search

nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.
https://nf-co.re/chipseq
MIT License
186 stars 145 forks source link

PhantomPeakQualTools step can't be completed #144

Closed CadenZhao closed 4 years ago

CadenZhao commented 4 years ago

When I run nextflow run nf-core/chipseq -profile test,conda, it stopped at

issue

The PhantomPeakQualTools step can't be completed.

The log file is below

.nextflow.log 
 

Mar-09 22:55:42.037 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/chipseq -profile test,conda
Mar-09 22:55:42.143 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.01.0
Mar-09 22:55:43.007 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xiangjie/.nextflow/assets/nf-core/chipseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/chipseq.git
Mar-09 22:55:43.019 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xiangjie/.nextflow/assets/nf-core/chipseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/chipseq.git
Mar-09 22:55:43.310 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xiangjie/.nextflow/assets/nf-core/chipseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/chipseq.git
Mar-09 22:55:43.310 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/chipseq` [angry_kirch] - revision: 21be314954 [master]
Mar-09 22:55:45.010 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/xiangjie/.nextflow/assets/nf-core/chipseq/nextflow.config
Mar-09 22:55:45.012 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/xiangjie/.nextflow/assets/nf-core/chipseq/nextflow.config
Mar-09 22:55:45.025 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,conda`
Mar-09 22:55:46.642 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [denbi_qbic, genotoul, bigpurple, uppmax, docker, gis, conda, singularity, munin, prince, czbiohub_aws, hebbe, cfc, uzh, ccga_med, debug, test, genouest, cbe, ccga_dx, crick, google, czbiohub_aws_highpriority, kraken, phoenix, shh, awsbatch, pasteur, uct_hex, binac]
Mar-09 22:55:46.717 [main] DEBUG nextflow.Session - Session uuid: 4f383c1e-13b0-40a3-a276-2c5d53981fba
Mar-09 22:55:46.717 [main] DEBUG nextflow.Session - Run name: angry_kirch
Mar-09 22:55:46.718 [main] DEBUG nextflow.Session - Executor pool size: 112
Mar-09 22:55:46.744 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 20.01.0 build 5264
  Created: 12-02-2020 10:14 UTC (18:14 CDT)
  System: Linux 3.10.0-862.11.6.el7.x86_64
  Runtime: Groovy 2.5.8 on OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12
  Encoding: UTF-8 (UTF-8)
  Process: 114090@platinum [192.168.5.14]
  CPUs: 112 - Mem: 503.6 GB (285.1 GB) - Swap: 128 GB (0)
Mar-09 22:55:46.766 [main] DEBUG nextflow.Session - Work-dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work [xfs]
Mar-09 22:55:46.802 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Mar-09 22:55:46.804 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-09 22:55:47.035 [main] DEBUG nextflow.Session - Session start invoked
Mar-09 22:55:47.046 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/results/pipeline_info/execution_trace.txt
Mar-09 22:55:48.308 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-09 22:55:48.322 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: MakeGeneBED, BigWig, output_documentation, Preseq, PlotProfile, PhantomPeakQualTools, CheckDesign, BWAIndex, ConsensusPeakSetAnnotate, FastQC, MergeBAMFilter, PeakQC, TrimGalore, get_software_versions, CollectMultipleMetrics, BWAMem, MergeBAM, MultiQC, AnnotatePeaks, MergeBAMRemoveOrphan, ConsensusPeakSetDESeq, PlotFingerprint, MACSCallPeak, MakeGenomeFilter, ConsensusPeakSet, IGV, SortBAM, MakeTSSBED
Mar-09 22:55:53.083 [main] INFO  nextflow.Nextflow - ----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/chipseq v1.1.0
----------------------------------------------------

