqc
|
|
2859
|
status=ACTIVE
|
|
2860
|
port 0: (value) - ; channel: multiqc_config
|
|
2861
|
port 1: (value) - ; channel: fastqc
|
|
2862
|
port 2: (value) - ; channel: trimgalore/*
|
|
2863
|
port 3: (value) - ; channel: alignment/*
|
|
2864
|
port 4: (value) - ; channel: rseqc/*
|
|
2865
|
port 5: (value) - ; channel: rseqc/*
|
|
2866
|
port 6: (value) - ; channel: preseq/*
|
|
2867
|
port 7: (value) - ; channel: dupradar/*
|
|
2868
|
port 8: (value) - ; channel: featureCounts/*
|
|
2869
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2870
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2871
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2872
|
port 12: (value) - ; channel: software_versions/*
|
|
2873
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2874
|
port 14: (cntrl) OPEN; channel: $
|
|
2875
|
|
|
2876
|
[process] output_documentation
|
|
2877
|
status=ACTIVE
|
|
2878
|
port 0: (value) - ; channel: output_docs
|
|
2879
|
port 1: (value) - ; channel: prefix
|
|
2880
|
port 2: (cntrl) OPEN; channel: $
|
|
2881
|
|
|
2882
|
Apr-24 17:04:43.622 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below
|
|
2883
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2884
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2885
|
~> TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: -; ]
|
|
2886
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2887
|
Apr-24 17:08:23.629 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842319.srvslshpc001; id: 42; name: genebody_coverage (sample39AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/89/4b5c517f4b65464afbd6125ae9a5ed started: 1524574448277; exited: 2018-04-24T15:08:23Z; ]
|
|
2888
|
Apr-24 17:09:41.789 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2889
|
[process] multiqc
|
|
2890
|
status=ACTIVE
|
|
2891
|
port 0: (value) - ; channel: multiqc_config
|
|
2892
|
port 1: (value) - ; channel: fastqc
|
|
2893
|
port 2: (value) - ; channel: trimgalore/*
|
|
2894
|
port 3: (value) - ; channel: alignment/*
|
|
2895
|
port 4: (value) - ; channel: rseqc/*
|
|
2896
|
port 5: (value) - ; channel: rseqc/*
|
|
2897
|
port 6: (value) - ; channel: preseq/*
|
|
2898
|
port 7: (value) - ; channel: dupradar/*
|
|
2899
|
port 8: (value) - ; channel: featureCounts/*
|
|
2900
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2901
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2902
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2903
|
port 12: (value) - ; channel: software_versions/*
|
|
2904
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2905
|
port 14: (cntrl) OPEN; channel: $
|
|
2906
|
|
|
2907
|
[process] output_documentation
|
|
2908
|
status=ACTIVE
|
|
2909
|
port 0: (value) - ; channel: output_docs
|
|
2910
|
port 1: (value) - ; channel: prefix
|
|
2911
|
port 2: (cntrl) OPEN; channel: $
|
|
2912
|
|
|
2913
|
Apr-24 17:09:43.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below
|
|
2914
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2915
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2916
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2917
|
Apr-24 17:14:41.873 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2918
|
[process] multiqc
|
|
2919
|
status=ACTIVE
|
|
2920
|
port 0: (value) - ; channel: multiqc_config
|
|
2921
|
port 1: (value) - ; channel: fastqc
|
|
2922
|
port 2: (value) - ; channel: trimgalore/*
|
|
2923
|
port 3: (value) - ; channel: alignment/*
|
|
2924
|
port 4: (value) - ; channel: rseqc/*
|
|
2925
|
port 5: (value) - ; channel: rseqc/*
|
|
2926
|
port 6: (value) - ; channel: preseq/*
|
|
2927
|
port 7: (value) - ; channel: dupradar/*
|
|
2928
|
port 8: (value) - ; channel: featureCounts/*
|
|
2929
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2930
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2931
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2932
|
port 12: (value) - ; channel: software_versions/*
|
|
2933
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2934
|
port 14: (cntrl) OPEN; channel: $
