Sep-10 12:52:30.399 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/chipseq -profile test,conda Sep-10 12:52:30.583 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.10.0 Sep-10 12:52:31.591 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/stain/.nextflow/assets/nf-core/chipseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/chipseq.git Sep-10 12:52:31.611 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/stain/.nextflow/assets/nf-core/chipseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/chipseq.git Sep-10 12:52:31.786 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/stain/.nextflow/assets/nf-core/chipseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/chipseq.git Sep-10 12:52:31.787 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/chipseq` [pensive_dubinsky] - revision: 0f487ed76d [master] Sep-10 12:52:55.109 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/stain/.nextflow/assets/nf-core/chipseq/nextflow.config Sep-10 12:52:55.110 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/stain/.nextflow/assets/nf-core/chipseq/nextflow.config Sep-10 12:52:55.124 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,conda` Sep-10 12:52:56.742 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, denbi_qbic, bi, genotoul, bigpurple, uppmax, docker, gis, utd_ganymede, conda, singularity, icr_davros, munin, prince, czbiohub_aws, hebbe, cfc, uzh, ccga_med, debug, test, genouest, cbe, ebc, ccga_dx, crick, google, kraken, phoenix, shh, awsbatch, pasteur, uct_hpc, test_full, binac] Sep-10 12:52:56.834 [main] DEBUG nextflow.extension.OperatorEx - Dataflow extension methods: branch,buffer,chain,choice,collate,collect,collectFile,combine,concat,count,countBy,countFasta,countFastq,countLines,countText,cross,distinct,filter,first,flatMap,flatten,fork,groupBy,groupTuple,ifEmpty,into,join,last,map,max,mean,merge,min,mix,phase,print,println,randomSample,reduce,separate,set,splitCsv,splitFasta,splitFastq,splitText,spread,subscribe,sum,take,tap,toDouble,toFloat,toInteger,toList,toLong,toSortedList,transpose,unique,until,view Sep-10 12:52:56.844 [main] DEBUG nextflow.Session - Session uuid: 05f2add8-5039-4497-8924-62458a2bd0a6 Sep-10 12:52:56.844 [main] DEBUG nextflow.Session - Run name: pensive_dubinsky Sep-10 12:52:56.845 [main] DEBUG nextflow.Session - Executor pool size: 4 Sep-10 12:53:06.920 [main] DEBUG nextflow.cli.CmdRun - Version: 19.10.0 build 5170 Created: 21-10-2019 15:07 UTC (16:07 BST) System: Linux 5.4.0-47-generic Runtime: Groovy 2.5.8 on OpenJDK 64-Bit Server VM 11.0.8+10-post-Ubuntu-0ubuntu120.04 Encoding: UTF-8 (UTF-8) Process: 307982@biggie.ds.s11.no [192.168.2.218] CPUs: 4 - Mem: 15.6 GB (6.9 GB) - Swap: 2 GB (2 GB) Sep-10 12:53:06.945 [main] DEBUG nextflow.Session - Work-dir: /home/stain/src/92/work [zfs] Sep-10 12:53:06.986 [main] DEBUG nextflow.Session - Observer factory: TowerFactory Sep-10 12:53:06.992 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Sep-10 12:53:07.485 [main] DEBUG nextflow.Session - Session start invoked Sep-10 12:53:07.522 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/stain/src/92/results/pipeline_info/execution_trace.txt Sep-10 12:53:09.296 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Sep-10 12:53:10.530 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/chipseq v1.2.1 ---------------------------------------------------- Sep-10 12:53:10.574 [main] INFO nextflow.Nextflow - Run Name : pensive_dubinsky Data Type : Paired-End Design File : https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv Genome : Not supplied Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf MACS2 Genome Size : 1.2E+7 Min Consensus Reps : 1 MACS2 Narrow Peaks : No MACS2 Broad Cutoff : 0.1 Trim R1 : 0 bp Trim R2 : 0 bp Trim 3' R1 : 0 bp Trim 3' R2 : 0 bp NextSeq Trim : 0 bp Fingerprint Bins : 100 Save Genome Index : No Max Resources : 6 GB memory, 2 cpus, 12h time per job Output Dir : ./results Launch Dir : /home/stain/src/92 Working Dir : /home/stain/src/92/work Script Dir : /home/stain/.nextflow/assets/nf-core/chipseq User : stain Config Profile : test,conda Config Description : Minimal test dataset to check pipeline function Sep-10 12:53:10.593 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Sep-10 12:53:10.870 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:10.871 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:10.885 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Sep-10 12:53:10.901 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=15.6 GB; capacity=4; pollInterval=100ms; dumpInterval=5m Sep-10 12:53:11.177 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CHECK_DESIGN -- maxForks: 4 Sep-10 12:53:11.536 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name BWA_INDEX Sep-10 12:53:11.559 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.559 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:11.561 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BWA_INDEX -- maxForks: 4 Sep-10 12:53:11.599 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name MAKE_GENE_BED Sep-10 12:53:11.603 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.604 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:11.623 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MAKE_GENE_BED -- maxForks: 4 Sep-10 12:53:11.665 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.674 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:11.677 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MAKE_GENOME_FILTER -- maxForks: 4 Sep-10 12:53:11.813 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name FASTQC Sep-10 12:53:11.819 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.841 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:11.847 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > FASTQC -- maxForks: 4 Sep-10 12:53:11.883 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name TRIMGALORE Sep-10 12:53:11.888 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.888 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:11.889 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > TRIMGALORE -- maxForks: 4 Sep-10 12:53:11.913 [Actor Thread 3] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=12; maxQueueSize=36; keepAlive=1m Sep-10 12:53:11.959 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name BWA_MEM Sep-10 12:53:11.961 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.961 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:11.964 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BWA_MEM -- maxForks: 4 Sep-10 12:53:11.970 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv to work dir: /home/stain/src/92/work/stage/c6/c1bbf8ff75be5c895992ce7b24701a/design.csv Sep-10 12:53:11.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SORT_BAM Sep-10 12:53:11.991 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:11.994 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.013 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > SORT_BAM -- maxForks: 4 Sep-10 12:53:12.072 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa to work dir: /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 12:53:12.117 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MERGED_BAM Sep-10 12:53:12.118 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.118 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.121 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MERGED_BAM -- maxForks: 4 Sep-10 12:53:12.161 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MERGED_BAM_FILTER Sep-10 12:53:12.163 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.163 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.164 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MERGED_BAM_FILTER -- maxForks: 4 Sep-10 12:53:12.180 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MERGED_BAM_REMOVE_ORPHAN Sep-10 12:53:12.181 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.191 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.193 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MERGED_BAM_REMOVE_ORPHAN -- maxForks: 4 Sep-10 12:53:12.215 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PRESEQ Sep-10 12:53:12.216 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name PRESEQ Sep-10 12:53:12.216 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.221 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf to work dir: /home/stain/src/92/work/stage/51/92d7396f0d182420a585a93e70f261/genes.gtf Sep-10 12:53:12.224 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PRESEQ -- maxForks: 4 Sep-10 12:53:12.314 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PICARD_METRICS Sep-10 12:53:12.316 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.316 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.335 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PICARD_METRICS -- maxForks: 4 Sep-10 12:53:12.