Mar-09 22:55:53.105 [main] INFO  nextflow.Nextflow - Run Name            : angry_kirch
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          : /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq
Working Dir         : /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work
Script Dir          : /home/xiangjie/.nextflow/assets/nf-core/chipseq
User                : xiangjie
Config Profile      : test,conda
Config Description  : Minimal test dataset to check pipeline function
Mar-09 22:55:53.107 [main] INFO  nextflow.Nextflow - ----------------------------------------------------
Mar-09 22:55:53.291 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.301 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Mar-09 22:55:53.309 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=112; memory=503.6 GB; capacity=112; pollInterval=100ms; dumpInterval=5m
Mar-09 22:55:53.395 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CheckDesign -- maxForks: 112; blocking: false
Mar-09 22:55:53.687 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name BWAIndex
Mar-09 22:55:53.689 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.689 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.691 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BWAIndex -- maxForks: 112; blocking: false
Mar-09 22:55:53.697 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name MakeGeneBED
Mar-09 22:55:53.699 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.699 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.703 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MakeGeneBED -- maxForks: 112; blocking: false
Mar-09 22:55:53.708 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.709 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.712 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MakeTSSBED -- maxForks: 112; blocking: false
Mar-09 22:55:53.722 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.722 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.724 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MakeGenomeFilter -- maxForks: 112; blocking: false
Mar-09 22:55:53.742 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name FastQC
Mar-09 22:55:53.743 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.743 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.745 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > FastQC -- maxForks: 112; blocking: false
Mar-09 22:55:53.759 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name TrimGalore
Mar-09 22:55:53.760 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.760 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.762 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > TrimGalore -- maxForks: 112; blocking: false
Mar-09 22:55:53.780 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name BWAMem
Mar-09 22:55:53.782 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.782 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.787 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BWAMem -- maxForks: 112; blocking: false
Mar-09 22:55:53.794 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name SortBAM
Mar-09 22:55:53.795 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.795 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.797 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > SortBAM -- maxForks: 112; blocking: false
Mar-09 22:55:53.818 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MergeBAM
Mar-09 22:55:53.819 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.819 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.820 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MergeBAM -- maxForks: 112; blocking: false
Mar-09 22:55:53.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MergeBAMFilter
Mar-09 22:55:53.838 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.838 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.840 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MergeBAMFilter -- maxForks: 112; blocking: false
Mar-09 22:55:53.852 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MergeBAMRemoveOrphan
Mar-09 22:55:53.852 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.852 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.854 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MergeBAMRemoveOrphan -- maxForks: 112; blocking: false
Mar-09 22:55:53.861 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name Preseq
Mar-09 22:55:53.861 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.861 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.863 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Preseq -- maxForks: 112; blocking: false
Mar-09 22:55:53.867 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name CollectMultipleMetrics
Mar-09 22:55:53.868 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.868 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.869 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > CollectMultipleMetrics -- maxForks: 112; blocking: false
Mar-09 22:55:53.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name BigWig
Mar-09 22:55:53.882 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.882 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.884 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > BigWig -- maxForks: 112; blocking: false
Mar-09 22:55:53.891 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name PlotProfile
Mar-09 22:55:53.892 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.892 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.895 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PlotProfile -- maxForks: 112; blocking: false
Mar-09 22:55:53.902 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PhantomPeakQualTools
Mar-09 22:55:53.902 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.903 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.905 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PhantomPeakQualTools -- maxForks: 112; blocking: false
Mar-09 22:55:53.928 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name PlotFingerprint
Mar-09 22:55:53.929 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.929 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.930 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PlotFingerprint -- maxForks: 112; blocking: false
Mar-09 22:55:53.938 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name MACSCallPeak
Mar-09 22:55:53.938 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.938 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.940 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MACSCallPeak -- maxForks: 112; blocking: false
Mar-09 22:55:53.946 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name AnnotatePeaks
Mar-09 22:55:53.946 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.946 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.947 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > AnnotatePeaks -- maxForks: 112; blocking: false
Mar-09 22:55:53.953 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name PeakQC
Mar-09 22:55:53.954 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.954 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.956 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PeakQC -- maxForks: 112; blocking: false
Mar-09 22:55:53.966 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name ConsensusPeakSet
Mar-09 22:55:53.966 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.966 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.968 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > ConsensusPeakSet -- maxForks: 112; blocking: false
