Jul-16 16:05:41.681 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /home/hd/hd_hd/hd_ow424/my-pipelines/nf-core/rnaseq-master/ --reads 'data/*_R{1,2}.fastq.gz' --genome GRCh37 -profile conda -c custom.conf -resume Jul-16 16:05:42.086 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.08.0-SNAPSHOT Jul-16 16:05:46.267 [main] INFO nextflow.cli.CmdRun - Launching `/home/hd/hd_hd/hd_ow424/my-pipelines/nf-core/rnaseq-master/main.nf` [distraught_mirzakhani] - revision: 653dedd4d2 Jul-16 16:05:46.319 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/hd/hd_hd/hd_ow424/my-pipelines/nf-core/rnaseq-master/nextflow.config Jul-16 16:05:46.329 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/custom.conf Jul-16 16:05:46.331 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/hd/hd_hd/hd_ow424/my-pipelines/nf-core/rnaseq-master/nextflow.config Jul-16 16:05:46.334 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/custom.conf Jul-16 16:05:46.374 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `conda` Jul-16 16:05:54.140 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `conda` Jul-16 16:05:54.193 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [czbiohub_aws, hebbe, cfc, uppmax_devel, uzh, debug, test, bigpurple, crick, uppmax, docker, czbiohub_aws_highpriority, gis, phoenix, shh, ccga, mendel, conda, uct_hex, awsbatch, singularity, munin, binac, prince] Jul-16 16:05:54.684 [main] DEBUG nextflow.Session - Session uuid: b46ec13c-3ea6-4fb5-bf06-d7fa84540c88 Jul-16 16:05:54.686 [main] DEBUG nextflow.Session - Run name: distraught_mirzakhani Jul-16 16:05:54.687 [main] DEBUG nextflow.Session - Executor pool size: 32 Jul-16 16:05:55.071 [main] DEBUG nextflow.cli.CmdRun - Version: 19.08.0-SNAPSHOT build 5104 Created: 16-07-2019 13:25 UTC (15:25 CEST) System: Linux 3.10.0-862.3.3.el7.x86_64 Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS Encoding: UTF-8 (ANSI_X3.4-1968) Process: 19378@login3 [172.30.23.51] CPUs: 32 - Mem: 62.8 GB (274.1 MB) - Swap: 0 (0) Jul-16 16:05:55.565 [main] DEBUG nextflow.Session - Work-dir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work [fhgfs] Jul-16 16:05:57.447 [main] DEBUG nextflow.Session - Session start invoked Jul-16 16:05:57.475 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/results/pipeline_info/execution_trace.txt Jul-16 16:05:58.869 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jul-16 16:05:59.331 [PathVisitor-1] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider Jul-16 16:05:59.349 [PathVisitor-4] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: data/; pattern: *_R{1,2}.fastq.gz; options: [:] Jul-16 16:05:59.450 [PathVisitor-1] DEBUG nextflow.file.FileHelper - AWS S3 config details: {} Jul-16 16:05:59.467 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/rnaseq v1.3 ---------------------------------------------------- Jul-16 16:05:59.479 [main] INFO nextflow.Nextflow - Run Name : distraught_mirzakhani Reads : data/*_R{1,2}.fastq.gz Data Type : Paired-End Genome : GRCh37 Strandedness : None Trimming : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 Aligner : STAR STAR Index : s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ GTF Annotation : s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf BED Annotation : s3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed Save prefs : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No Max Resources : 128 GB memory, 16 cpus, 10d time per job Output dir : ./results Launch dir : /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0 Working dir : /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work Script dir : /home/hd/hd_hd/hd_ow424/my-pipelines/nf-core/rnaseq-master User : hd_ow424 Config Profile : conda Jul-16 16:05:59.481 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Jul-16 16:06:00.220 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:multiqc|get_software_versions` matches process get_software_versions Jul-16 16:06:00.225 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:00.226 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:00.243 [main] DEBUG nextflow.executor.Executor - [warm up] executor > moab Jul-16 16:06:00.258 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'moab' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Jul-16 16:06:00.274 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'moab' > queue-stat-interval: 1m Jul-16 16:06:00.532 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 32 Jul-16 16:06:00.651 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:00.652 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:00.655 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 32 Jul-16 16:06:00.758 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name trim_galore Jul-16 16:06:00.