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 Apr-24 13:24:29.424 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.28.0 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 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 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 Apr-24 13:24:31.703 [main] INFO nextflow.cli.CmdRun - Launching `uct-cbio/RNAseq` [mad_ptolemy] - revision: 718fb1aff1 [dev] Apr-24 13:24:33.369 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/nextflow.config Apr-24 13:24:33.372 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq/nextflow.config Apr-24 13:24:33.388 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `uct_hex` 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] Apr-24 13:24:34.388 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by cli option `-with-singularity null` Apr-24 13:24:34.455 [main] DEBUG nextflow.Session - Session uuid: 623be393-8589-433d-8914-7a3b6390d0af Apr-24 13:24:34.456 [main] DEBUG nextflow.Session - Run name: mad_ptolemy Apr-24 13:24:34.459 [main] DEBUG nextflow.Session - Executor pool size: 64 Apr-24 13:24:34.593 [main] DEBUG nextflow.cli.CmdRun - Version: 0.28.0 build 4779 Modified: 10-03-2018 12:13 UTC (14:13 SAST) System: Linux 3.0.101-108.10-default Runtime: Groovy 2.4.13 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13 Encoding: UTF-8 (UTF-8) Process: 47974@srvslshpc600.uct.ac.za [137.158.155.219] CPUs: 64 - Mem: 126 GB (82.5 GB) - Swap: 0 (0) Apr-24 13:24:34.628 [main] DEBUG nextflow.Session - Work-dir: /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir [UNKNOWN (0x19830326)] Apr-24 13:24:36.058 [main] DEBUG nextflow.Session - Session start invoked Apr-24 13:24:36.064 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start 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 Apr-24 13:24:36.088 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Apr-24 13:24:37.508 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution 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: [:] Apr-24 13:24:37.831 [main] INFO nextflow.Nextflow - =================================== Apr-24 13:24:37.832 [main] INFO nextflow.Nextflow - nfcore/RNAseq ~ version 1.5dev Apr-24 13:24:37.833 [main] INFO nextflow.Nextflow - =================================== Apr-24 13:24:37.844 [main] INFO nextflow.Nextflow - Run Name : mad_ptolemy Reads : /researchdata/fhgfs/katie/NGI-RNAseq-test/*_R{1,2}.fastq.gz Data Type : Paired-End Genome : GRCh37 Strandedness : None Trim R1 : 0 Trim R2 : 0 Trim 3' R1 : 0 Trim 3' R2 : 0 Aligner : STAR STAR Index : /scratch/DB/bio/rna-seq/references/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ GTF Annotation : /scratch/DB/bio/rna-seq/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf BED Annotation : /scratch/DB/bio/rna-seq/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed Save Reference : No Save Trimmed : No Save Intermeds : No Max Memory : 256 GB Max CPUs : 64 Max Time : 24d 20h 31m 24s Output dir : /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-outdir Working dir : /researchdata/fhgfs/katie/NGI-RNAseq-test/nf-workdir Container : /scratch/DB/bio/singularity-containers/uct-cbio-rnaseq.img Pipeline Release: dev Current home : /home/kviljoen Current user : kviljoen Current path : /researchdata/fhgfs/katie/NGI-RNAseq-test R libraries : false Script dir : /home/kviljoen/.nextflow/assets/uct-cbio/RNAseq Config Profile : uct_hex E-mail Address : katie.viljoen@uct.ac.za Apr-24 13:24:37.845 [main] INFO nextflow.Nextflow - ========================================= Apr-24 13:24:37.987 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:37.988 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.006 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.010 [main] INFO nextflow.executor.Executor - [warm up] executor > pbs Apr-24 13:24:38.019 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbs' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Apr-24 13:24:38.023 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor Apr-24 13:24:38.024 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: pbs) Apr-24 13:24:38.028 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: pbs Apr-24 13:24:38.029 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.080 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc) Apr-24 13:24:38.084 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 64 Apr-24 13:24:38.124 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.125 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.126 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.127 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.130 [main] DEBUG nextflow.Session - >>> barrier register (process: trim_galore) Apr-24 13:24:38.133 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 64 Apr-24 13:24:38.236 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.237 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.238 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.240 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.242 [main] DEBUG nextflow.Session - >>> barrier register (process: star) Apr-24 13:24:38.243 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > star -- maxForks: 64 Apr-24 13:24:38.279 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.279 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.281 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.282 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.283 [main] DEBUG nextflow.Session - >>> barrier register (process: rseqc) Apr-24 13:24:38.284 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > rseqc -- maxForks: 64 Apr-24 13:24:38.306 