Mar-09 22:55:53.973 [Actor Thread 5] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=336; maxQueueSize=1008; keepAlive=1m
Mar-09 22:55:53.974 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name ConsensusPeakSetAnnotate
Mar-09 22:55:53.975 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.975 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.976 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > ConsensusPeakSetAnnotate -- maxForks: 112; blocking: false
Mar-09 22:55:53.984 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 22:55:53.987 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name ConsensusPeakSetDESeq
Mar-09 22:55:53.988 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.988 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:53.989 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > ConsensusPeakSetDESeq -- maxForks: 112; blocking: false
Mar-09 22:55:53.999 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:53.999 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:54.000 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > IGV -- maxForks: 112; blocking: false
Mar-09 22:55:54.003 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions
Mar-09 22:55:54.004 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:54.004 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:54.005 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 112; blocking: false
Mar-09 22:55:54.033 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:54.033 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:54.035 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > MultiQC -- maxForks: 112; blocking: false
Mar-09 22:55:54.041 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-09 22:55:54.041 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-09 22:55:54.042 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 112; blocking: false
Mar-09 22:55:54.048 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Mar-09 22:55:54.048 [main] DEBUG nextflow.Session - Session await
Mar-09 22:55:54.099 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/9d/953ae071434ac7240c7a0b1f66aeff/genes.gtf
Mar-09 22:55:54.160 [Actor Thread 14] INFO  nextflow.conda.CondaCache - Creating Conda env: /home/xiangjie/.nextflow/assets/nf-core/chipseq/environment.yml [cache /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/conda/nf-core-chipseq-1.1.0-92988ce42e87fb63720162cc5576644a]
Mar-09 22:55:54.216 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/b5/fb1a830741ff00d5f46c75f95b2d21/design.csv
Mar-09 22:55:55.983 [Actor Thread 5] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa
Mar-09 22:55:56.098 [Actor Thread 7] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf
Mar-09 22:58:09.614 [Actor Thread 14] DEBUG nextflow.conda.CondaCache - Conda create complete env=/home/xiangjie/.nextflow/assets/nf-core/chipseq/environment.yml path=/platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/conda/nf-core-chipseq-1.1.0-92988ce42e87fb63720162cc5576644a
Mar-09 22:58:09.782 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:09.791 [Task submitter] INFO  nextflow.Session - [c4/daabc1] Submitted process > output_documentation
Mar-09 22:58:09.810 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:09.811 [Task submitter] INFO  nextflow.Session - [52/1babca] Submitted process > MakeGenomeFilter (genome.fa)
Mar-09 22:58:09.824 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:09.825 [Task submitter] INFO  nextflow.Session - [b7/96aec0] Submitted process > CheckDesign (design.csv)
Mar-09 22:58:09.836 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:09.837 [Task submitter] INFO  nextflow.Session - [1d/c32184] Submitted process > get_software_versions
Mar-09 22:58:09.846 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:09.846 [Task submitter] INFO  nextflow.Session - [92/ff59da] Submitted process > MakeGeneBED (genes.gtf)
Mar-09 22:58:09.854 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:09.855 [Task submitter] INFO  nextflow.Session - [a0/855280] Submitted process > BWAIndex (genome.fa)
Mar-09 22:58:12.899 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: MakeGenomeFilter (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/52/1babcad2ec2dc8f1e472f1fd407037]
Mar-09 22:58:13.015 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/c4/daabc1e8c14fba7bb63658f4a64748]
Mar-09 22:58:13.042 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: CheckDesign (design.csv); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/b7/96aec0de3177198ba329fe22ebda04]
Mar-09 22:58:13.269 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: MakeGeneBED (genes.gtf); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/92/ff59daa01c55f6b42424d4bce55a1f]
Mar-09 22:58:13.298 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:13.298 [Task submitter] INFO  nextflow.Session - [d8/8d3ccf] Submitted process > MakeTSSBED (genes.bed)
Mar-09 22:58:16.251 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/1d/c321846b2cd39c470f18002ec36d45]
Mar-09 22:58:16.491 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: MakeTSSBED (genes.bed); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/d8/8d3ccf3062c0af1762629fe03afad6]
Mar-09 22:58:20.547 [FileTransfer-thread-14] 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: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/04/2187e1a5a360f5f9e91d3027c4952f/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz
Mar-09 22:58:20.670 [FileTransfer-thread-15] 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: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/12/fecec59ee8a6d63b6f722240c4ebc5/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz
Mar-09 22:58:21.310 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: BWAIndex (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/a0/8552803edeafa18ed120f78ad946cc]
Mar-09 22:58:22.670 [Actor Thread 6] 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_R1.fastq.gz
Mar-09 22:58:24.670 [Actor Thread 16] 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
Mar-09 22:58:25.531 [FileTransfer-thread-16] 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: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/1c/5065d02265e8113da4aaf7c76223f0/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz
Mar-09 22:58:25.822 [FileTransfer-thread-17] 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: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/0a/8e9e678abfc0f3e3598c9276074b4f/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz
Mar-09 22:58:27.632 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:27.633 [Task submitter] INFO  nextflow.Session - [ca/7f687e] Submitted process > FastQC (SPT5_INPUT_R1_T1)
Mar-09 22:58:27.670 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:27.671 [Task submitter] INFO  nextflow.Session - [1a/37d46f] Submitted process > TrimGalore (SPT5_INPUT_R1_T1)
Mar-09 22:58:27.822 [Actor Thread 4] 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
Mar-09 22:58:28.946 [FileTransfer-thread-18] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_1.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/5e/011f923a4739c3ccf8d9253c347feb/SRR1822153_1.fastq.gz
Mar-09 22:58:29.823 [Actor Thread 7] 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
Mar-09 22:58:30.063 [FileTransfer-thread-19] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_2.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/33/3525f65343080c9645d39b5c7ccb23/SRR1822153_2.fastq.gz