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BIGWIG Sep-10 12:53:12.452 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.452 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.470 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BIGWIG -- maxForks: 4 Sep-10 12:53:12.610 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name PLOTPROFILE Sep-10 12:53:12.611 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.626 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.636 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PLOTPROFILE -- maxForks: 4 Sep-10 12:53:12.671 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PHANTOMPEAKQUALTOOLS Sep-10 12:53:12.687 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.687 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.706 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PHANTOMPEAKQUALTOOLS -- maxForks: 4 Sep-10 12:53:12.868 [Actor Thread 11] INFO nextflow.conda.CondaCache - Creating Conda env: /home/stain/.nextflow/assets/nf-core/chipseq/environment.yml [cache /home/stain/src/92/work/conda/nf-core-chipseq-1.2.1-124f0f8d69d9dfbfcea852493605e617] Sep-10 12:53:12.893 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name PLOTFINGERPRINT Sep-10 12:53:12.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:12.918 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:12.924 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PLOTFINGERPRINT -- maxForks: 4 Sep-10 12:53:12.995 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MACS2 Sep-10 12:53:13.005 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.006 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.014 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MACS2 -- maxForks: 4 Sep-10 12:53:13.061 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MACS2_ANNOTATE Sep-10 12:53:13.069 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.075 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.086 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MACS2_ANNOTATE -- maxForks: 4 Sep-10 12:53:13.112 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MACS2_QC Sep-10 12:53:13.113 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.113 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.114 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MACS2_QC -- maxForks: 4 Sep-10 12:53:13.133 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name CONSENSUS_PEAKS Sep-10 12:53:13.134 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.134 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.136 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CONSENSUS_PEAKS -- maxForks: 4 Sep-10 12:53:13.146 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name CONSENSUS_PEAKS_ANNOTATE Sep-10 12:53:13.147 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.147 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.149 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CONSENSUS_PEAKS_ANNOTATE -- maxForks: 4 Sep-10 12:53:13.172 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name CONSENSUS_PEAKS_COUNTS Sep-10 12:53:13.173 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.173 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.174 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CONSENSUS_PEAKS_COUNTS -- maxForks: 4 Sep-10 12:53:13.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name CONSENSUS_PEAKS_DESEQ2 Sep-10 12:53:13.185 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.185 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.186 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CONSENSUS_PEAKS_DESEQ2 -- maxForks: 4 Sep-10 12:53:13.204 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.204 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.206 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > IGV -- maxForks: 4 Sep-10 12:53:13.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions Sep-10 12:53:13.213 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.213 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.214 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 4 Sep-10 12:53:13.665 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.665 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.667 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MULTIQC -- maxForks: 4 Sep-10 12:53:13.679 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Sep-10 12:53:13.679 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Sep-10 12:53:13.680 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 4 Sep-10 12:53:13.701 [main] DEBUG nextflow.script.BaseScript - No entry workflow defined Sep-10 12:53:13.706 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Sep-10 12:53:13.707 [main] DEBUG nextflow.Session - Session await Sep-10 12:53:13.925 [Actor Thread 14] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.047 s; total time: 0.048 s Sep-10 12:53:13.942 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/bbfd50ba89f65365ec7acf68c469fc29.collect-file Sep-10 12:53:13.958 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-16564487043894895853 Sep-10 12:53:14.071 [Actor Thread 9] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa Sep-10 12:53:14.221 [Actor Thread 8] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf Sep-10 12:56:25.376 [Actor Thread 11] DEBUG nextflow.conda.CondaCache - Conda create complete env=/home/stain/.nextflow/assets/nf-core/chipseq/environment.yml path=/home/stain/src/92/work/conda/nf-core-chipseq-1.2.1-124f0f8d69d9dfbfcea852493605e617 Sep-10 12:56:25.562 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:25.571 [Task submitter] INFO nextflow.Session - [00/157ada] Submitted process > MAKE_GENE_BED (genes.gtf) Sep-10 12:56:25.614 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:25.623 [Task submitter] INFO nextflow.Session - [a0/139af8] Submitted process > CHECK_DESIGN (design.csv) Sep-10 12:56:29.434 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: CHECK_DESIGN (design.csv); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a0/139af8786326422813b8b84b1d0ad5] Sep-10 12:56:29.462 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:29.474 [Task submitter] INFO nextflow.Session - [59/f71c9f] Submitted process > output_documentation Sep-10 12:56:29.934 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: MAKE_GENE_BED (genes.gtf); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/00/157ada5c09e886786739e93123e386] Sep-10 12:56:29.942 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:29.949 [Task submitter] INFO nextflow.Session - [3f/286e4e] Submitted process > get_software_versions Sep-10 12:56:30.448 [FileTransfer-thread-7] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz to work dir: /home/stain/src/92/work/stage/6c/bc46129277bc857808f8d0a8dc70bc/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz Sep-10 12:56:30.599 [FileTransfer-thread-8] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz to work dir: /home/stain/src/92/work/stage/b9/cc3910b06d5d5509cf70ee20116887/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz Sep-10 12:56:31.559 [FileTransfer-thread-9] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz to work dir: /home/stain/src/92/work/stage/80/6e2de2c76e7232fdfeddb2fa175a1e/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz Sep-10 12:56:31.603 [FileTransfer-thread-10] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz to work dir: /home/stain/src/92/work/stage/d1/d3c74ca076d4b11763b63bad8c82b1/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz Sep-10 12:56:32.386 [FileTransfer-thread-11] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_1.fastq.gz to work dir: /home/stain/src/92/work/stage/a6/c03e392a9d5730bb17d65ec0bf3ea3/SRR1822153_1.fastq.gz Sep-10 12:56:32.593 [FileTransfer-thread-12] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_2.fastq.gz to work dir: /home/stain/src/92/work/stage/a8/06bc6eddfc5dd2918d6eb480551c21/SRR1822153_2.fastq.gz Sep-10 12:56:33.076 [FileTransfer-thread-13] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_1.fastq.gz to work dir: /home/stain/src/92/work/stage/95/507684ae8140dd9cef82fd31ac6804/SRR1822154_1.fastq.gz Sep-10 12:56:33.274 [FileTransfer-thread-14] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_2.fastq.gz to work dir: /home/stain/src/92/work/stage/12/285fd71e8db192b0bb66b79ab9d1d5/SRR1822154_2.fastq.gz Sep-10 12:56:33.602 [Actor Thread 17] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz Sep-10 12:56:33.603 [Actor Thread 4] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz Sep-10 12:56:34.144 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/59/f71c9fa6f5927891a9f70201975225] Sep-10 12:56:34.155 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:34.155 [Task submitter] INFO nextflow.Session - [55/92a4f2] Submitted process > BWA_INDEX (genome.fa) Sep-10 12:56:34.593 [Actor Thread 16] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_1.fastq.gz Sep-10 12:56:34.978 [FileTransfer-thread-4] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_1.fastq.gz to work dir: /home/stain/src/92/work/stage/19/f84a871d248d4557d38acc1f0abbae/SRR1822157_1.fastq.gz Sep-10 12:56:35.214 [FileTransfer-thread-5] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_2.fastq.gz to work dir: /home/stain/src/92/work/stage/93/29aa300cd376107765b931c34d49a1/SRR1822157_2.fastq.gz Sep-10 12:56:35.274 [Actor Thread 12] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_1.fastq.gz Sep-10 12:56:35.603 [Actor Thread 17] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz Sep-10 12:56:36.594 [Actor Thread 16] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_2.fastq.gz Sep-10 12:56:37.214 [Actor Thread 6] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_1.fastq.gz Sep-10 12:56:37.275 [Actor Thread 12] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_2.fastq.gz Sep-10 12:56:38.206 [FileTransfer-thread-6] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_1.fastq.gz to work dir: /home/stain/src/92/work/stage/a1/73abcbafb3a2f511abbdf9713843e9/SRR1822158_1.fastq.gz Sep-10 12:56:38.436 [FileTransfer-thread-7] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_2.fastq.gz to work dir: /home/stain/src/92/work/stage/23/2bc32121a618bc26830aa35b5d4dd2/SRR1822158_2.fastq.gz Sep-10 12:56:39.214 [Actor Thread 6] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_2.fastq.gz Sep-10 12:56:40.436 [Actor Thread 16] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_1.fastq.gz Sep-10 12:56:41.541 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/3f/286e4ec8d41d8d096e79e8a5088fea] Sep-10 12:56:41.550 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:41.550 [Task submitter] INFO nextflow.Session - [34/1d5b54] Submitted process > MAKE_GENOME_FILTER (genome.fa) Sep-10 12:56:45.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: MAKE_GENOME_FILTER (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/34/1d5b5463cb52d6be900de32d4c4485] Sep-10 12:56:45.289 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:45.296 [Task submitter] INFO nextflow.Session - [e1/a217d0] Submitted process > FASTQC (SPT5_INPUT_R1_T1) Sep-10 12:56:50.428 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: BWA_INDEX (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/55/92a4f245b291092fad52cecf278800] Sep-10 12:56:50.451 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:56:50.452 [Task submitter] INFO nextflow.Session - [04/a99077] Submitted process > TRIMGALORE (SPT5_INPUT_R1_T1) Sep-10 12:57:01.155 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: FASTQC (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e1/a217d0b79e692f46f48bbe341f2f15] Sep-10 12:57:01.183 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:57:01.183 [Task submitter] INFO nextflow.Session - [bf/715e9e] Submitted process > FASTQC (SPT5_T0_R1_T1) Sep-10 12:57:13.977 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: TRIMGALORE (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/04/a990774f181426ac14d06fdb7dfe1a] Sep-10 12:57:13.983 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:57:13.983 [Task submitter] INFO nextflow.Session - [48/a3a1ab] Submitted process > TRIMGALORE (SPT5_T0_R1_T1) Sep-10 12:57:18.093 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: FASTQC (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/bf/715e9ef6507e9ca3b0e0de4ab2ed2f] Sep-10 12:57:18.099 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:57:18.099 [Task submitter] INFO nextflow.Session - [e4/1fd169] Submitted process > TRIMGALORE (SPT5_INPUT_R2_T1) Sep-10 12:57:40.571 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: TRIMGALORE (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/48/a3a1ab1b82b7419ce649c754fc9e71] Sep-10 12:57:40.581 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:57:40.582 [Task submitter] INFO nextflow.Session - [f0/0c96b3] Submitted process > FASTQC (SPT5_INPUT_R2_T1) Sep-10 12:57:42.359 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: TRIMGALORE (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e4/1fd169dfc17dbbeeebd4b9585095ae] Sep-10 12:57:42.364 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:57:42.365 [Task submitter] INFO nextflow.Session - [21/c72960] Submitted process > TRIMGALORE (SPT5_T0_R2_T1) Sep-10 12:57:54.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: FASTQC (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/f0/0c96b3f7a1953416b9e78a6fcbbf93] Sep-10 12:57:54.878 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:57:54.885 [Task submitter] INFO nextflow.Session - [61/31369d] Submitted process > FASTQC (SPT5_T0_R2_T1) Sep-10 12:58:09.321 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: TRIMGALORE (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/21/c7296069b7878889feb93e086c279f] Sep-10 12:58:09.326 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:58:09.331 [Task submitter] INFO nextflow.Session - [3e/c3dc21] Submitted process > FASTQC (SPT5_T15_R2_T1) Sep-10 12:58:10.637 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: FASTQC (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/61/31369dbe2c8facec99908a51f29747] Sep-10 12:58:10.644 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:58:10.646 [Task submitter] INFO nextflow.Session - [5c/92aafc] Submitted process > TRIMGALORE (SPT5_T15_R2_T1) Sep-10 12:58:11.138 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below ~> TaskHandler[id: 17; name: FASTQC (SPT5_T15_R2_T1); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/3e/c3dc213310ea0917fa450c41c9e9dc] ~> TaskHandler[id: 18; name: TRIMGALORE (SPT5_T15_R2_T1); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/5c/92aafc701dbce3c06a4765f862123c] Sep-10 12:58:27.180 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: FASTQC (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/3e/c3dc213310ea0917fa450c41c9e9dc] Sep-10 12:58:27.200 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:58:27.205 [Task submitter] INFO nextflow.Session - [a1/70bf36] Submitted process > TRIMGALORE (SPT5_T15_R1_T1) Sep-10 12:58:39.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: TRIMGALORE (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/5c/92aafc701dbce3c06a4765f862123c] Sep-10 12:58:39.339 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:58:39.340 [Task submitter] INFO nextflow.Session - [be/022ad6] Submitted process > FASTQC (SPT5_T15_R1_T1) Sep-10 12:58:55.