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.306 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.311 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.312 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.315 [main] DEBUG nextflow.Session - >>> barrier register (process: genebody_coverage) Apr-24 13:24:38.316 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > genebody_coverage -- maxForks: 64 Apr-24 13:24:38.333 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.334 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.335 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.336 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.338 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq) Apr-24 13:24:38.346 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 64 Apr-24 13:24:38.372 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.373 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.378 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.379 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.386 [main] DEBUG nextflow.Session - >>> barrier register (process: markDuplicates) Apr-24 13:24:38.387 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDuplicates -- maxForks: 64 Apr-24 13:24:38.630 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.631 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.632 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.633 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.636 [main] DEBUG nextflow.Session - >>> barrier register (process: dupradar) Apr-24 13:24:38.639 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dupradar -- maxForks: 64 Apr-24 13:24:38.662 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.663 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.663 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.665 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.670 [main] DEBUG nextflow.Session - >>> barrier register (process: featureCounts) Apr-24 13:24:38.671 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 64 Apr-24 13:24:38.697 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.698 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.699 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.700 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.701 [main] DEBUG nextflow.Session - >>> barrier register (process: merge_featureCounts) Apr-24 13:24:38.702 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_featureCounts -- maxForks: 64 Apr-24 13:24:38.713 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.714 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.715 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.716 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.718 [main] DEBUG nextflow.Session - >>> barrier register (process: stringtieFPKM) Apr-24 13:24:38.719 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringtieFPKM -- maxForks: 64 Apr-24 13:24:38.758 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.759 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.759 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.760 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.762 [main] DEBUG nextflow.Session - >>> barrier register (process: sample_correlation) Apr-24 13:24:38.763 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sample_correlation -- maxForks: 64 Apr-24 13:24:38.776 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local Apr-24 13:24:38.777 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Apr-24 13:24:38.782 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Apr-24 13:24:38.783 [main] INFO nextflow.executor.Executor - [warm up] executor > local 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 Apr-24 13:24:38.796 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor Apr-24 13:24:38.797 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Apr-24 13:24:38.798 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local Apr-24 13:24:38.800 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions) Apr-24 13:24:38.800 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 64 Apr-24 13:24:38.806 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: local Apr-24 13:24:38.807 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Apr-24 13:24:38.808 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Apr-24 13:24:38.809 [main] DEBUG nextflow.Session - >>> barrier register (process: workflow_summary_mqc) Apr-24 13:24:38.810 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > workflow_summary_mqc -- maxForks: 64 Apr-24 13:24:38.830 [Actor Thread 6] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.VersionNumber -- 0.28.0 Apr-24 13:24:38.838 [Task submitter] INFO nextflow.Session - [81/2834d4] Submitted process > workflow_summary_mqc Apr-24 13:24:38.855 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.856 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.859 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.860 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.863 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc) Apr-24 13:24:38.864 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 64 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] Apr-24 13:24:38.883 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: pbs Apr-24 13:24:38.885 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'pbs' Apr-24 13:24:38.887 [main] DEBUG nextflow.executor.Executor - Initializing executor: pbs Apr-24 13:24:38.889 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m Apr-24 13:24:38.894 [main] DEBUG nextflow.Session - >>> barrier register (process: output_documentation) Apr-24 