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:trim_galore` matches process trim_galore Jul-16 16:06:00.761 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:00.762 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:00.765 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > trim_galore -- maxForks: 32 Jul-16 16:06:00.785 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:high_memory` matches label `high_memory` for process with name star Jul-16 16:06:00.788 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:00.789 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:00.791 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > star -- maxForks: 32 Jul-16 16:06:00.955 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches label `mid_memory` for process with name rseqc Jul-16 16:06:00.957 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:00.958 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:00.960 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > rseqc -- maxForks: 32 Jul-16 16:06:00.970 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:00.971 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:00.974 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bam_subsample -- maxForks: 32 Jul-16 16:06:01.246 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:mid_memory` matches label `mid_memory` for process with name genebody_coverage Jul-16 16:06:01.249 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:01.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:01.252 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > genebody_coverage -- maxForks: 32 Jul-16 16:06:01.262 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:01.263 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:01.266 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 32 Jul-16 16:06:01.526 [Actor Thread 7] DEBUG nextflow.conda.CondaCache - Conda found local env for environment=/home/hd/hd_hd/hd_ow424/my-pipelines/nf-core/rnaseq-master/environment.yml; path=/beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/conda/nf-core-rnaseq-1.3-61052e18a9b5f4580cd5fc073c4f40c0 Jul-16 16:06:01.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:markDuplicates` matches process markDuplicates Jul-16 16:06:01.530 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:01.532 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:01.534 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDuplicates -- maxForks: 32 Jul-16 16:06:02.045 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name dupradar Jul-16 16:06:02.054 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.055 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.064 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dupradar -- maxForks: 32 Jul-16 16:06:02.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name featureCounts Jul-16 16:06:02.227 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.228 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.230 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > featureCounts -- maxForks: 32 Jul-16 16:06:02.236 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.237 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.241 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > merge_featureCounts -- maxForks: 32 Jul-16 16:06:02.311 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.313 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.315 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > stringtieFPKM -- maxForks: 32 Jul-16 16:06:02.445 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:low_memory` matches label `low_memory` for process with name sample_correlation Jul-16 16:06:02.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.448 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.450 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > sample_correlation -- maxForks: 32 Jul-16 16:06:02.508 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:multiqc|get_software_versions` matches process multiqc Jul-16 16:06:02.511 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.512 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.516 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 32 Jul-16 16:06:02.528 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: moab Jul-16 16:06:02.529 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'moab' Jul-16 16:06:02.534 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 32 Jul-16 16:06:02.540 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Jul-16 