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: TRIMGALORE (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a1/70bf366821f68b8b95378153889db5] Sep-10 12:58:55.679 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:58:55.679 [Task submitter] INFO nextflow.Session - [95/fd6cbf] Submitted process > BWA_MEM (SPT5_INPUT_R1_T1) Sep-10 12:58:56.904 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: FASTQC (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/be/022ad6920de21cbf8c93e357badbdf] Sep-10 12:58:56.917 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:58:56.918 [Task submitter] INFO nextflow.Session - [a5/0fb53b] Submitted process > BWA_MEM (SPT5_T0_R1_T1) Sep-10 12:59:06.920 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: BWA_MEM (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/95/fd6cbfd833dd24f2b8d4216e90192a] Sep-10 12:59:06.939 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:06.939 [Task submitter] INFO nextflow.Session - [5c/9d3f6a] Submitted process > BWA_MEM (SPT5_INPUT_R2_T1) Sep-10 12:59:09.876 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: BWA_MEM (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a5/0fb53b1ec0e985aa3e1e058481c58d] Sep-10 12:59:09.882 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:09.882 [Task submitter] INFO nextflow.Session - [a1/a9ae84] Submitted process > BWA_MEM (SPT5_T0_R2_T1) Sep-10 12:59:17.624 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: BWA_MEM (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/5c/9d3f6a0c00fc130ab2d9edbef688d3] Sep-10 12:59:17.629 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:17.630 [Task submitter] INFO nextflow.Session - [ea/8d626f] Submitted process > BWA_MEM (SPT5_T15_R2_T1) Sep-10 12:59:23.338 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: BWA_MEM (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a1/a9ae845d78236ca4a4b70b9dbf5fa6] Sep-10 12:59:23.343 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:23.345 [Task submitter] INFO nextflow.Session - [1b/db658c] Submitted process > BWA_MEM (SPT5_T15_R1_T1) Sep-10 12:59:31.455 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: BWA_MEM (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ea/8d626f74e28db73a875c39629ca3cd] Sep-10 12:59:31.462 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:31.465 [Task submitter] INFO nextflow.Session - [7c/53671b] Submitted process > SORT_BAM (SPT5_INPUT_R1_T1) Sep-10 12:59:36.280 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: BWA_MEM (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/1b/db658c5522b8dab8a76601d7db29a7] Sep-10 12:59:36.285 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:36.291 [Task submitter] INFO nextflow.Session - [86/61e059] Submitted process > SORT_BAM (SPT5_T0_R1_T1) Sep-10 12:59:37.411 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: SORT_BAM (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/7c/53671be7fb3d099b2a13e44ac4ca20] Sep-10 12:59:37.415 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:37.415 [Task submitter] INFO nextflow.Session - [5b/bd5826] Submitted process > SORT_BAM (SPT5_INPUT_R2_T1) Sep-10 12:59:40.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: SORT_BAM (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/86/61e059753a1df75a6bb1df49691350] Sep-10 12:59:40.858 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:40.863 [Task submitter] INFO nextflow.Session - [c9/741bb9] Submitted process > SORT_BAM (SPT5_T0_R2_T1) Sep-10 12:59:42.021 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: SORT_BAM (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/5b/bd582683564791141c0c03b080bb11] Sep-10 12:59:42.025 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:42.026 [Task submitter] INFO nextflow.Session - [93/52da3f] Submitted process > SORT_BAM (SPT5_T15_R2_T1) Sep-10 12:59:45.397 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: SORT_BAM (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/c9/741bb9a82d317097707762e5f7ba67] Sep-10 12:59:45.401 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:45.402 [Task submitter] INFO nextflow.Session - [a2/74e365] Submitted process > SORT_BAM (SPT5_T15_R1_T1) Sep-10 12:59:46.777 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: SORT_BAM (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/93/52da3ff86d103581079d37639d7e30] Sep-10 12:59:49.304 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: SORT_BAM (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a2/74e365dacc9117906c19f497b4b09b] Sep-10 12:59:49.334 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:49.334 [Task submitter] INFO nextflow.Session - [a0/83ea26] Submitted process > MERGED_BAM (SPT5_T0_R1) Sep-10 12:59:49.342 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 12:59:49.342 [Task submitter] INFO nextflow.Session - [18/7f78a9] Submitted process > MERGED_BAM (SPT5_INPUT_R1) Sep-10 13:00:09.207 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: MERGED_BAM (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a0/83ea2611c219cd19a003abbfc5c96f] Sep-10 13:00:09.242 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:09.243 [Task submitter] INFO nextflow.Session - [a0/5b8bb4] Submitted process > MERGED_BAM (SPT5_T0_R2) Sep-10 13:00:10.443 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: MERGED_BAM (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/18/7f78a96014a6590cb37cd60a9d6151] Sep-10 13:00:10.448 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:10.448 [Task submitter] INFO nextflow.Session - [20/d306ec] Submitted process > MERGED_BAM (SPT5_INPUT_R2) Sep-10 13:00:26.730 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: MERGED_BAM (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/a0/5b8bb4a74ab57eeb47c041a245137f] Sep-10 13:00:26.737 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:26.737 [Task submitter] INFO nextflow.Session - [41/b46a47] Submitted process > MERGED_BAM (SPT5_T15_R1) Sep-10 13:00:29.041 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: MERGED_BAM (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/20/d306ec9628fc88328366ab31440ac2] Sep-10 13:00:29.046 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:29.046 [Task submitter] INFO nextflow.Session - [17/674501] Submitted process > MERGED_BAM (SPT5_T15_R2) Sep-10 13:00:43.281 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: MERGED_BAM (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/41/b46a474bff7892f3851375891e3dd3] Sep-10 13:00:43.289 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:43.289 [Task submitter] INFO nextflow.Session - [b4/65bc40] Submitted process > PRESEQ (SPT5_T0_R1) Sep-10 13:00:46.300 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: MERGED_BAM (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/17/674501cdeedbb3303fccdda0154349] Sep-10 13:00:46.307 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:46.311 [Task submitter] INFO nextflow.Session - [84/7667d4] Submitted process > MERGED_BAM_FILTER (SPT5_T0_R1) Sep-10 13:00:51.586 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: PRESEQ (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/b4/65bc40e814bcea8cc24a82ac0c516d] Sep-10 13:00:51.590 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:51.590 [Task submitter] INFO nextflow.Session - [ba/46b523] Submitted process > PRESEQ (SPT5_INPUT_R1) Sep-10 13:00:52.247 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: MERGED_BAM_FILTER (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/84/7667d48cc6a4d2bf728663b6e0a845] Sep-10 13:00:52.251 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:00:52.260 [Task submitter] INFO nextflow.Session - [6e/ba78a5] Submitted process > MERGED_BAM_FILTER (SPT5_INPUT_R1) Sep-10 13:01:01.004 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: MERGED_BAM_FILTER (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/6e/ba78a577eaa5e68d5a34db5ae7c188] Sep-10 13:01:01.009 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:01.010 [Task submitter] INFO