13:24:38.895 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 64 Apr-24 13:24:38.897 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Apr-24 13:24:38.902 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Apr-24 13:24:38.902 [main] DEBUG nextflow.Session - Session await Apr-24 13:24:38.906 [Task submitter] INFO nextflow.Session - [4a/6b391a] Submitted process > get_software_versions Apr-24 13:24:38.965 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: workflow_summary_mqc) 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 Apr-24 13:24:43.885 [Task submitter] INFO nextflow.Session - [8a/402e2e] Submitted process > fastqc (sample37) 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] Apr-24 13:24:44.666 [Actor Thread 18] DEBUG nextflow.Session - <<< barrier arrive (process: get_software_versions) 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 Apr-24 13:24:47.122 [Task submitter] INFO nextflow.Session - [44/9020e4] Submitted process > fastqc (sample40) 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 Apr-24 13:24:47.160 [Task submitter] INFO nextflow.Session - [7f/3e00fc] Submitted process > trim_galore (sample41) 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 Apr-24 13:24:47.191 [Task submitter] INFO nextflow.Session - [4d/c3b6f7] Submitted process > trim_galore (sample40) 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 Apr-24 13:24:47.235 [Task submitter] INFO nextflow.Session - [0f/155001] Submitted process > fastqc (sample38) 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 Apr-24 13:24:47.305 [Task submitter] INFO nextflow.Session - [cf/fd065a] Submitted process > fastqc (sample39) 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 Apr-24 13:24:47.344 [Task submitter] INFO nextflow.Session - [41/11c319] Submitted process > trim_galore (sample38) 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 Apr-24 13:24:47.425 [Task submitter] INFO nextflow.Session - [71/fa68aa] Submitted process > fastqc (sample41) 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 Apr-24 13:24:47.511 [Task submitter] INFO nextflow.Session - [6f/55d00a] Submitted process > trim_galore (sample39) 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 Apr-24 13:24:47.540 [Task submitter] INFO nextflow.Session - [ac/d8cf85] Submitted process > trim_galore (sample37) Apr-24 13:29:38.956 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:29:43.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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; ] 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; ] Apr-24 13:34:38.923 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:34:43.076 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 7 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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; ] Apr-24 13:37:03.092 [Actor Thread 20] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc) Apr-24 13:39:38.943 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:39:43.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 13:44:38.960 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:44:43.097 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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 Apr-24 13:49:31.243 [Task submitter] INFO nextflow.Session - [8f/480101] Submitted process > star (sample37) Apr-24 13:49:38.989 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:49:43.110 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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 Apr-24 13:50:28.191 [Task submitter] INFO nextflow.Session - [98/1630fc] Submitted process > star (sample38) Apr-24 13:54:39.003 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:54:43.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 13:59:39.007 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN; channel: reads port 1: (value) - ; channel: index port 2: (value) - ; channel: gtf port 3: (value) - ; channel: wherearemyfiles port 4: (cntrl) OPEN; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 13:59:43.127 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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 Apr-24 14:01:18.225 [Task submitter] INFO nextflow.Session - [31/a2fe86] Submitted process > star (sample40) 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; ] 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 Apr-24 14:02:28.277 [Task submitter] INFO nextflow.Session - [25/113d9b] Submitted process > star (sample41) 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; ] Apr-24 14:03:53.151 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: trim_galore) 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 Apr-24 14:03:53.213 [Task submitter] INFO nextflow.Session - [a7/97254c] Submitted process > star (sample39) Apr-24 14:04:39.102 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:04:43.136 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 14:09:39.190 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:09:43.142 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 14:14:39.197 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:14:43.150 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 5 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 14:16:48.686 [Actor Thread 38] INFO nextflow.Nextflow - Passed alignment > star (sample37) >> 95.88% << 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 Apr-24 14:16:51.776 [Task submitter] INFO nextflow.Session - [48/f5722e] Submitted process > preseq (sample37AlignedByCoord.out) 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 Apr-24 14:16:51.821 [Task submitter] INFO nextflow.Session - [86/089c84] Submitted process > markDuplicates (sample37AlignedByCoord.out) 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 Apr-24 14:16:51.869 [Task submitter] INFO nextflow.Session - [5e/8884c7] Submitted process > stringtieFPKM (sample37AlignedByCoord.out) 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 Apr-24 14:16:51.905 [Task submitter] INFO nextflow.Session - [4e/0b1fbd] Submitted process > featureCounts (sample37AlignedByCoord.out) 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 Apr-24 14:16:51.972 [Task submitter] INFO nextflow.Session - [df/c16f93] Submitted process > genebody_coverage (sample37AlignedByCoord.out) 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 Apr-24 14:16:52.023 [Task submitter] INFO nextflow.Session - [1d/848400] Submitted process > rseqc (sample37AlignedByCoord.out) Apr-24 14:19:39.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:19:43.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 14:24:39.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:24:43.176 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 14:29:38.722 [Actor Thread 38] INFO nextflow.Nextflow - Passed alignment > star (sample41) >> 97.27% << 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 Apr-24 14:29:38.774 [Task submitter] INFO nextflow.Session - [61/b53bbb] Submitted process > markDuplicates (sample41AlignedByCoord.out) 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 Apr-24 14:29:38.807 [Task submitter] INFO nextflow.Session - [b4/fa71ee] Submitted process > featureCounts (sample41AlignedByCoord.out) 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 Apr-24 14:29:38.843 [Task submitter] INFO nextflow.Session - [87/5d9fb6] Submitted process > preseq (sample41AlignedByCoord.out) 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 Apr-24 14:29:38.901 [Task submitter] INFO nextflow.Session - [bd/783d84] Submitted process > stringtieFPKM (sample41AlignedByCoord.out) 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 Apr-24 14:29:38.942 [Task submitter] INFO nextflow.Session - [b0/7aa70c] Submitted process > rseqc (sample41AlignedByCoord.out) 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 Apr-24 14:29:38.974 [Task submitter] INFO nextflow.Session - [59/f12334] Submitted process > genebody_coverage (sample41AlignedByCoord.out) Apr-24 14:29:39.307 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:29:43.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 15 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. Apr-24 14:34:39.404 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:34:43.207 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 15 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] Apr-24 14:34:58.271 [Actor Thread 55] INFO nextflow.Nextflow - Passed alignment > star (sample40) >> 97.30% << 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 Apr-24 14:35:03.311 [Task submitter] INFO nextflow.Session - [b8/4046a2] Submitted process > preseq (sample40AlignedByCoord.out) 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 Apr-24 14:35:03.338 [Task submitter] INFO nextflow.Session - [a5/d4109c] Submitted process > markDuplicates (sample40AlignedByCoord.out) 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 Apr-24 14:35:03.363 [Task submitter] INFO nextflow.Session - [b8/05430f] Submitted process > genebody_coverage (sample40AlignedByCoord.out) 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 Apr-24 14:35:03.387 [Task submitter] INFO nextflow.Session - [a8/79b168] Submitted process > rseqc (sample40AlignedByCoord.out) 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 Apr-24 14:35:03.440 [Task submitter] INFO nextflow.Session - [06/9dc499] Submitted process > stringtieFPKM (sample40AlignedByCoord.out) 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 Apr-24 14:35:03.468 [Task submitter] INFO nextflow.Session - [49/d847cb] Submitted process > featureCounts (sample40AlignedByCoord.out) 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; ] 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; ] Apr-24 14:39:39.463 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:39:43.227 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 18 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] 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; ] 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; ] 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; ] Apr-24 14:44:39.557 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] rseqc status=ACTIVE port 0: (queue) OPEN; channel: bam_rseqc port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN; channel: bam_geneBodyCoverage port 1: (value) - ; channel: bed12 port 2: (cntrl) OPEN; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN; channel: bam_preseq port 1: (cntrl) OPEN; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN; channel: bam port 1: (cntrl) OPEN; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN; channel: bam_featurecounts port 1: (value) - ; channel: gtf port 2: (value) - ; channel: biotypes_header port 3: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN; channel: bam_stringtieFPKM port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:44:43.246 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 14 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] 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; ] 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) 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 Apr-24 14:45:21.324 [Task submitter] INFO nextflow.Session - [b1/cac4bc] Re-submitted process > markDuplicates (sample40AlignedByCoord.out) 