Mar-09 22:58:32.063 [Actor Thread 6] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_1.fastq.gz
Mar-09 22:58:34.064 [Actor Thread 16] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822153_2.fastq.gz
Mar-09 22:58:35.919 [FileTransfer-thread-20] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_1.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/4c/04fda47e32a4c8d1adb3a57948f60c/SRR1822154_1.fastq.gz
Mar-09 22:58:36.279 [FileTransfer-thread-21] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_2.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/52/ccf11e351bbce4c8a8f1c96c59f7c2/SRR1822154_2.fastq.gz
Mar-09 22:58:38.279 [Actor Thread 17] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_1.fastq.gz
Mar-09 22:58:38.794 [FileTransfer-thread-22] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_1.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/6c/49ec149172e2ed7a54b38a810f5b70/SRR1822157_1.fastq.gz
Mar-09 22:58:38.832 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: FastQC (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/ca/7f687ed90225e73c9761fab33a34af]
Mar-09 22:58:39.911 [FileTransfer-thread-27] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_2.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/f3/ca70627254cce50064281fb129ffcd/SRR1822157_2.fastq.gz
Mar-09 22:58:40.279 [Actor Thread 17] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822154_2.fastq.gz
Mar-09 22:58:41.910 [Actor Thread 19] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_1.fastq.gz
Mar-09 22:58:42.762 [FileTransfer-thread-28] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_1.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/a4/c079da1ae8270f7981a748c2904579/SRR1822158_1.fastq.gz
Mar-09 22:58:42.928 [FileTransfer-thread-29] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_2.fastq.gz to work dir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/90/3fa3f48d72d7e39a668146298c15e4/SRR1822158_2.fastq.gz
Mar-09 22:58:43.911 [Actor Thread 20] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822157_2.fastq.gz
Mar-09 22:58:44.928 [Actor Thread 23] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_1.fastq.gz
Mar-09 22:58:46.827 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: TrimGalore (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/1a/37d46fff8ee7c849988f3234bb5100]
Mar-09 22:58:46.902 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:46.903 [Task submitter] INFO  nextflow.Session - [7b/1dea03] Submitted process > BWAMem (SPT5_INPUT_R1_T1)
Mar-09 22:58:46.929 [Actor Thread 21] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/testdata/SRR1822158_2.fastq.gz
Mar-09 22:58:51.199 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:51.200 [Task submitter] INFO  nextflow.Session - [a1/7b2ed4] Submitted process > FastQC (SPT5_INPUT_R2_T1)
Mar-09 22:58:51.210 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:51.211 [Task submitter] INFO  nextflow.Session - [fc/bf5b1f] Submitted process > TrimGalore (SPT5_INPUT_R2_T1)
Mar-09 22:58:55.292 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: BWAMem (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/7b/1dea0317c6a9aba56bd5bfdca62d95]
Mar-09 22:58:55.313 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:55.313 [Task submitter] INFO  nextflow.Session - [16/d8b7f6] Submitted process > SortBAM (SPT5_INPUT_R1_T1)
Mar-09 22:58:57.349 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:57.349 [Task submitter] INFO  nextflow.Session - [90/575bab] Submitted process > FastQC (SPT5_T0_R1_T1)
Mar-09 22:58:57.358 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:58:57.359 [Task submitter] INFO  nextflow.Session - [28/24b72d] Submitted process > TrimGalore (SPT5_T0_R1_T1)
Mar-09 22:58:59.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: SortBAM (SPT5_INPUT_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/16/d8b7f68931d88d5072eededcb53c4c]
Mar-09 22:59:01.198 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: FastQC (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/a1/7b2ed43d1b118650abd13831a603d2]
Mar-09 22:59:01.962 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:01.963 [Task submitter] INFO  nextflow.Session - [29/640af4] Submitted process > FastQC (SPT5_T15_R1_T1)
Mar-09 22:59:01.971 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:01.972 [Task submitter] INFO  nextflow.Session - [a6/851e4d] Submitted process > TrimGalore (SPT5_T15_R1_T1)
Mar-09 22:59:03.785 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:03.785 [Task submitter] INFO  nextflow.Session - [22/f383f7] Submitted process > FastQC (SPT5_T0_R2_T1)
Mar-09 22:59:03.793 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:03.793 [Task submitter] INFO  nextflow.Session - [9d/1431fa] Submitted process > TrimGalore (SPT5_T0_R2_T1)
Mar-09 22:59:04.908 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:04.908 [Task submitter] INFO  nextflow.Session - [c5/c75cff] Submitted process > TrimGalore (SPT5_T15_R2_T1)
Mar-09 22:59:04.916 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:04.916 [Task submitter] INFO  nextflow.Session - [e9/4db589] Submitted process > FastQC (SPT5_T15_R2_T1)
Mar-09 22:59:08.299 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: TrimGalore (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/fc/bf5b1f730a148d3d9cb54fdea57352]
Mar-09 22:59:08.327 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:08.327 [Task submitter] INFO  nextflow.Session - [f3/c6489d] Submitted process > BWAMem (SPT5_INPUT_R2_T1)
Mar-09 22:59:09.069 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: FastQC (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/90/575babb732930ff9bac9aca9d56ffe]
Mar-09 22:59:13.843 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: FastQC (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/29/640af492b57b858f03bc23378a93b9]
Mar-09 22:59:15.740 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: FastQC (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/22/f383f7b7f1e5d9b9d3be4135cc51c8]
Mar-09 22:59:16.779 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: FastQC (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/e9/4db5892172a4497a52fb8462354c4a]
Mar-09 22:59:17.261 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: BWAMem (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/f3/c6489d5b0f9894985b9d352dfbf411]
Mar-09 22:59:17.280 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:17.281 [Task submitter] INFO  nextflow.Session - [65/29f35c] Submitted process > SortBAM (SPT5_INPUT_R2_T1)
Mar-09 22:59:18.437 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: TrimGalore (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/28/24b72dc0dcc346e23ae98462555243]
Mar-09 22:59:18.459 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:18.460 [Task submitter] INFO  nextflow.Session - [36/5fd5f7] Submitted process > BWAMem (SPT5_T0_R1_T1)
Mar-09 22:59:21.548 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: SortBAM (SPT5_INPUT_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/65/29f35ccb2b6b045b858698a3b0b2bf]
Mar-09 22:59:23.535 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: TrimGalore (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/a6/851e4dc26f6d97feb10a0f18b3006a]
Mar-09 22:59:23.556 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:23.556 [Task submitter] INFO  nextflow.Session - [42/da1d40] Submitted process > BWAMem (SPT5_T15_R1_T1)
Mar-09 22:59:24.825 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: TrimGalore (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9d/1431fa396ae1165c76b4d6abbe06e0]