|
|
2935
|
|
|
2936
|
[process] output_documentation
|
|
2937
|
status=ACTIVE
|
|
2938
|
port 0: (value) - ; channel: output_docs
|
|
2939
|
port 1: (value) - ; channel: prefix
|
|
2940
|
port 2: (cntrl) OPEN; channel: $
|
|
2941
|
|
|
2942
|
Apr-24 17:14:43.639 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below
|
|
2943
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2944
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2945
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2946
|
Apr-24 17:19:41.974 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2947
|
[process] multiqc
|
|
2948
|
status=ACTIVE
|
|
2949
|
port 0: (value) - ; channel: multiqc_config
|
|
2950
|
port 1: (value) - ; channel: fastqc
|
|
2951
|
port 2: (value) - ; channel: trimgalore/*
|
|
2952
|
port 3: (value) - ; channel: alignment/*
|
|
2953
|
port 4: (value) - ; channel: rseqc/*
|
|
2954
|
port 5: (value) - ; channel: rseqc/*
|
|
2955
|
port 6: (value) - ; channel: preseq/*
|
|
2956
|
port 7: (value) - ; channel: dupradar/*
|
|
2957
|
port 8: (value) - ; channel: featureCounts/*
|
|
2958
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2959
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2960
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2961
|
port 12: (value) - ; channel: software_versions/*
|
|
2962
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2963
|
port 14: (cntrl) OPEN; channel: $
|
|
2964
|
|
|
2965
|
[process] output_documentation
|
|
2966
|
status=ACTIVE
|
|
2967
|
port 0: (value) - ; channel: output_docs
|
|
2968
|
port 1: (value) - ; channel: prefix
|
|
2969
|
port 2: (cntrl) OPEN; channel: $
|
|
2970
|
|
|
2971
|
Apr-24 17:19:43.645 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below
|
|
2972
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
2973
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
2974
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
2975
|
Apr-24 17:24:42.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
2976
|
[process] multiqc
|
|
2977
|
status=ACTIVE
|
|
2978
|
port 0: (value) - ; channel: multiqc_config
|
|
2979
|
port 1: (value) - ; channel: fastqc
|
|
2980
|
port 2: (value) - ; channel: trimgalore/*
|
|
2981
|
port 3: (value) - ; channel: alignment/*
|
|
2982
|
port 4: (value) - ; channel: rseqc/*
|
|
2983
|
port 5: (value) - ; channel: rseqc/*
|
|
2984
|
port 6: (value) - ; channel: preseq/*
|
|
2985
|
port 7: (value) - ; channel: dupradar/*
|
|
2986
|
port 8: (value) - ; channel: featureCounts/*
|
|
2987
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
2988
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
2989
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
2990
|
port 12: (value) - ; channel: software_versions/*
|
|
2991
|
port 13: (value) - ; channel: workflow_summary/*
|
|
2992
|
port 14: (cntrl) OPEN; channel: $
|
|
2993
|
|
|
2994
|
[process] output_documentation
|
|
2995
|
status=ACTIVE
|
|
2996
|
port 0: (value) - ; channel: output_docs
|
|
2997
|
port 1: (value) - ; channel: prefix
|
|
2998
|
port 2: (cntrl) OPEN; channel: $
|
|
2999
|
|
|
3000
|
Apr-24 17:24:43.658 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below
|
|
3001
|
~> TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: -; ]
|
|
3002
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
3003
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3004
|
Apr-24 17:29:13.665 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842306.srvslshpc001; id: 29; name: genebody_coverage (sample41AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/59/f123347650e1834aa7ec8977ee460e started: 1524573058259; exited: 2018-04-24T15:29:13Z; ]
|
|
3005
|
Apr-24 17:29:42.151 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3006
|
[process] multiqc
|
|
3007
|
status=ACTIVE
|
|
3008
|
port 0: (value) - ; channel: multiqc_config
|
|
3009
|
port 1: (value) - ; channel: fastqc
|
|
3010
|
port 2: (value) - ; channel: trimgalore/*
|
|
3011
|
port 3: (value) - ; channel: alignment/*
|
|
3012
|