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; ] Apr-24 14:46:58.323 [Actor Thread 79] INFO nextflow.Nextflow - Passed alignment > star (sample39) >> 97.57% << 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 Apr-24 14:46:58.450 [Task submitter] INFO nextflow.Session - [cc/c538b4] Submitted process > stringtieFPKM (sample39AlignedByCoord.out) 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 Apr-24 14:46:58.593 [Task submitter] INFO nextflow.Session - [a1/4544b7] Submitted process > markDuplicates (sample39AlignedByCoord.out) 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 Apr-24 14:46:58.759 [Task submitter] INFO nextflow.Session - [3b/a48c0c] Submitted process > preseq (sample39AlignedByCoord.out) 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 Apr-24 14:46:58.814 [Task submitter] INFO nextflow.Session - [34/91dbe0] Submitted process > featureCounts (sample39AlignedByCoord.out) 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 Apr-24 14:46:58.842 [Task submitter] INFO nextflow.Session - [50/a9d819] Submitted process > rseqc (sample39AlignedByCoord.out) 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 Apr-24 14:46:58.864 [Task submitter] INFO nextflow.Session - [89/4b5c51] Submitted process > genebody_coverage (sample39AlignedByCoord.out) 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; ] Apr-24 14:48:33.298 [Actor Thread 90] INFO nextflow.Nextflow - Passed alignment > star (sample38) >> 97.36% << Apr-24 14:48:33.298 [Actor Thread 83] DEBUG nextflow.Session - <<< barrier arrive (process: star) 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 Apr-24 14:48:33.335 [Task submitter] INFO nextflow.Session - [f5/975056] Submitted process > genebody_coverage (sample38AlignedByCoord.out) 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 Apr-24 14:48:33.439 [Task submitter] INFO nextflow.Session - [bb/d8291f] Submitted process > rseqc (sample38AlignedByCoord.out) 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 Apr-24 14:48:33.498 [Task submitter] INFO nextflow.Session - [3b/3b36e2] Submitted process > preseq (sample38AlignedByCoord.out) 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 Apr-24 14:48:33.535 [Task submitter] INFO nextflow.Session - [de/7484a4] Submitted process > stringtieFPKM (sample38AlignedByCoord.out) 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 Apr-24 14:48:33.559 [Task submitter] INFO nextflow.Session - [a3/d55720] Submitted process > markDuplicates (sample38AlignedByCoord.out) 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 Apr-24 14:48:33.613 [Task submitter] INFO nextflow.Session - [a8/1d7f16] Submitted process > featureCounts (sample38AlignedByCoord.out) 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; ] 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 Apr-24 14:49:33.540 [Task submitter] INFO nextflow.Session - [fc/c14f95] Submitted process > dupradar (sample37Aligned.sortedByCoord.out.markDups) Apr-24 14:49:39.649 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:49:43.265 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 23 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] 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 Apr-24 14:49:48.324 [Task submitter] INFO nextflow.Session - [24/7338ef] Submitted process > dupradar (sample41Aligned.sortedByCoord.out.markDups) 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; ] 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; ] Apr-24 14:54:39.656 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:54:43.283 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 21 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. Apr-24 14:59:39.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 14:59:43.302 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 21 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] Apr-24 15:04:39.747 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:04:43.323 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 20 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] Apr-24 15:09:39.772 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:09:43.340 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 19 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] 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; ] 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 Apr-24 15:14:33.388 [Task submitter] INFO nextflow.Session - [ff/cec112] Submitted process > dupradar (sample40Aligned.sortedByCoord.out.markDups) 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; ] Apr-24 15:14:39.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:14:43.354 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 17 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. Apr-24 15:19:39.953 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) - ; channel: input_files port 1: (cntrl) OPEN; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) - ; channel: input_files port 1: (value) - ; channel: num_bams port 2: (value) - ; channel: mdsplot_header port 3: (value) - ; channel: heatmap_header port 4: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:19:43.379 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 17 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] 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; ] Apr-24 15:21:23.391 [Actor Thread 125] DEBUG nextflow.Session - <<< barrier arrive (process: stringtieFPKM) 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; ] 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 Apr-24 15:21:58.446 [Task submitter] INFO nextflow.Session - [8d/e72fbf] Submitted process > dupradar (sample39Aligned.sortedByCoord.out.markDups) 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; ] Apr-24 15:23:18.393 [Actor Thread 129] DEBUG nextflow.Session - <<< barrier arrive (process: preseq) 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; ] Apr-24 15:24:18.395 [Actor Thread 129] DEBUG nextflow.Session - <<< barrier arrive (process: featureCounts) 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 Apr-24 15:24:18.439 [Task submitter] INFO nextflow.Session - [9b/84b3f4] Submitted process > merge_featureCounts (sample41AlignedByCoord.out_gene.featureCounts) 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 Apr-24 15:24:18.471 [Task submitter] INFO nextflow.Session - [1a/cf18a4] Submitted process > sample_correlation (sample41.sortedByCoord.out_gene.featureCounts.txt) Apr-24 15:24:40.040 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:24:43.