Mar-09 22:59:24.844 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:24.845 [Task submitter] INFO  nextflow.Session - [3c/4f3597] Submitted process > BWAMem (SPT5_T0_R2_T1)
Mar-09 22:59:26.386 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: TrimGalore (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/c5/c75cff1cb6029f7cd201fba3d6c662]
Mar-09 22:59:26.406 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:26.407 [Task submitter] INFO  nextflow.Session - [18/152a21] Submitted process > BWAMem (SPT5_T15_R2_T1)
Mar-09 22:59:27.637 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: BWAMem (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/5fd5f757a37536aff73b00c062b0cf]
Mar-09 22:59:27.652 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:27.653 [Task submitter] INFO  nextflow.Session - [2c/0951fa] Submitted process > SortBAM (SPT5_T0_R1_T1)
Mar-09 22:59:31.909 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: SortBAM (SPT5_T0_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/2c/0951fa31b95b02f023fe7e8c8214d5]
Mar-09 22:59:32.392 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: BWAMem (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/42/da1d40429d49da49fbf39185fc0695]
Mar-09 22:59:32.408 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:32.408 [Task submitter] INFO  nextflow.Session - [ef/5114cc] Submitted process > SortBAM (SPT5_T15_R1_T1)
Mar-09 22:59:34.254 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: BWAMem (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/3c/4f35976813acd1fc39c21de8fe03fb]
Mar-09 22:59:34.270 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:34.271 [Task submitter] INFO  nextflow.Session - [2c/b4f5a4] Submitted process > SortBAM (SPT5_T0_R2_T1)
Mar-09 22:59:35.470 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: BWAMem (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/18/152a21483277f535ac2d979cbab170]
Mar-09 22:59:35.485 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:35.486 [Task submitter] INFO  nextflow.Session - [eb/e07dd4] Submitted process > SortBAM (SPT5_T15_R2_T1)
Mar-09 22:59:36.754 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: SortBAM (SPT5_T15_R1_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/ef/5114cc1d2cde82fb537b3a78772522]
Mar-09 22:59:38.681 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: SortBAM (SPT5_T0_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/2c/b4f5a4512f8b947387f6f88b0c10f3]
Mar-09 22:59:40.109 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: SortBAM (SPT5_T15_R2_T1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/eb/e07dd4d5c94993fd024d4885ff95ba]
Mar-09 22:59:40.149 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:40.150 [Task submitter] INFO  nextflow.Session - [21/fa4bc3] Submitted process > MergeBAM (SPT5_T0_R2)
Mar-09 22:59:40.157 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:40.158 [Task submitter] INFO  nextflow.Session - [f3/276c14] Submitted process > MergeBAM (SPT5_INPUT_R2)
Mar-09 22:59:40.165 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:40.165 [Task submitter] INFO  nextflow.Session - [7f/5c89c1] Submitted process > MergeBAM (SPT5_T0_R1)
Mar-09 22:59:40.171 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:40.172 [Task submitter] INFO  nextflow.Session - [06/66c67e] Submitted process > MergeBAM (SPT5_INPUT_R1)
Mar-09 22:59:40.177 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:40.178 [Task submitter] INFO  nextflow.Session - [1b/78cda7] Submitted process > MergeBAM (SPT5_T15_R1)
Mar-09 22:59:40.183 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:40.184 [Task submitter] INFO  nextflow.Session - [d4/0a7ddf] Submitted process > MergeBAM (SPT5_T15_R2)
Mar-09 22:59:52.147 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: MergeBAM (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/1b/78cda748a8683187f9a970efbe5081]
Mar-09 22:59:52.165 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.165 [Task submitter] INFO  nextflow.Session - [40/50c134] Submitted process > Preseq (SPT5_T15_R1)
Mar-09 22:59:52.200 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.201 [Task submitter] INFO  nextflow.Session - [a9/3f4fc0] Submitted process > MergeBAMFilter (SPT5_T15_R1)
Mar-09 22:59:52.218 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: MergeBAM (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/21/fa4bc3aca5188a75ad616a8d2d5a77]
Mar-09 22:59:52.236 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.236 [Task submitter] INFO  nextflow.Session - [40/aef57b] Submitted process > Preseq (SPT5_T0_R2)
Mar-09 22:59:52.242 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.242 [Task submitter] INFO  nextflow.Session - [9b/5b43e1] Submitted process > MergeBAMFilter (SPT5_T0_R2)
Mar-09 22:59:52.438 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: MergeBAM (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/7f/5c89c139e392c9f2000e547cf11361]
Mar-09 22:59:52.456 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.457 [Task submitter] INFO  nextflow.Session - [6a/4e5569] Submitted process > Preseq (SPT5_T0_R1)
Mar-09 22:59:52.464 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.464 [Task submitter] INFO  nextflow.Session - [9a/f25102] Submitted process > MergeBAMFilter (SPT5_T0_R1)
Mar-09 22:59:52.536 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: MergeBAM (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/d4/0a7ddf4e228fa990d6803396638ae6]
Mar-09 22:59:52.552 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.552 [Task submitter] INFO  nextflow.Session - [ed/c03d37] Submitted process > Preseq (SPT5_T15_R2)
Mar-09 22:59:52.557 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.557 [Task submitter] INFO  nextflow.Session - [4c/f4eaf1] Submitted process > MergeBAMFilter (SPT5_T15_R2)
Mar-09 22:59:52.588 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: MergeBAM (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/f3/276c1484dea8defd33def21641d60e]
Mar-09 22:59:52.603 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.603 [Task submitter] INFO  nextflow.Session - [c1/6bea15] Submitted process > Preseq (SPT5_INPUT_R2)
Mar-09 22:59:52.610 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.611 [Task submitter] INFO  nextflow.Session - [14/b5e389] Submitted process > MergeBAMFilter (SPT5_INPUT_R2)
Mar-09 22:59:52.656 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: MergeBAM (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/06/66c67e8b7f7d1258781175e51127c2]
Mar-09 22:59:52.676 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.676 [Task submitter] INFO  nextflow.Session - [d5/3aab0e] Submitted process > Preseq (SPT5_INPUT_R1)
Mar-09 22:59:52.683 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:52.683 [Task submitter] INFO  nextflow.Session - [8e/521f11] Submitted process > MergeBAMFilter (SPT5_INPUT_R1)
Mar-09 22:59:57.880 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: MergeBAMFilter (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9b/5b43e15025c5d79b3bad59c8b69502]
Mar-09 22:59:57.897 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:57.897 [Task submitter] INFO  nextflow.Session - [84/6b064a] Submitted process > MergeBAMRemoveOrphan (SPT5_T0_R2)
Mar-09 22:59:58.264 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: MergeBAMFilter (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/f251026f07c434d8d6655bcc589d55]
Mar-09 22:59:58.281 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:58.281 [Task submitter] INFO  nextflow.Session - [4f/2a4681] Submitted process > MergeBAMRemoveOrphan (SPT5_T0_R1)