port 4: (value) - ; channel: rseqc/*
|
|
3013
|
port 5: (value) - ; channel: rseqc/*
|
|
3014
|
port 6: (value) - ; channel: preseq/*
|
|
3015
|
port 7: (value) - ; channel: dupradar/*
|
|
3016
|
port 8: (value) - ; channel: featureCounts/*
|
|
3017
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3018
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3019
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3020
|
port 12: (value) - ; channel: software_versions/*
|
|
3021
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3022
|
port 14: (cntrl) OPEN; channel: $
|
|
3023
|
|
|
3024
|
[process] output_documentation
|
|
3025
|
status=ACTIVE
|
|
3026
|
port 0: (value) - ; channel: output_docs
|
|
3027
|
port 1: (value) - ; channel: prefix
|
|
3028
|
port 2: (cntrl) OPEN; channel: $
|
|
3029
|
|
|
3030
|
Apr-24 17:29:43.666 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 2 -- pending tasks are shown below
|
|
3031
|
~> TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: -; ]
|
|
3032
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3033
|
Apr-24 17:33:18.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842309.srvslshpc001; id: 33; name: genebody_coverage (sample40AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/b8/05430f0d785abb6a3e82308a5e3d36 started: 1524573463220; exited: 2018-04-24T15:33:16Z; ]
|
|
3034
|
Apr-24 17:34:42.239 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3035
|
[process] multiqc
|
|
3036
|
status=ACTIVE
|
|
3037
|
port 0: (value) - ; channel: multiqc_config
|
|
3038
|
port 1: (value) - ; channel: fastqc
|
|
3039
|
port 2: (value) - ; channel: trimgalore/*
|
|
3040
|
port 3: (value) - ; channel: alignment/*
|
|
3041
|
port 4: (value) - ; channel: rseqc/*
|
|
3042
|
port 5: (value) - ; channel: rseqc/*
|
|
3043
|
port 6: (value) - ; channel: preseq/*
|
|
3044
|
port 7: (value) - ; channel: dupradar/*
|
|
3045
|
port 8: (value) - ; channel: featureCounts/*
|
|
3046
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3047
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3048
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3049
|
port 12: (value) - ; channel: software_versions/*
|
|
3050
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3051
|
port 14: (cntrl) OPEN; channel: $
|
|
3052
|
|
|
3053
|
[process] output_documentation
|
|
3054
|
status=ACTIVE
|
|
3055
|
port 0: (value) - ; channel: output_docs
|
|
3056
|
port 1: (value) - ; channel: prefix
|
|
3057
|
port 2: (cntrl) OPEN; channel: $
|
|
3058
|
|
|
3059
|
Apr-24 17:34:43.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3060
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3061
|
Apr-24 17:39:42.324 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3062
|
[process] multiqc
|
|
3063
|
status=ACTIVE
|
|
3064
|
port 0: (value) - ; channel: multiqc_config
|
|
3065
|
port 1: (value) - ; channel: fastqc
|
|
3066
|
port 2: (value) - ; channel: trimgalore/*
|
|
3067
|
port 3: (value) - ; channel: alignment/*
|
|
3068
|
port 4: (value) - ; channel: rseqc/*
|
|
3069
|
port 5: (value) - ; channel: rseqc/*
|
|
3070
|
port 6: (value) - ; channel: preseq/*
|
|
3071
|
port 7: (value) - ; channel: dupradar/*
|
|
3072
|
port 8: (value) - ; channel: featureCounts/*
|
|
3073
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3074
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3075
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3076
|
port 12: (value) - ; channel: software_versions/*
|
|
3077
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3078
|
port 14: (cntrl) OPEN; channel: $
|
|
3079
|
|
|
3080
|
[process] output_documentation
|
|
3081
|
status=ACTIVE
|
|
3082
|
port 0: (value) - ; channel: output_docs
|
|
3083
|
port 1: (value) - ; channel: prefix
|
|
3084
|
port 2: (cntrl) OPEN; channel: $
|
|
3085
|
|
|
3086
|
Apr-24 17:39:43.682 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3087
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3088
|
Apr-24 17:44:42.409 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3089
|
[process] multiqc