nextflow.Session - [18/6418d9] Submitted process > MERGED_BAM_FILTER (SPT5_T0_R2) Sep-10 13:01:06.852 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: MERGED_BAM_FILTER (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/18/6418d9a865d369652575ace3fbfe03] Sep-10 13:01:06.863 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:06.863 [Task submitter] INFO nextflow.Session - [00/578290] Submitted process > PRESEQ (SPT5_T0_R2) Sep-10 13:01:09.042 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: PRESEQ (SPT5_INPUT_R1); status: COMPLETED; exit: 1; error: -; workDir: /home/stain/src/92/work/ba/46b5238e3fccff4fdcd2af2a95310f] Sep-10 13:01:09.054 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:09.054 [Task submitter] INFO nextflow.Session - [7e/c53e66] Submitted process > PRESEQ (SPT5_INPUT_R2) Sep-10 13:01:09.065 [Task monitor] INFO nextflow.processor.TaskProcessor - [ba/46b523] NOTE: Process `PRESEQ (SPT5_INPUT_R1)` terminated with an error exit status (1) -- Error is ignored Sep-10 13:01:09.066 [Task monitor] DEBUG nextflow.trace.TraceRecord - Not a valid trace `realtime` value: '2' Sep-10 13:01:15.071 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: PRESEQ (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/00/57829019113b3d2bcac42788b23308] Sep-10 13:01:15.075 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:15.075 [Task submitter] INFO nextflow.Session - [ea/bf3171] Submitted process > MERGED_BAM_FILTER (SPT5_INPUT_R2) Sep-10 13:01:23.478 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: MERGED_BAM_FILTER (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ea/bf31719fb1020f723405815cf5fdb7] Sep-10 13:01:23.483 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:23.484 [Task submitter] INFO nextflow.Session - [eb/7f68c9] Submitted process > PRESEQ (SPT5_T15_R1) Sep-10 13:01:25.955 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: PRESEQ (SPT5_INPUT_R2); status: COMPLETED; exit: 1; error: -; workDir: /home/stain/src/92/work/7e/c53e66ddf4ef897cd0d3f1dc70b45c] Sep-10 13:01:25.956 [Task monitor] INFO nextflow.processor.TaskProcessor - [7e/c53e66] NOTE: Process `PRESEQ (SPT5_INPUT_R2)` terminated with an error exit status (1) -- Error is ignored Sep-10 13:01:25.957 [Task monitor] DEBUG nextflow.trace.TraceRecord - Not a valid trace `realtime` value: '2' Sep-10 13:01:25.960 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:25.961 [Task submitter] INFO nextflow.Session - [30/efad13] Submitted process > MERGED_BAM_FILTER (SPT5_T15_R1) Sep-10 13:01:25.988 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below ~> TaskHandler[id: 48; name: PRESEQ (SPT5_T15_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/c4/34c7e6346e7929bc2dc4a192b53244] ~> TaskHandler[id: 47; name: MERGED_BAM_FILTER (SPT5_T15_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/98/46e072df3a7dedd81212ece2ed4d8d] ~> TaskHandler[id: 49; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_T0_R1); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/52/5d9786705629ee9b8cbc8b0f5b7631] ~> TaskHandler[id: 50; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_INPUT_R1); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/6e/b5ca3ca579a6d1e26364ec9ac8f05d] ~> TaskHandler[id: 51; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_T0_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/3f/c7d0d71a1b19c161d8d77a0942a4a0] ~> TaskHandler[id: 52; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_INPUT_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/32/8acc3d02a6432984277cfbe2548d26] Sep-10 13:01:31.250 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: PRESEQ (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/eb/7f68c9a21bb256577acc0a230b7283] Sep-10 13:01:31.256 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:31.257 [Task submitter] INFO nextflow.Session - [c4/34c7e6] Submitted process > PRESEQ (SPT5_T15_R2) Sep-10 13:01:31.934 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: MERGED_BAM_FILTER (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/30/efad13b2c77ee41363a6c38386ac7e] Sep-10 13:01:31.938 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:31.938 [Task submitter] INFO nextflow.Session - [98/46e072] Submitted process > MERGED_BAM_FILTER (SPT5_T15_R2) Sep-10 13:01:38.735 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: MERGED_BAM_FILTER (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/98/46e072df3a7dedd81212ece2ed4d8d] Sep-10 13:01:38.740 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:38.746 [Task submitter] INFO nextflow.Session - [52/5d9786] Submitted process > MERGED_BAM_REMOVE_ORPHAN (SPT5_T0_R1) Sep-10 13:01:39.572 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: PRESEQ (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/c4/34c7e6346e7929bc2dc4a192b53244] Sep-10 13:01:39.576 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:39.576 [Task submitter] INFO nextflow.Session - [6e/b5ca3c] Submitted process > MERGED_BAM_REMOVE_ORPHAN (SPT5_INPUT_R1) Sep-10 13:01:43.997 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/52/5d9786705629ee9b8cbc8b0f5b7631] Sep-10 13:01:44.001 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:44.001 [Task submitter] INFO nextflow.Session - [3f/c7d0d7] Submitted process > MERGED_BAM_REMOVE_ORPHAN (SPT5_T0_R2) Sep-10 13:01:44.513 [FileTransfer-thread-18] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:01:46.165 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/6e/b5ca3ca579a6d1e26364ec9ac8f05d] Sep-10 13:01:46.170 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:46.170 [Task submitter] INFO nextflow.Session - [32/8acc3d] Submitted process > MERGED_BAM_REMOVE_ORPHAN (SPT5_INPUT_R2) Sep-10 13:01:46.358 [FileTransfer-thread-36] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:01:49.544 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/3f/c7d0d71a1b19c161d8d77a0942a4a0] Sep-10 13:01:49.548 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:49.549 [Task submitter] INFO nextflow.Session - [26/fb502b] Submitted process > MERGED_BAM_REMOVE_ORPHAN (SPT5_T15_R1) Sep-10 13:01:49.705 [FileTransfer-thread-18] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:01:53.238 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/32/8acc3d02a6432984277cfbe2548d26] Sep-10 13:01:53.242 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:53.242 [Task submitter] INFO nextflow.Session - [2f/c60b2d] Submitted process > MERGED_BAM_REMOVE_ORPHAN (SPT5_T15_R2) Sep-10 13:01:53.425 [FileTransfer-thread-31] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:01:55.885 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/26/fb502b6ef8aa85fcee3fe38cfcc773] Sep-10 13:01:55.889 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:55.895 [Task submitter] INFO nextflow.Session - [93/950ed5] Submitted process > PHANTOMPEAKQUALTOOLS (SPT5_T0_R1) Sep-10 13:01:56.039 [FileTransfer-thread-18] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:01:59.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: MERGED_BAM_REMOVE_ORPHAN (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/2f/c60b2d2b4456d095e7e5e8ea50d11f] Sep-10 13:01:59.035 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:01:59.035 [Task submitter] INFO nextflow.Session - [e7/aae1ce] Submitted process > BIGWIG (SPT5_T0_R1) Sep-10 13:01:59.196 [FileTransfer-thread-31] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:02:03.