Mar-09 22:59:58.479 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: MergeBAMFilter (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/a9/3f4fc0dc599c69f9c33ea9293bcdd3]
Mar-09 22:59:58.494 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:58.495 [Task submitter] INFO  nextflow.Session - [9f/96d4a6] Submitted process > MergeBAMRemoveOrphan (SPT5_T15_R1)
Mar-09 22:59:58.611 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: Preseq (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/c1/6bea159b9d304dcc94913c568431c9]
Mar-09 22:59:58.762 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: Preseq (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/d5/3aab0e762967aaa093b7fb487d2636]
Mar-09 22:59:58.873 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: MergeBAMFilter (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/f4eaf1ec2254a33ffa8c952a45c66b]
Mar-09 22:59:58.889 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 22:59:58.890 [Task submitter] INFO  nextflow.Session - [ed/61ae0f] Submitted process > MergeBAMRemoveOrphan (SPT5_T15_R2)
Mar-09 22:59:58.906 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: Preseq (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/40/50c134344780fecec188f5c8823f75]
Mar-09 22:59:58.917 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: Preseq (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/40/aef57bfd290e4362d7fa2f1df3be6f]
Mar-09 22:59:59.126 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: Preseq (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/6a/4e5569164f87b8ed875e21477fd553]
Mar-09 22:59:59.177 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: Preseq (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/ed/c03d37b72773e18c1bfde23be7343a]
Mar-09 23:00:00.330 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: MergeBAMFilter (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/521f11e1909e640ffb2b8b6be00b7f]
Mar-09 23:00:00.348 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:00.349 [Task submitter] INFO  nextflow.Session - [d7/efde1a] Submitted process > MergeBAMRemoveOrphan (SPT5_INPUT_R1)
Mar-09 23:00:00.457 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: MergeBAMFilter (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/14/b5e38935e6d103c9289a7f2e2d4d40]
Mar-09 23:00:00.475 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:00.475 [Task submitter] INFO  nextflow.Session - [f0/069415] Submitted process > MergeBAMRemoveOrphan (SPT5_INPUT_R2)
Mar-09 23:00:02.139 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: MergeBAMRemoveOrphan (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/84/6b064a1c4c527562466b7431d02c23]
Mar-09 23:00:02.162 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:02.163 [Task submitter] INFO  nextflow.Session - [36/7a8919] Submitted process > PhantomPeakQualTools (SPT5_T0_R2)
Mar-09 23:00:02.187 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:02.187 [Task submitter] INFO  nextflow.Session - [7a/403016] Submitted process > BigWig (SPT5_T0_R2)
Mar-09 23:00:02.445 [FileTransfer-thread-121] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:02.455 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:02.456 [Task submitter] INFO  nextflow.Session - [6f/7a92d1] Submitted process > CollectMultipleMetrics (SPT5_T0_R2)
Mar-09 23:00:02.755 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: MergeBAMRemoveOrphan (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4f/2a468193fa3be60eb13cf2bdf61eb5]
Mar-09 23:00:02.774 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:02.774 [Task submitter] INFO  nextflow.Session - [04/0adccf] Submitted process > PhantomPeakQualTools (SPT5_T0_R1)
Mar-09 23:00:02.780 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:02.781 [Task submitter] INFO  nextflow.Session - [85/032865] Submitted process > BigWig (SPT5_T0_R1)
Mar-09 23:00:02.996 [FileTransfer-thread-127] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:03.006 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.007 [Task submitter] INFO  nextflow.Session - [f0/64b6f5] Submitted process > CollectMultipleMetrics (SPT5_T0_R1)
Mar-09 23:00:03.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: MergeBAMRemoveOrphan (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9f/96d4a6cedc5bb7dc10b1bab0b6b48c]
Mar-09 23:00:03.086 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.086 [Task submitter] INFO  nextflow.Session - [fd/f4e1c3] Submitted process > BigWig (SPT5_T15_R1)
Mar-09 23:00:03.095 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.096 [Task submitter] INFO  nextflow.Session - [36/e35714] Submitted process > PhantomPeakQualTools (SPT5_T15_R1)
Mar-09 23:00:03.313 [FileTransfer-thread-133] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:03.324 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.325 [Task submitter] INFO  nextflow.Session - [83/0bc7f5] Submitted process > CollectMultipleMetrics (SPT5_T15_R1)
Mar-09 23:00:03.526 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: MergeBAMRemoveOrphan (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/ed/61ae0f454db611886e53079a1e3506]
Mar-09 23:00:03.550 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.550 [Task submitter] INFO  nextflow.Session - [8e/dbffc6] Submitted process > PhantomPeakQualTools (SPT5_T15_R2)
Mar-09 23:00:03.558 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.558 [Task submitter] INFO  nextflow.Session - [2f/fe4538] Submitted process > BigWig (SPT5_T15_R2)
Mar-09 23:00:03.767 [FileTransfer-thread-139] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:03.778 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:03.779 [Task submitter] INFO  nextflow.Session - [9f/ec5106] Submitted process > CollectMultipleMetrics (SPT5_T15_R2)
Mar-09 23:00:05.614 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: MergeBAMRemoveOrphan (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/d7/efde1a6f16274125ce21d9f769497b]
Mar-09 23:00:05.641 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.641 [Task submitter] INFO  nextflow.Session - [98/620a33] Submitted process > BigWig (SPT5_INPUT_R1)
Mar-09 23:00:05.650 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.651 [Task submitter] INFO  nextflow.Session - [9a/0b4483] Submitted process > PhantomPeakQualTools (SPT5_INPUT_R1)
Mar-09 23:00:05.684 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.684 [Task submitter] INFO  nextflow.Session - [b2/241911] Submitted process > PlotFingerprint (SPT5_T15_R1 vs SPT5_INPUT_R1)
Mar-09 23:00:05.691 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.691 [Task submitter] INFO  nextflow.Session - [2f/216356] Submitted process > PlotFingerprint (SPT5_T0_R1 vs SPT5_INPUT_R1)
Mar-09 23:00:05.696 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.696 [Task submitter] INFO  nextflow.Session - [6e/2a3f2c] Submitted process > MACSCallPeak (SPT5_T0_R1 vs SPT5_INPUT_R1)
Mar-09 23:00:05.700 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.700 [Task submitter] INFO  nextflow.Session - [6d/c5868a] Submitted process > MACSCallPeak (SPT5_T15_R1 vs SPT5_INPUT_R1)
Mar-09 23:00:05.848 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: MergeBAMRemoveOrphan (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/f0/0694159cc8950be2c8b836a5ea5c70]
Mar-09 23:00:05.856 [FileTransfer-thread-150] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:05.861 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.861 [Task submitter] INFO  nextflow.Session - [4c/91bfcf] Submitted process > PhantomPeakQualTools (SPT5_INPUT_R2)