|
|
3090
|
status=ACTIVE
|
|
3091
|
port 0: (value) - ; channel: multiqc_config
|
|
3092
|
port 1: (value) - ; channel: fastqc
|
|
3093
|
port 2: (value) - ; channel: trimgalore/*
|
|
3094
|
port 3: (value) - ; channel: alignment/*
|
|
3095
|
port 4: (value) - ; channel: rseqc/*
|
|
3096
|
port 5: (value) - ; channel: rseqc/*
|
|
3097
|
port 6: (value) - ; channel: preseq/*
|
|
3098
|
port 7: (value) - ; channel: dupradar/*
|
|
3099
|
port 8: (value) - ; channel: featureCounts/*
|
|
3100
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3101
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3102
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3103
|
port 12: (value) - ; channel: software_versions/*
|
|
3104
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3105
|
port 14: (cntrl) OPEN; channel: $
|
|
3106
|
|
|
3107
|
[process] output_documentation
|
|
3108
|
status=ACTIVE
|
|
3109
|
port 0: (value) - ; channel: output_docs
|
|
3110
|
port 1: (value) - ; channel: prefix
|
|
3111
|
port 2: (cntrl) OPEN; channel: $
|
|
3112
|
|
|
3113
|
Apr-24 17:44:43.696 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3114
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3115
|
Apr-24 17:49:42.509 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3116
|
[process] multiqc
|
|
3117
|
status=ACTIVE
|
|
3118
|
port 0: (value) - ; channel: multiqc_config
|
|
3119
|
port 1: (value) - ; channel: fastqc
|
|
3120
|
port 2: (value) - ; channel: trimgalore/*
|
|
3121
|
port 3: (value) - ; channel: alignment/*
|
|
3122
|
port 4: (value) - ; channel: rseqc/*
|
|
3123
|
port 5: (value) - ; channel: rseqc/*
|
|
3124
|
port 6: (value) - ; channel: preseq/*
|
|
3125
|
port 7: (value) - ; channel: dupradar/*
|
|
3126
|
port 8: (value) - ; channel: featureCounts/*
|
|
3127
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3128
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3129
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3130
|
port 12: (value) - ; channel: software_versions/*
|
|
3131
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3132
|
port 14: (cntrl) OPEN; channel: $
|
|
3133
|
|
|
3134
|
[process] output_documentation
|
|
3135
|
status=ACTIVE
|
|
3136
|
port 0: (value) - ; channel: output_docs
|
|
3137
|
port 1: (value) - ; channel: prefix
|
|
3138
|
port 2: (cntrl) OPEN; channel: $
|
|
3139
|
|
|
3140
|
Apr-24 17:49:43.704 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3141
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3142
|
Apr-24 17:54:42.602 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3143
|
[process] multiqc
|
|
3144
|
status=ACTIVE
|
|
3145
|
port 0: (value) - ; channel: multiqc_config
|
|
3146
|
port 1: (value) - ; channel: fastqc
|
|
3147
|
port 2: (value) - ; channel: trimgalore/*
|
|
3148
|
port 3: (value) - ; channel: alignment/*
|
|
3149
|
port 4: (value) - ; channel: rseqc/*
|
|
3150
|
port 5: (value) - ; channel: rseqc/*
|
|
3151
|
port 6: (value) - ; channel: preseq/*
|
|
3152
|
port 7: (value) - ; channel: dupradar/*
|
|
3153
|
port 8: (value) - ; channel: featureCounts/*
|
|
3154
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3155
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3156
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3157
|
port 12: (value) - ; channel: software_versions/*
|
|
3158
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3159
|
port 14: (cntrl) OPEN; channel: $
|
|
3160
|
|
|
3161
|
[process] output_documentation
|
|
3162
|
status=ACTIVE
|
|
3163
|
port 0: (value) - ; channel: output_docs
|
|
3164
|
port 1: (value) - ; channel: prefix
|
|
3165
|
port 2: (cntrl) OPEN; channel: $
|
|
3166
|
|
|
3167
|
Apr-24 17:54:43.708 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3168
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3169
|
Apr-24 17:59:42.690 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3170
|
[process] multiqc
|
|
3171
|
status=ACTIVE
|
|
3172
|
port 0: (value) - ; channel: multiqc_config
|
|
3173
|
port 1: (value) - ; channel: fastqc
|
|