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 15 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] Apr-24 15:27:13.406 [Actor Thread 136] DEBUG nextflow.Session - <<< barrier arrive (process: merge_featureCounts) 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; ] Apr-24 15:27:18.438 [Actor Thread 136] DEBUG nextflow.Session - <<< barrier arrive (process: sample_correlation) Apr-24 15:29:40.130 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] dupradar status=ACTIVE port 0: (queue) OPEN; channel: bam_md port 1: (value) - ; channel: gtf port 2: (cntrl) OPEN; channel: $ [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:29:43.409 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 13 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] Apr-24 15:32:03.420 [Actor Thread 139] DEBUG nextflow.Session - <<< barrier arrive (process: markDuplicates) 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 Apr-24 15:32:03.531 [Task submitter] INFO nextflow.Session - [af/842ef0] Submitted process > dupradar (sample38Aligned.sortedByCoord.out.markDups) Apr-24 15:34:40.215 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:34:43.420 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 13 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] .. remaining tasks omitted. 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; ] 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; ] Apr-24 15:39:40.298 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:39:43.433 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 11 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 15:44:40.386 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:44:43.446 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 15:49:40.470 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:49:43.464 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 10 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 15:54:40.553 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:54:43.478 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 9 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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; ] Apr-24 15:57:43.500 [Actor Thread 147] DEBUG nextflow.Session - <<< barrier arrive (process: rseqc) 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; ] Apr-24 15:59:40.651 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 15:59:43.490 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 6 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] 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; ] Apr-24 16:04:13.506 [Actor Thread 151] DEBUG nextflow.Session - <<< barrier arrive (process: dupradar) Apr-24 16:04:40.732 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:04:43.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:09:40.810 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:09:43.511 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:14:40.893 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:14:43.519 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:19:40.971 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:19:43.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:24:41.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:24:43.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:29:41.134 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:29:43.554 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:34:41.221 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:34:43.565 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:39:41.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:39:43.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:44:41.397 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:44:43.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:49:41.496 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:49:43.598 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:54:41.585 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:54:43.606 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 16:59:41.679 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 16:59:43.612 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 17:04:41.769 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:04:43.622 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 4 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 17:09:41.789 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:09:43.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 17:14:41.873 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:14:43.639 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 17:19:41.974 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:19:43.645 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] Apr-24 17:24:42.