16:06:02.541 [main] DEBUG nextflow.Session - Session await Jul-16 16:06:04.332 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [MOAB] submitted process fastqc (C20_TNF_GTCCGC) > jobId: 884646; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3 Jul-16 16:06:04.364 [Task submitter] INFO nextflow.Session - [46/6dfdc9] Submitted process > fastqc (C20_TNF_GTCCGC) Jul-16 16:06:04.725 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [MOAB] submitted process trim_galore (C20_CCGTCC) > jobId: 884647; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/fb/f1e19b43dfb58df2f23d3cbdb5a402 Jul-16 16:06:04.726 [Task submitter] INFO nextflow.Session - [fb/f1e19b] Submitted process > trim_galore (C20_CCGTCC) Jul-16 16:06:05.025 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [MOAB] submitted process trim_galore (C20_TNF_GTCCGC) > jobId: 884648; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/42/6f9014543d8db34680696ae5492cda Jul-16 16:06:05.026 [Task submitter] INFO nextflow.Session - [42/6f9014] Submitted process > trim_galore (C20_TNF_GTCCGC) Jul-16 16:06:05.339 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [MOAB] submitted process get_software_versions > jobId: 884649; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/0f/9d213b04242b3d6bac847fe5e1a2d5 Jul-16 16:06:05.341 [Task submitter] INFO nextflow.Session - [0f/9d213b] Submitted process > get_software_versions Jul-16 16:06:05.650 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [MOAB] submitted process fastqc (C20_CCGTCC) > jobId: 884650; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/d8/2ff6a140702108d0544285b4a59404 Jul-16 16:06:05.652 [Task submitter] INFO nextflow.Session - [d8/2ff6a1] Submitted process > fastqc (C20_CCGTCC) Jul-16 16:06:05.948 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [MOAB] submitted process output_documentation (1) > jobId: 884651; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/8d/ce3910ea832f88df5b4cfc64e94b0f Jul-16 16:06:05.950 [Task submitter] INFO nextflow.Session - [8d/ce3910] Submitted process > output_documentation (1) Jul-16 16:06:50.357 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 884646; id: 3; name: fastqc (C20_TNF_GTCCGC); status: COMPLETED; exit: 1; error: -; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3 started: 1563286005347; exited: 2019-07-16T14:06:46Z; ] Jul-16 16:06:50.503 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'fastqc (C20_TNF_GTCCGC)' -- Cause: java.nio.file.NoSuchFileException: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3/.command.out Jul-16 16:06:50.523 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'fastqc (C20_TNF_GTCCGC)' -- Cause: java.nio.file.NoSuchFileException: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3/.command.err Jul-16 16:06:50.583 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'fastqc (C20_TNF_GTCCGC)' Caused by: Process `fastqc (C20_TNF_GTCCGC)` terminated with an error exit status (1) Command executed: fastqc -q C20_TNF_GTCCGC_R1.fastq.gz C20_TNF_GTCCGC_R2.fastq.gz Command exit status: 1 Command output: (empty) Command wrapper: # Job ID | 884646 # Job name | nf-fastqc_(C20_TNF_GTCCGC) # Job state | Completed (1) # Host list | m09s0604:2 # TimeSubmit | 2019-07-16 16:06:02 # TimeStart | 2019-07-16 16:06:09 # TimeQueued | 00:00:07 [elig. 00:00:00] # WallTime | 00:00:38 of 2:00:00 # Nodes:ppn:feature | 1:2:standard # Memory task, MB | 0 [requested 4096] # Memory job, MB | 0 [requested 8192] # CPU load job avg, (0.00-1.00)*tasks | 0 # CPU efficiency, 0-100% | 0 % [requested cores 2] # Node efficiency, 0-100% | 0 % [reserved cores 16] # #================================================ # JOB ANALYSIS: notes, problems and solutions #================================================ # # * NOTE: walltime usage/request ratio is under "0.01": # -> 38 sec / 7200 sec = 0.005278 # -> 0.005278 < 0.01 # Advice: request less walltime, it could force the job's start. # # * NOTE: some of the parameters are equal "0", # see "Memory" and "CPU load". # Advice: because of the small job's running time # please ignore it. # # * NOTE: the node efficiency of your Job is below optimum, # see "Node efficiency". # Advice: you should parallelize your jobs or start more tasks # inside the job (see /opt/bwhpc/common/system/moab-examples/). # #================================================ # SUPPORT info #================================================ # # Wiki: # https://www.bwhpc.de/wiki/index.php/Category:BwForCluster_MLS&WISO # Queuing system: # https://www.bwhpc.de/wiki/index.php/BwForCluster_MLS&WISO_Production_Batch_Jobs # E-mail: # mls-wiso@bwhpc.de # # Detailed information about the