3174
|
port 2: (value) - ; channel: trimgalore/*
|
|
3175
|
port 3: (value) - ; channel: alignment/*
|
|
3176
|
port 4: (value) - ; channel: rseqc/*
|
|
3177
|
port 5: (value) - ; channel: rseqc/*
|
|
3178
|
port 6: (value) - ; channel: preseq/*
|
|
3179
|
port 7: (value) - ; channel: dupradar/*
|
|
3180
|
port 8: (value) - ; channel: featureCounts/*
|
|
3181
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3182
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3183
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3184
|
port 12: (value) - ; channel: software_versions/*
|
|
3185
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3186
|
port 14: (cntrl) OPEN; channel: $
|
|
3187
|
|
|
3188
|
[process] output_documentation
|
|
3189
|
status=ACTIVE
|
|
3190
|
port 0: (value) - ; channel: output_docs
|
|
3191
|
port 1: (value) - ; channel: prefix
|
|
3192
|
port 2: (cntrl) OPEN; channel: $
|
|
3193
|
|
|
3194
|
Apr-24 17:59:43.712 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3195
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3196
|
Apr-24 18:04:42.786 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3197
|
[process] multiqc
|
|
3198
|
status=ACTIVE
|
|
3199
|
port 0: (value) - ; channel: multiqc_config
|
|
3200
|
port 1: (value) - ; channel: fastqc
|
|
3201
|
port 2: (value) - ; channel: trimgalore/*
|
|
3202
|
port 3: (value) - ; channel: alignment/*
|
|
3203
|
port 4: (value) - ; channel: rseqc/*
|
|
3204
|
port 5: (value) - ; channel: rseqc/*
|
|
3205
|
port 6: (value) - ; channel: preseq/*
|
|
3206
|
port 7: (value) - ; channel: dupradar/*
|
|
3207
|
port 8: (value) - ; channel: featureCounts/*
|
|
3208
|
port 9: (value) - ; channel: featureCounts_biotype/*
|
|
3209
|
port 10: (value) - ; channel: stringtie/stringtie_log*
|
|
3210
|
port 11: (value) - ; channel: sample_correlation_results/*
|
|
3211
|
port 12: (value) - ; channel: software_versions/*
|
|
3212
|
port 13: (value) - ; channel: workflow_summary/*
|
|
3213
|
port 14: (cntrl) OPEN; channel: $
|
|
3214
|
|
|
3215
|
[process] output_documentation
|
|
3216
|
status=ACTIVE
|
|
3217
|
port 0: (value) - ; channel: output_docs
|
|
3218
|
port 1: (value) - ; channel: prefix
|
|
3219
|
port 2: (cntrl) OPEN; channel: $
|
|
3220
|
|
|
3221
|
Apr-24 18:04:43.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3222
|
~> TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: -; ]
|
|
3223
|
Apr-24 18:06:48.721 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842320.srvslshpc001; id: 44; name: genebody_coverage (sample38AlignedByCoord.out); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/f5/975056d916d5670b08bdcee7296ab1 started: 1524574988314; exited: 2018-04-24T16:06:45Z; ]
|
|
3224
|
Apr-24 18:06:48.729 [Actor Thread 156] DEBUG nextflow.Session - <<< barrier arrive (process: genebody_coverage)
|
|
3225
|
Apr-24 18:06:56.949 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process multiqc (sample41_R1) > jobId: 1842341.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/72/b84ed1cabf9f47272dd314f4d6ca09
|
|
3226
|
Apr-24 18:06:56.950 [Task submitter] INFO nextflow.Session - [72/b84ed1] Submitted process > multiqc (sample41_R1)
|
|
3227
|
Apr-24 18:09:42.880 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
|
|
3228
|
[process] output_documentation
|
|
3229
|
status=ACTIVE
|
|
3230
|
port 0: (value) - ; channel: output_docs
|
|
3231
|
port 1: (value) - ; channel: prefix
|
|
3232
|
port 2: (cntrl) OPEN; channel: $
|
|
3233
|
|
|
3234
|
Apr-24 18:09:43.720 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below
|
|
3235
|
~> TaskHandler[jobId: 1842341.srvslshpc001; id: 56; name: multiqc (sample41_R1); status: RUNNING; exit: -; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/72/b84ed1cabf9f47272dd314f4d6ca09 started: 1524586148720; exited: -; ]
|
|
3236
|
Apr-24 18:11:38.727 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842341.srvslshpc001; id: 56; name: multiqc (sample41_R1); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/72/b84ed1cabf9f47272dd314f4d6ca09 started: 1524586148720; exited: 2018-04-24T16:11:36Z; ]