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: BIGWIG (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e7/aae1ce78f04ffcf1afb067e536bc4b] Sep-10 13:02:03.636 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:03.640 [Task submitter] INFO nextflow.Session - [87/f4d9b4] Submitted process > PICARD_METRICS (SPT5_T0_R1) Sep-10 13:02:05.920 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: PHANTOMPEAKQUALTOOLS (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/93/950ed5fda145752429739aeff99e85] Sep-10 13:02:05.924 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:05.931 [Task submitter] INFO nextflow.Session - [1a/29c342] Submitted process > BIGWIG (SPT5_INPUT_R1) Sep-10 13:02:13.537 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: BIGWIG (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/1a/29c342e7b15ca197e5943250049d3a] Sep-10 13:02:13.542 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:13.546 [Task submitter] INFO nextflow.Session - [e2/327bfd] Submitted process > PHANTOMPEAKQUALTOOLS (SPT5_INPUT_R1) Sep-10 13:02:15.130 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: PICARD_METRICS (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/87/f4d9b4950e55bf8948e9fe1e5be065] Sep-10 13:02:15.137 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:15.137 [Task submitter] INFO nextflow.Session - [17/fd3850] Submitted process > PLOTFINGERPRINT (SPT5_T0_R1 vs SPT5_INPUT_R1) Sep-10 13:02:25.507 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: PHANTOMPEAKQUALTOOLS (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e2/327bfd1f639bd49dbc4106c6d1d2fc] Sep-10 13:02:25.518 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:25.519 [Task submitter] INFO nextflow.Session - [03/ff7efa] Submitted process > MACS2 (SPT5_T0_R1 vs SPT5_INPUT_R1) Sep-10 13:02:33.460 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: MACS2 (SPT5_T0_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/03/ff7efa127feec986408310e8bda72f] Sep-10 13:02:33.467 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:33.467 [Task submitter] INFO nextflow.Session - [4b/6887ed] Submitted process > PICARD_METRICS (SPT5_INPUT_R1) Sep-10 13:02:34.006 [FileTransfer-thread-36] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:02:34.072 [FileTransfer-thread-18] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /home/stain/src/92/work/stage/51/92d7396f0d182420a585a93e70f261/genes.gtf Sep-10 13:02:45.249 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: PICARD_METRICS (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/4b/6887edb016e053dc59a14d457c2e4b] Sep-10 13:02:45.255 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:45.255 [Task submitter] INFO nextflow.Session - [42/5456ea] Submitted process > PHANTOMPEAKQUALTOOLS (SPT5_T0_R2) Sep-10 13:02:53.165 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: PHANTOMPEAKQUALTOOLS (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/42/5456ea7551cb7c32c211c1c6511228] Sep-10 13:02:53.169 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:53.169 [Task submitter] INFO nextflow.Session - [27/db9456] Submitted process > BIGWIG (SPT5_T0_R2) Sep-10 13:02:57.023 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: BIGWIG (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/27/db9456de6541143ec608c5f04e1a2b] Sep-10 13:02:57.031 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:57.031 [Task submitter] INFO nextflow.Session - [3a/671f05] Submitted process > PICARD_METRICS (SPT5_T0_R2) Sep-10 13:02:59.492 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: PLOTFINGERPRINT (SPT5_T0_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/17/fd385048178a6fc506620877c6938a] Sep-10 13:02:59.498 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:02:59.499 [Task submitter] INFO nextflow.Session - [ff/1bf441] Submitted process > BIGWIG (SPT5_INPUT_R2) Sep-10 13:03:07.395 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: BIGWIG (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ff/1bf4419daa9bec262d8c6958ab5eaa] Sep-10 13:03:07.401 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:07.401 [Task submitter] INFO nextflow.Session - [ce/288494] Submitted process > PHANTOMPEAKQUALTOOLS (SPT5_INPUT_R2) Sep-10 13:03:08.000 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: PICARD_METRICS (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/3a/671f0593defd2ce8b6c66debc901c7] Sep-10 13:03:08.006 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:08.006 [Task submitter] INFO nextflow.Session - [86/dbe579] Submitted process > MACS2 (SPT5_T0_R2 vs SPT5_INPUT_R2) Sep-10 13:03:11.219 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below ~> TaskHandler[id: 67; name: PHANTOMPEAKQUALTOOLS (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/ce/288494752cda977e54e32b846ca489] ~> TaskHandler[id: 68; name: MACS2 (SPT5_T0_R2 vs SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/86/dbe579e8575d83ed63a9486bae37fe] Sep-10 13:03:15.401 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: MACS2 (SPT5_T0_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/86/dbe579e8575d83ed63a9486bae37fe] Sep-10 13:03:15.421 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:15.421 [Task submitter] INFO nextflow.Session - [70/024eb1] Submitted process > PLOTFINGERPRINT (SPT5_T0_R2 vs SPT5_INPUT_R2) Sep-10 13:03:15.705 [FileTransfer-thread-37] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:03:15.766 [FileTransfer-thread-32] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /home/stain/src/92/work/stage/51/92d7396f0d182420a585a93e70f261/genes.gtf Sep-10 13:03:20.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: PHANTOMPEAKQUALTOOLS (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ce/288494752cda977e54e32b846ca489] Sep-10 13:03:20.624 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:20.631 [Task submitter] INFO nextflow.Session - [b5/9ba593] Submitted process > PICARD_METRICS (SPT5_INPUT_R2) Sep-10 13:03:32.023 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: PICARD_METRICS (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/b5/9ba59369250842a5f4abda4d43d745] Sep-10 13:03:32.033 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:32.033 [Task submitter] INFO nextflow.Session - [75/0ddfaf] Submitted process > PHANTOMPEAKQUALTOOLS (SPT5_T15_R1) Sep-10 13:03:41.279 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: PHANTOMPEAKQUALTOOLS (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/75/0ddfaf7dbba46073bbb4c511888b84] Sep-10 13:03:41.287 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:41.287 [Task submitter] INFO nextflow.Session - [0d/15fba4] Submitted process > BIGWIG (SPT5_T15_R1) Sep-10 13:03:45.223 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: BIGWIG (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/0d/15fba4000edabbdbb8f29d804dbad4] Sep-10 13:03:45.227 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:45.228 [Task submitter] INFO nextflow.Session - [e8/c7dfee] Submitted process > PLOTFINGERPRINT (SPT5_T15_R1 vs SPT5_INPUT_R1) Sep-10 13:03:57.481 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: PLOTFINGERPRINT (SPT5_T0_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/70/024eb177ee473ecfe3505873393e2e] Sep-10 13:03:57.488 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:03:57.488 [Task submitter] INFO nextflow.Session - [53/a7f0c7] Submitted process > MACS2 (SPT5_T15_R1 vs SPT5_INPUT_R1) Sep-10 13:04:05.523 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: MACS2 (SPT5_T15_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/53/a7f0c7a4d45bc345466a7e1c32612d] Sep-10 13:04:05.529 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:05.531 [Task submitter] INFO nextflow.Session - [ae/351ea9] Submitted process > PICARD_METRICS (SPT5_T15_R1) Sep-10 13:04:05.798 [FileTransfer-thread-31] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:04:05.860 [FileTransfer-thread-18] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /home/stain/src/92/work/stage/51/92d7396f0d182420a585a93e70f261/genes.gtf Sep-10 13:04:17.563 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: PICARD_METRICS (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ae/351ea96910eebf145df42ff510752e] Sep-10 13:04:17.568 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:17.568 [Task submitter] INFO nextflow.Session - [e7/82015b] Submitted process > PHANTOMPEAKQUALTOOLS (SPT5_T15_R2) Sep-10 13:04:26.330 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: PHANTOMPEAKQUALTOOLS (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e7/82015b8b24b6b9c8323e34d9aa2d26] Sep-10 13:04:26.341 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:26.342 [Task submitter] INFO nextflow.Session - [be/4eaebd] Submitted process > MACS2 (SPT5_T15_R2 vs SPT5_INPUT_R2) Sep-10 13:04:26.426 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: PLOTFINGERPRINT (SPT5_T15_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e8/c7dfee4e9d8fe5aef5c5488bb4ad30] Sep-10 13:04:26.443 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:26.444 [Task submitter] INFO nextflow.Session - [61/3209cb] Submitted process > BIGWIG (SPT5_T15_R2) Sep-10 13:04:31.687 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: BIGWIG (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/61/3209cbfc48773800ea43710cbefc99] Sep-10 13:04:31.692 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:31.692 [Task submitter] INFO nextflow.Session - [79/2670ee] Submitted process > PLOTFINGERPRINT (SPT5_T15_R2 vs SPT5_INPUT_R2) Sep-10 13:04:35.065 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: MACS2 (SPT5_T15_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/be/4eaebd136f463746c5223583404564] Sep-10 13:04:35.074 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:35.074 [Task submitter] INFO nextflow.Session - [97/2d093f] Submitted process > PICARD_METRICS (SPT5_T15_R2) Sep-10 13:04:35.298 [FileTransfer-thread-35] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:04:35.369 [FileTransfer-thread-30] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /home/stain/src/92/work/stage/51/92d7396f0d182420a585a93e70f261/genes.gtf Sep-10 13:04:45.952 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: PICARD_METRICS (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/97/2d093f187ddca0096f53f328bf7354] Sep-10 13:04:45.955 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:04:45.956 [Task submitter] INFO nextflow.Session - [75/a683f1] Submitted process > PLOTPROFILE (SPT5_T0_R1) Sep-10 13:05:17.694 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: PLOTFINGERPRINT (SPT5_T15_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/79/2670ee589ff993e1bfd0e9d33e7683] Sep-10 13:05:17.702 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:05:17.706 [Task submitter] INFO nextflow.Session - [61/b05864] Submitted process > PLOTPROFILE (SPT5_INPUT_R1) Sep-10 13:08:11.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below ~> TaskHandler[id: 81; name: PLOTPROFILE (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/75/a683f1ea45d06b92ea8483f9de6636] ~> TaskHandler[id: 82; name: PLOTPROFILE (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/61/b05864a4dbd581a5d170ed2210d31a] Sep-10 13:11:43.946 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: PLOTPROFILE (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/75/a683f1ea45d06b92ea8483f9de6636] Sep-10 13:11:43.955 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:11:43.956 [Task submitter] INFO nextflow.Session - [40/2629f7] Submitted process > MACS2_ANNOTATE (SPT5_T0_R1 vs SPT5_INPUT_R1) Sep-10 13:11:43.958 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 8 -- tasks to be submitted are shown below ~> TaskHandler[id: 84; name: PLOTPROFILE (SPT5_T0_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/72/4ba4e7feb9a4d964cff313f56b33c4] ~> TaskHandler[id: 85; name: PLOTPROFILE (SPT5_INPUT_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/ad/2c47a1d51b8f773b44831dd538dab7] ~> TaskHandler[id: 86; name: MACS2_ANNOTATE (SPT5_T0_R2 vs SPT5_INPUT_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/ec/d1de3eaa896acca3ef7a7f0975af69] ~> TaskHandler[id: 87; name: PLOTPROFILE (SPT5_T15_R1); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/ca/fbf7fba943af55e3c7970d66518da9] ~> TaskHandler[id: 88; name: MACS2_ANNOTATE (SPT5_T15_R1 vs SPT5_INPUT_R1); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/47/9ffee34eea9496facedc8db00d82f0] ~> TaskHandler[id: 89; name: PLOTPROFILE (SPT5_T15_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/93/adeaf4ba0622f2f9de04bd39bb049d] ~> TaskHandler[id: 91; name: CONSENSUS_PEAKS (SPT5); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/e9/d5c26f43b1c83664cc8d729f101a05] ~> TaskHandler[id: 90; name: MACS2_ANNOTATE (SPT5_T15_R2 vs SPT5_INPUT_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/4d/d3c0a642e5c0ba6ffddb77aaf72953] Sep-10 13:11:53.101 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: MACS2_ANNOTATE (SPT5_T0_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/40/2629f71afcaaca81519e52e4bbdad0] Sep-10 13:11:53.111 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:11:53.111 [Task submitter] INFO nextflow.Session - [72/4ba4e7] Submitted process > PLOTPROFILE (SPT5_T0_R2) Sep-10 13:12:22.764 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: PLOTPROFILE (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/61/b05864a4dbd581a5d170ed2210d31a] Sep-10 13:12:22.772 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:12:22.773 [Task submitter] INFO nextflow.Session - [ad/2c47a1] Submitted process > PLOTPROFILE (SPT5_INPUT_R2) Sep-10 13:13:11.320 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below ~> TaskHandler[id: 84; name: PLOTPROFILE (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/72/4ba4e7feb9a4d964cff313f56b33c4] ~> TaskHandler[id: 85; name: PLOTPROFILE (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/ad/2c47a1d51b8f773b44831dd538dab7] Sep-10 13:18:11.420 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below ~> TaskHandler[id: 84; name: PLOTPROFILE (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/72/4ba4e7feb9a4d964cff313f56b33c4] ~> TaskHandler[id: 85; name: PLOTPROFILE (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/ad/2c47a1d51b8f773b44831dd538dab7] Sep-10 13:18:41.914 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: PLOTPROFILE (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/72/4ba4e7feb9a4d964cff313f56b33c4] Sep-10 13:18:41.918 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:18:41.919 [Task submitter] INFO nextflow.Session - [ec/d1de3e] Submitted process > MACS2_ANNOTATE (SPT5_T0_R2 vs SPT5_INPUT_R2) Sep-10 13:18:41.921 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below ~> TaskHandler[id: 87; name: PLOTPROFILE (SPT5_T15_R1); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/ca/fbf7fba943af55e3c7970d66518da9] ~> TaskHandler[id: 88; name: MACS2_ANNOTATE (SPT5_T15_R1 vs SPT5_INPUT_R1); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/47/9ffee34eea9496facedc8db00d82f0] ~> TaskHandler[id: 89; name: PLOTPROFILE (SPT5_T15_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/93/adeaf4ba0622f2f9de04bd39bb049d] ~> TaskHandler[id: 91; name: CONSENSUS_PEAKS (SPT5); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/e9/d5c26f43b1c83664cc8d729f101a05] ~> TaskHandler[id: 90; name: MACS2_ANNOTATE (SPT5_T15_R2 vs SPT5_INPUT_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/4d/d3c0a642e5c0ba6ffddb77aaf72953] Sep-10 13:18:50.376 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: MACS2_ANNOTATE (SPT5_T0_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ec/d1de3eaa896acca3ef7a7f0975af69] Sep-10 13:18:50.379 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:18:50.380 [Task submitter] INFO nextflow.Session - [ca/fbf7fb] Submitted process > PLOTPROFILE (SPT5_T15_R1) Sep-10 13:19:10.320 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: PLOTPROFILE (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ad/2c47a1d51b8f773b44831dd538dab7] Sep-10 13:19:10.331 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:19:10.331 [Task submitter] INFO nextflow.Session - [47/9ffee3] Submitted process > MACS2_ANNOTATE (SPT5_T15_R1 vs SPT5_INPUT_R1) Sep-10 13:19:21.555 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: MACS2_ANNOTATE (SPT5_T15_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/47/9ffee34eea9496facedc8db00d82f0] Sep-10 13:19:21.573 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:19:21.579 [Task submitter] INFO nextflow.Session - [93/adeaf4] Submitted process > PLOTPROFILE (SPT5_T15_R2) Sep-10 13:23:11.471 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- pending tasks are shown below ~> TaskHandler[id: 87; name: PLOTPROFILE (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/ca/fbf7fba943af55e3c7970d66518da9] ~> TaskHandler[id: 89; name: PLOTPROFILE (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /home/stain/src/92/work/93/adeaf4ba0622f2f9de04bd39bb049d] Sep-10 13:25:58.428 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: PLOTPROFILE (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ca/fbf7fba943af55e3c7970d66518da9] Sep-10 13:25:58.433 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:25:58.434 [Task submitter] INFO nextflow.Session - [e9/d5c26f] Submitted process > CONSENSUS_PEAKS (SPT5) Sep-10 13:25:58.436 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 90; name: MACS2_ANNOTATE (SPT5_T15_R2 vs SPT5_INPUT_R2); status: NEW; exit: -; error: -; workDir: /home/stain/src/92/work/4d/d3c0a642e5c0ba6ffddb77aaf72953] Sep-10 13:26:04.176 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: CONSENSUS_PEAKS (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/e9/d5c26f43b1c83664cc8d729f101a05] Sep-10 13:26:04.179 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:04.179 [Task submitter] INFO nextflow.Session - [4d/d3c0a6] Submitted process > MACS2_ANNOTATE (SPT5_T15_R2 vs SPT5_INPUT_R2) Sep-10 13:26:04.921 [FileTransfer-thread-74] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:26:04.985 [FileTransfer-thread-63] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /home/stain/src/92/work/stage/51/92d7396f0d182420a585a93e70f261/genes.gtf Sep-10 13:26:12.335 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: PLOTPROFILE (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/93/adeaf4ba0622f2f9de04bd39bb049d] Sep-10 13:26:12.373 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:12.374 [Task submitter] INFO nextflow.Session - [48/070bc1] Submitted process > CONSENSUS_PEAKS_COUNTS (SPT5) Sep-10 13:26:16.015 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: MACS2_ANNOTATE (SPT5_T15_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/4d/d3c0a642e5c0ba6ffddb77aaf72953] Sep-10 13:26:16.021 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:16.025 [Task submitter] INFO nextflow.Session - [3d/128e0a] Submitted process > CONSENSUS_PEAKS_ANNOTATE (SPT5) Sep-10 13:26:17.441 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: CONSENSUS_PEAKS_COUNTS (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/48/070bc11d8a2809e44b66b107782288] Sep-10 13:26:17.449 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:17.449 [Task submitter] INFO nextflow.Session - [2e/c38082] Submitted process > MACS2_QC Sep-10 13:26:26.633 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: CONSENSUS_PEAKS_ANNOTATE (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/3d/128e0afe5322a62c262334011f0a78] Sep-10 13:26:26.638 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:26.639 [Task submitter] INFO nextflow.Session - [ef/d1ca38] Submitted process > CONSENSUS_PEAKS_DESEQ2 (SPT5) Sep-10 13:26:27.208 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: MACS2_QC; status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/2e/c38082f875fe2b118056863d3a0be6] Sep-10 13:26:46.467 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: CONSENSUS_PEAKS_DESEQ2 (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/ef/d1ca3831745b50b2efc1dcc7fd5817] Sep-10 13:26:46.536 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:46.536 [Task submitter] INFO nextflow.Session - [68/199ec6] Submitted process > MULTIQC (1) Sep-10 13:26:46.690 [FileTransfer-thread-70] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /home/stain/src/92/work/stage/57/5a4505658752a6830794aab2cddf0d/genome.fa Sep-10 13:26:46.700 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Sep-10 13:26:46.701 [Task submitter] INFO nextflow.Session - [08/d40313] Submitted process > IGV Sep-10 13:26:50.266 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: IGV; status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/08/d40313213a10b5f4ce80fc64d36896] Sep-10 13:26:59.183 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: MULTIQC (1); status: COMPLETED; exit: 0; error: -; workDir: /home/stain/src/92/work/68/199ec6aa2e3639d57438cd9f8737c8] Sep-10 13:26:59.187 [main] DEBUG nextflow.Session - Session await > all process finished Sep-10 13:26:59.189 [main] DEBUG nextflow.Session - Session await > all barriers passed Sep-10 13:27:00.121 [main] INFO nextflow.Nextflow - -Warning, pipeline completed, but with errored process(es) - Sep-10 13:27:00.121 [main] INFO nextflow.Nextflow - -Number of ignored errored process(es) : 2 - Sep-10 13:27:00.121 [main] INFO nextflow.Nextflow - -Number of successfully ran process(es) : 95 - Sep-10 13:27:00.121 [main] INFO nextflow.Nextflow - -[nf-core/chipseq] Pipeline completed successfully- Sep-10 13:27:00.141 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=95; failedCount=0; ignoredCount=2; cachedCount=0; succeedDuration=1h 49m 7s; failedDuration=1m 8s; cachedDuration=0ms] Sep-10 13:27:00.141 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Sep-10 13:27:00.147 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Sep-10 13:27:00.528 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":65.1,"min":65.1,"q1":65.1,"q2":65.1,"q3":65.1,"max":65.1,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"process":"CHECK_DESIGN","mem":{"mean":2408448,"min":2408448,"q1":2408448,"q2":2408448,"q3":2408448,"max":2408448,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"memUsage":{"mean":0.04,"min":0.04,"q1":0.04,"q2":0.04,"q3":0.04,"max":0.04,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"timeUsage":null,"vmem":{"mean":18571264,"min":18571264,"q1":18571264,"q2":18571264,"q3":18571264,"max":18571264,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"reads":{"mean":634390,"min":634390,"q1":634390,"q2":634390,"q3":634390,"max":634390,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"cpu":{"mean":65.1,"min":65.1,"q1":65.1,"q2":65.1,"q3":65.1,"max":65.1,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"time":{"mean":80,"min":80,"q1":80,"q2":80,"q3":80,"max":80,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"},"writes":{"mean":1812,"min":1812,"q1":1812,"q2":1812,"q3":1812,"max":1812,"minLabel":"CHECK_DESIGN (design.csv)","maxLabel":"CHECK_DESIGN (design.csv)","q1Label":"CHECK_DESIGN (design.csv)","q2Label":"CHECK_DESIGN (design.csv)","q3Label":"CHECK_DESIGN (design.csv)"}},{"cpuUsage":{"mean":49.5,"min":49.5,"q1":49.5,"q2":49.5,"q3":49.5,"max":49.5,"minLabel":"MAKE_GENE_BED (genes.gtf)","maxLabel":"MAKE_GENE_BED (genes.gtf)","q1Label":"MAKE_GENE_BED (genes.gtf)","q2Label":"MAKE_GENE_BED (genes.gtf)","q3Label":"MAKE_GENE_BED (genes.gtf)"},"process":"MAKE_GENE_BED","mem":{"mean":10010624,"min":10010624,"q1":10010624,"q2":10010624,"q3":10010624,"max":10010624,"minLabel":"MAKE_GENE_BED (genes.gtf)","maxLabel":"MAKE_GENE_BED (genes.gtf)","q1Label":"MAKE_GENE_BED (genes.gtf)","q2Label":"MAKE_GENE_BED (genes.gtf)","q3Label":"MAKE_GENE_BED (genes.gtf)"},"memUsage":{"mean":0.16,"min":0.16,"q1":0.16,"q2":0.16,"q3":0.16,"max":0.16,"minLabel":"MAKE_GENE_BED (genes.gtf)","maxLabel":"MAKE_GENE_BED (genes.gtf)","q1Label":"MAKE_GENE_BED (genes.gtf)","q2Label":"MAKE_GENE_BED (genes.gtf)","q3Label":"MAKE_GENE_BED (genes.gtf)"},"timeUsage":null,"vmem":{"mean":44683264,"min":44683264,"q1":44683264,"q2":44683264,"q3":44683264,"max":44683264,"minLabel":"MAKE_GENE_BED (genes.gtf)","maxLabel":"MAKE_GENE_BED (genes.gtf)","q1Label":"MAKE_GENE_BED (genes.gtf)","q2Label":"MAKE_GENE_BED (genes.gtf)","q3Label":"MAKE_GENE_BED (genes.gtf)"},"reads":{"mean":12278210,"min":12278210,"q1":12278210,"q2":12278210,"q3":12278210,"max":12278210,"minLabel":"MAKE_GENE_BED (genes.gtf)","maxLabel":"MAKE_GENE_BED (genes.gtf)","q1Label":"MAKE_GENE_BED (genes.gtf)","q2Label":"MAKE_GENE_BED (genes.gtf)","q3Label":"MAKE_GENE_BED (genes.gtf)"},"cpu":{"mean":99,"min":99,"q1":99,"q2":99,"q3":99,"max":99,"minLabel":"MAKE_GENE_BED (genes.gtf)","maxLabel":"MAKE_GENE_BED (genes.gtf)","q1Label":"MAKE_GENE_BED (genes.gtf)","q2Label":"MAKE_GENE_BED (genes.gtf)","q3Label":"MAKE_GENE_BED 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