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:24:43.658 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 3 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 17:29:42.151 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:29:43.666 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 2 -- pending tasks are shown below ~> 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: -; ] ~> 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: -; ] 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; ] Apr-24 17:34:42.239 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:34:43.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] Apr-24 17:39:42.324 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:39:43.682 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] Apr-24 17:44:42.409 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:44:43.696 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] Apr-24 17:49:42.509 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:49:43.704 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] Apr-24 17:54:42.602 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:54:43.708 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] Apr-24 17:59:42.690 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 17:59:43.712 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] Apr-24 18:04:42.786 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] multiqc status=ACTIVE port 0: (value) - ; channel: multiqc_config port 1: (value) - ; channel: fastqc port 2: (value) - ; channel: trimgalore/* port 3: (value) - ; channel: alignment/* port 4: (value) - ; channel: rseqc/* port 5: (value) - ; channel: rseqc/* port 6: (value) - ; channel: preseq/* port 7: (value) - ; channel: dupradar/* port 8: (value) - ; channel: featureCounts/* port 9: (value) - ; channel: featureCounts_biotype/* port 10: (value) - ; channel: stringtie/stringtie_log* port 11: (value) - ; channel: sample_correlation_results/* port 12: (value) - ; channel: software_versions/* port 13: (value) - ; channel: workflow_summary/* port 14: (cntrl) OPEN; channel: $ [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 18:04:43.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] 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; ] Apr-24 18:06:48.729 [Actor Thread 156] DEBUG nextflow.Session - <<< barrier arrive (process: genebody_coverage) 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 Apr-24 18:06:56.950 [Task submitter] INFO nextflow.Session - [72/b84ed1] Submitted process > multiqc (sample41_R1) Apr-24 18:09:42.880 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] output_documentation status=ACTIVE port 0: (value) - ; channel: output_docs port 1: (value) - ; channel: prefix port 2: (cntrl) OPEN; channel: $ Apr-24 18:09:43.720 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- pending tasks are shown below ~> 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: -; ] 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; ] Apr-24 18:11:38.745 [Actor Thread 161] DEBUG nextflow.Session - <<< barrier arrive (process: multiqc) 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 Apr-24 18:11:38.814 [Task submitter] INFO nextflow.Session - [23/16abf5] Submitted process > output_documentation (sample41_R1) 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; ] Apr-24 18:12:08.731 [Actor Thread 161] DEBUG nextflow.Session - <<< barrier arrive (process: output_documentation) Apr-24 18:12:08.732 [main] DEBUG nextflow.Session - Session await > all process finished Apr-24 18:12:08.774 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) Apr-24 18:12:13.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: pbs) Apr-24 18:12:13.725 [main] DEBUG nextflow.Session - Session await > all barriers passed Apr-24 18:12:14.058 [main] INFO nextflow.Nextflow - [nfcore/RNAseq] Sent summary e-mail to katie.viljoen@uct.ac.za (mail) Apr-24 18:12:14.086 [main] INFO nextflow.Nextflow - [nfcore/RNAseq] Pipeline Complete 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] Apr-24 18:12:14.108 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Apr-24 18:12:14.114 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Apr-24 18:12:14.260 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: {"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 (sample41AlignedByCoord.out_gene.featureCounts)"},"writes":null,"cpuUsage":{"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)"},"memUsage":{"mean":0.96,"min":0.96,"q1":0.96,"q2":0.96,"q3":0.96,"max":0.96,"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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(sample39)","q3Label":"star (sample41)"},"memUsage":{"mean":62.78,"min":62.74,"q1":62.75,"q2":62.75,"q3":62.76,"max":62.89,"minLabel":"star (sample37)","maxLabel":"star (sample38)","q1Label":"star (sample39)","q2Label":"star (sample41)","q3Label":"star (sample40)"},"timeUsage":{"mean":5.24,"min":3.02,"q1":4.21,"q2":5.35,"q3":6.59,"max":7.03,"minLabel":"star (sample41)","maxLabel":"star (sample38)","q1Label":"star (sample40)","q2Label":"star (sample37)","q3Label":"star (sample39)"}},"output_documentation":{"cpu":{"mean":37,"min":37,"q1":37,"q2":37,"q3":37,"max":37,"minLabel":"output_documentation (sample41_R1)","maxLabel":"output_documentation (sample41_R1)","q1Label":"output_documentation (sample41_R1)","q2Label":"output_documentation (sample41_R1)","q3Label":"output_documentation (sample41_R1)"},"mem":{"mean":136699904,"min":136699904,"q1":136699904,"q2":136699904,"q3":136699904,"max":136699904,"minLabel":"output_documentation (sample41_R1)","maxLabel":"output_documentation 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