|
|
3237
|
Apr-24 18:11:38.745 [Actor Thread 161] DEBUG nextflow.Session - <<< barrier arrive (process: multiqc)
|
|
3238
|
Apr-24 18:11:38.813 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process output_documentation (sample41_R1) > jobId: 1842342.srvslshpc001; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/23/16abf585085ea9752dba9bb318bb87
|
|
3239
|
Apr-24 18:11:38.814 [Task submitter] INFO nextflow.Session - [23/16abf5] Submitted process > output_documentation (sample41_R1)
|
|
3240
|
Apr-24 18:12:08.728 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1842342.srvslshpc001; id: 57; name: output_documentation (sample41_R1); status: COMPLETED; exit: 0; error: -; workDir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir/23/16abf585085ea9752dba9bb318bb87 started: 1524586328725; exited: 2018-04-24T16:12:06Z; ]
|
|
3241
|
Apr-24 18:12:08.731 [Actor Thread 161] DEBUG nextflow.Session - <<< barrier arrive (process: output_documentation)
|
|
3242
|
Apr-24 18:12:08.732 [main] DEBUG nextflow.Session - Session await > all process finished
|
|
3243
|
Apr-24 18:12:08.774 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
|
|
3244
|
Apr-24 18:12:13.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: pbs)
|
|
3245
|
Apr-24 18:12:13.725 [main] DEBUG nextflow.Session - Session await > all barriers passed
|
|
3246
|
Apr-24 18:12:14.058 [main] INFO nextflow.Nextflow - [nfcore/RNAseq] Sent summary e-mail to katie.viljoen@uct.ac.za (mail)
|
|
3247
|
Apr-24 18:12:14.086 [main] INFO nextflow.Nextflow - [nfcore/RNAseq] Pipeline Complete
|
|
3248
|
Apr-24 18:12:14.107 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=56; failedCount=1; ignoredCount=0; cachedCount=0; succeedDuration=6d 19h 41m 15s; failedDuration=1h 40s; cachedDuration=0ms]
|
|
3249
|
Apr-24 18:12:14.108 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
|
|
3250
|
Apr-24 18:12:14.114 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
|
|
3251
|
Apr-24 18:12:14.260 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
|
|
3252
|
{"merge_featureCounts":{"cpu":{"mean":65,"min":65,"q1":65,"q2":65,"q3":65,"max":65,"minLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","maxLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q1Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q2Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q3Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)"},"mem":{"mean":82796544,"min":82796544,"q1":82796544,"q2":82796544,"q3":82796544,"max":82796544,"minLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","maxLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q1Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q2Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q3Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)"},"time":{"mean":3077,"min":3077,"q1":3077,"q2":3077,"q3":3077,"max":3077,"minLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","maxLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q1Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q2Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q3Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)"},"reads":{"mean":51288112,"min":51288112,"q1":51288112,"q2":51288112,"q3":51288112,"max":51288112,"minLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","maxLabel":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q1Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q2Label":"merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts)","q3Label":"merge_featureCounts 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Apr-24 18:12:16.014 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
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Apr-24 18:12:16.390 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
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Apr-24 18:12:16.408 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
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