job (available <24h after job exit): # checkjob -v 884646 # checkjob -v -v 884646 # #================================================ Work dir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` Jul-16 16:06:50.711 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `fastqc (C20_TNF_GTCCGC)` terminated with an error exit status (1) Jul-16 16:06:50.763 [Task monitor] DEBUG nextflow.Session - The following nodes are still active: [process] star status=ACTIVE port 0: (queue) OPEN ; channel: reads port 1: (value) bound ; channel: index port 2: (value) bound ; channel: gtf port 3: (value) bound ; channel: wherearemyfiles port 4: (cntrl) - ; channel: $ [process] rseqc status=ACTIVE port 0: (queue) OPEN ; channel: bam_rseqc port 1: (queue) OPEN ; channel: index port 2: (value) bound ; channel: bed12 port 3: (cntrl) - ; channel: $ [process] bam_subsample status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] genebody_coverage status=ACTIVE port 0: (queue) OPEN ; channel: bam port 1: (value) bound ; channel: bed12 port 2: (cntrl) - ; channel: $ [process] preseq status=ACTIVE port 0: (queue) OPEN ; channel: bam_preseq port 1: (cntrl) - ; channel: $ [process] markDuplicates status=ACTIVE port 0: (queue) OPEN ; channel: bam port 1: (cntrl) - ; channel: $ [process] dupradar status=ACTIVE port 0: (queue) OPEN ; channel: bam_md port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $ [process] featureCounts status=ACTIVE port 0: (queue) OPEN ; channel: bam_featurecounts port 1: (value) bound ; channel: gtf port 2: (value) bound ; channel: biotypes_header port 3: (cntrl) - ; channel: $ [process] merge_featureCounts status=ACTIVE port 0: (value) OPEN ; channel: input_files port 1: (cntrl) - ; channel: $ [process] stringtieFPKM status=ACTIVE port 0: (queue) OPEN ; channel: bam_stringtieFPKM port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $ [process] sample_correlation status=ACTIVE port 0: (value) OPEN ; channel: input_files port 1: (value) OPEN ; channel: num_bams port 2: (queue) OPEN ; channel: mdsplot_header port 3: (queue) OPEN ; channel: heatmap_header port 4: (cntrl) - ; channel: $ [process] multiqc status=ACTIVE port 0: (queue) OPEN ; channel: multiqc_config port 1: (value) OPEN ; channel: fastqc port 2: (value) OPEN ; channel: trimgalore/* port 3: (value) OPEN ; channel: alignment/* port 4: (value) OPEN ; channel: rseqc/* port 5: (value) OPEN ; channel: rseqc/* port 6: (value) OPEN ; channel: preseq/* port 7: (value) OPEN ; channel: dupradar/* port 8: (value) OPEN ; channel: featureCounts/* port 9: (value) OPEN ; channel: featureCounts_biotype/* port 10: (value) OPEN ; channel: stringtie/stringtie_log* port 11: (value) OPEN ; channel: sample_correlation_results/* port 12: (value) OPEN ; channel: software_versions/* port 13: (value) bound ; channel: workflow_summary port 14: (cntrl) - ; channel: $ Jul-16 16:06:50.767 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'fastqc (C20_TNF_GTCCGC)' -- Cause: java.nio.file.NoSuchFileException: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3/.command.err Jul-16 16:06:50.769 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'fastqc (C20_TNF_GTCCGC)' -- Cause: java.nio.file.NoSuchFileException: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3/.command.out Jul-16 16:06:50.787 [main] DEBUG nextflow.Session - Session await > all process finished Jul-16 16:06:50.788 [main] DEBUG nextflow.Session - Session await > all barriers passed Jul-16 16:06:50.796 [main] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'fastqc (C20_TNF_GTCCGC)' -- Cause: java.nio.file.NoSuchFileException: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3/.command.err Jul-16 16:06:50.799 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'fastqc (C20_TNF_GTCCGC)' -- Cause: java.nio.file.NoSuchFileException: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/46/6dfdc98db9deac0dd1f677357e2ee3/.command.out Jul-16 16:06:50.808 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 884647; id: 4; name: trim_galore (C20_CCGTCC); status: COMPLETED; exit: 1; error: -; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/fb/f1e19b43dfb58df2f23d3cbdb5a402 started: 1563286005413; exited: 2019-07-16T14:06:46Z; ] Jul-16 16:06:50.821 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 884648; id: 5; name: trim_galore (C20_TNF_GTCCGC); status: COMPLETED; exit: 1; error: -; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/42/6f9014543d8db34680696ae5492cda started: 1563286005422; exited: 2019-07-16T14:06:46Z; ] Jul-16 16:06:50.833 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 884649; id: 1; name: get_software_versions; status: COMPLETED; exit: 