Mar-09 23:00:05.879 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.880 [Task submitter] INFO  nextflow.Session - [1a/3b42f6] Submitted process > BigWig (SPT5_INPUT_R2)
Mar-09 23:00:05.885 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.885 [Task submitter] INFO  nextflow.Session - [a1/7d0059] Submitted process > PlotFingerprint (SPT5_T15_R2 vs SPT5_INPUT_R2)
Mar-09 23:00:05.889 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.889 [Task submitter] INFO  nextflow.Session - [dd/774d65] Submitted process > CollectMultipleMetrics (SPT5_INPUT_R1)
Mar-09 23:00:05.893 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.893 [Task submitter] INFO  nextflow.Session - [da/76a732] Submitted process > PlotFingerprint (SPT5_T0_R2 vs SPT5_INPUT_R2)
Mar-09 23:00:05.898 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.898 [Task submitter] INFO  nextflow.Session - [95/f7d0cd] Submitted process > MACSCallPeak (SPT5_T15_R2 vs SPT5_INPUT_R2)
Mar-09 23:00:05.906 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:05.906 [Task submitter] INFO  nextflow.Session - [6f/13850e] Submitted process > MACSCallPeak (SPT5_T0_R2 vs SPT5_INPUT_R2)
Mar-09 23:00:06.087 [FileTransfer-thread-151] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:06.094 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:06.095 [Task submitter] INFO  nextflow.Session - [91/43cbc0] Submitted process > CollectMultipleMetrics (SPT5_INPUT_R2)
Mar-09 23:00:06.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: BigWig (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/7a/4030168db0deaf09c23a27db6ff43c]
Mar-09 23:00:06.511 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:06.512 [Task submitter] INFO  nextflow.Session - [82/8a672f] Submitted process > PlotProfile (SPT5_T0_R2)
Mar-09 23:00:07.308 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: BigWig (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/85/0328651665f6f56b1a7dbb4f3e8bba]
Mar-09 23:00:07.327 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:07.328 [Task submitter] INFO  nextflow.Session - [41/ec12b7] Submitted process > PlotProfile (SPT5_T0_R1)
Mar-09 23:00:08.231 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: BigWig (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/fd/f4e1c3a72320ad5c9f18156ef988c2]
Mar-09 23:00:08.245 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:08.245 [Task submitter] INFO  nextflow.Session - [cd/6ff4da] Submitted process > PlotProfile (SPT5_T15_R1)
Mar-09 23:00:09.000 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: BigWig (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/2f/fe453843ee8405d58ed36a6be8e2ce]
Mar-09 23:00:09.010 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:09.011 [Task submitter] INFO  nextflow.Session - [55/609054] Submitted process > PlotProfile (SPT5_T15_R2)
Mar-09 23:00:10.269 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: CollectMultipleMetrics (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/6f/7a92d155d226f3b2d4a1d1e9a6ca39]
Mar-09 23:00:10.707 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: CollectMultipleMetrics (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/f0/64b6f5e0ac93e2fd96a6d24166d8f5]
Mar-09 23:00:11.829 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: CollectMultipleMetrics (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/83/0bc7f51ada113bd3b3fe68f693982f]
Mar-09 23:00:11.964 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: CollectMultipleMetrics (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9f/ec51065c19e7d841fc8ad9c3b48c69]
Mar-09 23:00:12.080 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: BigWig (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/98/620a33712cc505a4d268f84a59d0dc]
Mar-09 23:00:12.096 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:12.097 [Task submitter] INFO  nextflow.Session - [38/f78edd] Submitted process > PlotProfile (SPT5_INPUT_R1)
Mar-09 23:00:12.272 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: BigWig (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/1a/3b42f6badf0e6b81dd1b16d2fc49c3]
Mar-09 23:00:12.287 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:12.287 [Task submitter] INFO  nextflow.Session - [cd/c7d3ee] Submitted process > PlotProfile (SPT5_INPUT_R2)
Mar-09 23:00:13.189 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: MACSCallPeak (SPT5_T0_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/6f/13850e8d280427e49e35cc56fd8ff2]
Mar-09 23:00:13.221 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: MACSCallPeak (SPT5_T15_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/6d/c5868ad7bfbc7e6cc61fd32073aaa5]
Mar-09 23:00:13.272 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: MACSCallPeak (SPT5_T0_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/6e/2a3f2cd99f0c27731b6f3df8758d9e]
Mar-09 23:00:13.552 [FileTransfer-thread-215] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:13.670 [FileTransfer-thread-216] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/9d/953ae071434ac7240c7a0b1f66aeff/genes.gtf
Mar-09 23:00:13.708 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: MACSCallPeak (SPT5_T15_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/95/f7d0cd2d7541b621bdf592124041a2]
Mar-09 23:00:13.746 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:13.746 [Task submitter] INFO  nextflow.Session - [a0/f75e45] Submitted process > ConsensusPeakSet (SPT5)
Mar-09 23:00:13.785 [FileTransfer-thread-222] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:13.792 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:13.792 [Task submitter] INFO  nextflow.Session - [c5/0bc4b7] Submitted process > AnnotatePeaks (SPT5_T0_R1 vs SPT5_INPUT_R1)
Mar-09 23:00:13.797 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:13.797 [Task submitter] INFO  nextflow.Session - [7b/ad225f] Submitted process > AnnotatePeaks (SPT5_T0_R2 vs SPT5_INPUT_R2)
Mar-09 23:00:13.801 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:13.801 [Task submitter] INFO  nextflow.Session - [e5/a70d0c] Submitted process > AnnotatePeaks (SPT5_T15_R1 vs SPT5_INPUT_R1)
Mar-09 23:00:13.908 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: CollectMultipleMetrics (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/dd/774d650ff46dfd21363c93e768f484]
Mar-09 23:00:14.059 [FileTransfer-thread-232] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:14.175 [FileTransfer-thread-233] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/9d/953ae071434ac7240c7a0b1f66aeff/genes.gtf
Mar-09 23:00:14.183 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:14.184 [Task submitter] INFO  nextflow.Session - [1e/27b3ae] Submitted process > AnnotatePeaks (SPT5_T15_R2 vs SPT5_INPUT_R2)
Mar-09 23:00:14.312 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: CollectMultipleMetrics (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/91/43cbc03a34c47be8cd2385ea5a7fb8]
Mar-09 23:00:19.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: AnnotatePeaks (SPT5_T0_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/7b/ad225fe4a8bfce423786829249bec2]
Mar-09 23:00:19.316 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: AnnotatePeaks (SPT5_T15_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/e5/a70d0c26d84d28b3284d98114f391f]
Mar-09 23:00:19.416 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: AnnotatePeaks (SPT5_T0_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/c5/0bc4b765855b940f12da370835ae11]
Mar-09 23:00:19.877 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: AnnotatePeaks (SPT5_T15_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/1e/27b3aea8b14f0373ee60e222b7da79]
Mar-09 23:00:19.893 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:19.893 [Task submitter] INFO  nextflow.Session - [32/e0d752] Submitted process > PeakQC
Mar-09 23:00:21.343 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: ConsensusPeakSet (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/a0/f75e451fd1ad4c3b022be525ec2b1f]
Mar-09 23:00:21.372 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:21.373 [Task submitter] INFO  nextflow.Session - [2d/6837c0] Submitted process > ConsensusPeakSetDESeq (SPT5)
Mar-09 23:00:21.694 [FileTransfer-thread-252] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:21.809 [FileTransfer-thread-253] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/9d/953ae071434ac7240c7a0b1f66aeff/genes.gtf
Mar-09 23:00:21.820 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:21.820 [Task submitter] INFO  nextflow.Session - [dc/5110ba] Submitted process > ConsensusPeakSetAnnotate (SPT5)
Mar-09 23:00:27.473 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: ConsensusPeakSetAnnotate (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/dc/5110ba54887f4630e2b11b47bc7ca5]
Mar-09 23:00:35.698 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: PeakQC; status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/32/e0d752a79d1f4ea916a38473132e85]
Mar-09 23:00:38.520 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: PlotFingerprint (SPT5_T15_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/b2/2419118c61ec5e36c86a1c0b7cd0ac]
Mar-09 23:00:39.354 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: PlotFingerprint (SPT5_T0_R1 vs SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/2f/2163563f5344d21067dc367be1c382]
Mar-09 23:00:39.782 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: PlotFingerprint (SPT5_T0_R2 vs SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/da/76a73255a26a1a476c2bb695102e30]
Mar-09 23:00:40.500 [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: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/a1/7d0059c183348f5e37c7c4b699e108]
Mar-09 23:00:53.518 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 13 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
~> TaskHandler[id: 82; name: PlotProfile (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/82/8a672f9fb0d316e2afdc0b309c93e4]
~> TaskHandler[id: 83; name: PlotProfile (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/41/ec12b7dfebb81b394ba5a5c08553a6]
~> TaskHandler[id: 84; name: PlotProfile (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/cd/6ff4dad7055036e117a15e53b7e59f]
~> TaskHandler[id: 85; name: PlotProfile (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/55/60905484f6c184e426c3e76f02c407]
.. remaining tasks omitted.
Mar-09 23:00:54.034 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: ConsensusPeakSetDESeq (SPT5); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/2d/6837c02565e334638394ebbbc3ba39]
Mar-09 23:00:54.676 [FileTransfer-thread-293] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa at /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/stage/54/f9807b3c79659da66058c2597caf1b/genome.fa
Mar-09 23:00:54.690 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-09 23:00:54.690 [Task submitter] INFO  nextflow.Session - [67/504cd7] Submitted process > IGV
Mar-09 23:00:57.584 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: IGV; status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/67/504cd738b36cd77cbf244978fedfcd]
Mar-09 23:02:33.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: PlotProfile (SPT5_INPUT_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/38/f78edd958cf9bc25b666d0951ae540]
Mar-09 23:02:34.489 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: PlotProfile (SPT5_T0_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/41/ec12b7dfebb81b394ba5a5c08553a6]
Mar-09 23:02:34.507 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: PlotProfile (SPT5_T15_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/55/60905484f6c184e426c3e76f02c407]
Mar-09 23:02:35.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: PlotProfile (SPT5_INPUT_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/cd/c7d3ee3eb62ab339bdeff64a1e5ffe]
Mar-09 23:02:38.821 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: PlotProfile (SPT5_T15_R1); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/cd/6ff4dad7055036e117a15e53b7e59f]
Mar-09 23:02:57.837 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: PlotProfile (SPT5_T0_R2); status: COMPLETED; exit: 0; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/82/8a672f9fb0d316e2afdc0b309c93e4]
Mar-09 23:05:53.589 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:10:53.655 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:15:53.711 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:20:53.767 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:25:53.825 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:30:53.867 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:35:53.925 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]
Mar-09 23:40:53.975 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 57; name: PhantomPeakQualTools (SPT5_T0_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/7a8919079e6567baf7e2443aad78cf]
~> TaskHandler[id: 60; name: PhantomPeakQualTools (SPT5_T0_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/04/0adccfc029bdcb8727ab18e9953b84]
~> TaskHandler[id: 62; name: PhantomPeakQualTools (SPT5_T15_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/36/e3571405bd783412b64623396236dc]
~> TaskHandler[id: 65; name: PhantomPeakQualTools (SPT5_T15_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/8e/dbffc6f261aa42983a1a04be0f8ff8]
~> TaskHandler[id: 69; name: PhantomPeakQualTools (SPT5_INPUT_R1); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/9a/0b4483e81b7e3384efe685e7118e7e]
~> TaskHandler[id: 75; name: PhantomPeakQualTools (SPT5_INPUT_R2); status: RUNNING; exit: -; error: -; workDir: /platinum-2/xiangjie/omics_analysis_practice/nf-core/test-chipseq/work/4c/91bfcf9ca3edebd1f3cfe89d4093ea]

Thanks!

drpatelh commented 4 years ago

Hi @CadenZhao ! Apologies for the late response. I havent seen that error before...the test dataset is small enough where the pipeline should complete all of the processes without any issues.

In any case, I would definitely try and run the pipeline with -profile test,docker or -profile test,singularity instead because using Conda doesnt make the results entirely reproducible. Do you have either Docker or Singularity installed in your local environment? Im not sure that will solve the error you reported but it may be worth retrying the execution a couple of times to see if the error is reproducible.

drpatelh commented 4 years ago

Hi @CadenZhao ! Hoping you figured out how to fix this but if the issue persists please feel free to re-open.

CadenZhao commented 4 years ago

Sorry for the late response. I tried singularity and docker. I install singularity using conda and run the pipeline, it throws the following ERRORs. Even though I install squashfs-tools, the situation is totally the same. image When I set profile to Docker, I got this image Maybe it's network problem at home? Since I have never used docker and singularity, please help me if there is any simple mistake.

By the way, I can run through many other pipelines, like rnaseq, atacseq, hic, scrnaseq, hic, mag, etc. Thank you very much!