1; error: -; workDir: /beegfs/work/ws/hd_ow424-RNAseqMK1-0-0/work/0f/9d213b04242b3d6bac847fe5e1a2d5 started: 1563286005429; exited: 2019-07-16T14:06:46Z; ] Jul-16 16:06:51.360 [main] INFO nextflow.Nextflow - [nf-core/rnaseq] Pipeline completed with errors Jul-16 16:06:51.381 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (2) Jul-16 16:07:01.545 [main] DEBUG nextflow.Session - Failed to execute shutdown hook: org.codehaus.groovy.runtime.typehandling.GroovyCastException: Cannot cast object 'BatchCleanup[ ' with class 'java.lang.String' to class 'java.lang.StringBuilder' at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.continueCastOnSAM(DefaultTypeTransformation.java:414) at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.continueCastOnNumber(DefaultTypeTransformation.java:328) at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.castToType(DefaultTypeTransformation.java:242) at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.castToType(ScriptBytecodeAdapter.java:615) at nextflow.executor.BatchCleanup.toString(BatchCleanup.groovy:112) at org.codehaus.groovy.runtime.InvokerHelper.format(InvokerHelper.java:659) at org.codehaus.groovy.runtime.InvokerHelper.toString(InvokerHelper.java:148) at org.codehaus.groovy.runtime.InvokerHelper.write(InvokerHelper.java:547) at groovy.lang.GString.writeTo(GString.java:194) at groovy.lang.GString.toString(GString.java:151) at org.codehaus.groovy.runtime.typehandling.ShortTypeHandling.castToString(ShortTypeHandling.java:55) at nextflow.processor.TaskPollingMonitor.cleanup(TaskPollingMonitor.groovy:653) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1011) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:994) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97) at nextflow.processor.TaskPollingMonitor$_start_closure1.doCall(TaskPollingMonitor.groovy:286) at nextflow.processor.TaskPollingMonitor$_start_closure1.call(TaskPollingMonitor.groovy) at nextflow.Session.shutdown0(Session.groovy:737) at nextflow.Session.destroy(Session.groovy:689) at nextflow.script.ScriptRunner.terminate(ScriptRunner.groovy:297) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:134) at nextflow.cli.CmdRun.run(CmdRun.groovy:246) at nextflow.cli.Launcher.run(Launcher.groovy:451) at nextflow.cli.Launcher.main(Launcher.groovy:633) Jul-16 16:07:01.549 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=6; ignoredCount=0; cachedCount=0; succeedDuration=0ms; failedDuration=42.3s; cachedDuration=0ms] Jul-16 16:07:01.552 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Jul-16 16:07:01.644 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Jul-16 16:07:02.011 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: {"get_software_versions":{"cpu":null,"mem":null,"vmem":null,"time":{"mean":5403,"min":5403,"q1":5403,"q2":5403,"q3":5403,"max":5403,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":{"mean":0.08,"min":0.08,"q1":0.08,"q2":0.08,"q3":0.08,"max":0.08,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"}},"output_documentation":{"cpu":null,"mem":null,"vmem":null,"time":null,"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"fastqc":{"cpu":null,"mem":null,"vmem":null,"time":{"mean":4979,"min":4979,"q1":4979,"q2":4979,"q3":4979,"max":4979,"minLabel":"fastqc (C20_TNF_GTCCGC)","maxLabel":"fastqc (C20_TNF_GTCCGC)","q1Label":"fastqc (C20_TNF_GTCCGC)","q2Label":"fastqc (C20_TNF_GTCCGC)","q3Label":"fastqc (C20_TNF_GTCCGC)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":{"mean":0.07,"min":0.07,"q1":0.07,"q2":0.07,"q3":0.07,"max":0.07,"minLabel":"fastqc (C20_TNF_GTCCGC)","maxLabel":"fastqc (C20_TNF_GTCCGC)","q1Label":"fastqc (C20_TNF_GTCCGC)","q2Label":"fastqc (C20_TNF_GTCCGC)","q3Label":"fastqc (C20_TNF_GTCCGC)"}},"trim_galore":{"cpu":null,"mem":null,"vmem":null,"time":{"mean":5395,"min":5393,"q1":5394,"q2":5395,"q3":5396,"max":5397,"minLabel":"trim_galore (C20_CCGTCC)","maxLabel":"trim_galore (C20_TNF_GTCCGC)","q1Label":"trim_galore (C20_CCGTCC)","q2Label":"trim_galore (C20_CCGTCC)","q3Label":"trim_galore (C20_CCGTCC)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":{"mean":0.02,"min":0.02,"q1":0.02,"q2":0.02,"q3":0.02,"max":0.02,"minLabel":"trim_galore (C20_CCGTCC)","maxLabel":"trim_galore (C20_TNF_GTCCGC)","q1Label":"trim_galore (C20_CCGTCC)","q2Label":"trim_galore (C20_CCGTCC)","q3Label":"trim_galore (C20_CCGTCC)"}}} Jul-16 16:07:03.169 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Jul-16 16:07:03.589 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Jul-16 16:07:03.655 [main] DEBUG nextflow.Session - AWS S3 uploader shutdown Jul-16 16:07:03.757 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye