Nov-14 17:05:39.416 [main] DEBUG nextflow.cli.Launcher - $> /projects1/clusterhomes/fellows/.local/bin/nextflow run nf-core/eager --reads /projects1/users/fellows/nextflow/eager2/my_test/data/ABM006.A0101/*_R{1,2}*fastq.gz --pairedEnd --fasta /projects1/users/fellows/nextflow/eager2/my_test/references/hg19_MT.fasta --outdir /projects1/users/fellows/nextflow/eager2/my_test/output_eager2 -profile singularity --max_cpus 4 --max_memory 16G -r 2.0.2
Nov-14 17:05:39.574 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.32.0
Nov-14 17:05:40.596 [main] DEBUG nextflow.scm.AssetManager - Git config: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Nov-14 17:05:40.610 [main] DEBUG nextflow.scm.AssetManager - Git config: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Nov-14 17:05:41.127 [main] DEBUG nextflow.scm.AssetManager - Git config: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git
Nov-14 17:05:41.127 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/eager` [naughty_lorenz] - revision: c44b88110d [2.0.2]
Nov-14 17:05:42.098 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager/nextflow.config
Nov-14 17:05:42.101 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager/nextflow.config
Nov-14 17:05:42.114 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Nov-14 17:05:42.297 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, cfc, uzh, debug, test, conda, singularity, awsbatch, none, docker, binac]
Nov-14 17:05:42.355 [main] DEBUG nextflow.Session - Session uuid: 14088634-cbe4-46aa-bde8-fb92056dd379
Nov-14 17:05:42.356 [main] DEBUG nextflow.Session - Run name: naughty_lorenz
Nov-14 17:05:42.357 [main] DEBUG nextflow.Session - Executor pool size: 64
Nov-14 17:05:42.397 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 0.32.0 build 4897
  Modified: 27-09-2018 10:17 UTC (12:17 CEST)
  System: Linux 4.4.0-38-generic
  Runtime: Groovy 2.5.1 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_74-b02
  Encoding: UTF-8 (UTF-8)
  Process: 76919@mpi-cruncher5 [172.20.102.85]
  CPUs: 64 - Mem: 755.9 GB (711.6 GB) - Swap: 952 MB (367.9 MB)
Nov-14 17:05:42.425 [main] DEBUG nextflow.Session - Work-dir: /projects1/users/fellows/nextflow/eager2/my_test/work [gpfs]
Nov-14 17:05:42.615 [main] DEBUG nextflow.Session - Session start invoked
Nov-14 17:05:42.623 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
Nov-14 17:05:42.625 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /projects1/users/fellows/nextflow/eager2/my_test/output_eager2/pipeline_info/nf-core/eager_trace.txt
Nov-14 17:05:42.632 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
Nov-14 17:05:43.812 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-14 17:05:44.082 [main] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /projects1/users/fellows/nextflow/eager2/my_test/data/ABM006.A0101/; pattern: *_R{1,2}*fastq.gz; options: [:]
Nov-14 17:05:44.129 [main] INFO  nextflow.Nextflow - =========================================
Nov-14 17:05:44.132 [main] INFO  nextflow.Nextflow -  nf-core/eager v2.0.0dev
Nov-14 17:05:44.132 [main] INFO  nextflow.Nextflow - =========================================
Nov-14 17:05:44.136 [main] WARN  nextflow.script.ScriptBinding - Access to undefined parameter `max_time` -- Initialise it to a default value eg. `params.max_time = some_value`
Nov-14 17:05:44.142 [main] INFO  nextflow.Nextflow - Pipeline Name  : nf-core/eager
Pipeline Version: 2.0.2
Run Name       : naughty_lorenz
Reads          : /projects1/users/fellows/nextflow/eager2/my_test/data/ABM006.A0101/*_R{1,2}*fastq.gz
Fasta Ref      : /projects1/users/fellows/nextflow/eager2/my_test/references/hg19_MT.fasta
Data Type      : Paired-End
Max Memory     : 16G
Max CPUs       : 4
Max Time       : null
Output dir     : /projects1/users/fellows/nextflow/eager2/my_test/output_eager2
Working dir    : /projects1/users/fellows/nextflow/eager2/my_test/work
Container Engine: singularity
Container      : [:]
Current home   : /projects1/clusterhomes/fellows
Current user   : fellows
Current path   : /projects1/users/fellows/nextflow/eager2/my_test
Script dir     : /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager
Config Profile : singularity
Nov-14 17:05:44.144 [main] INFO  nextflow.Nextflow - =========================================
Nov-14 17:05:44.252 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.253 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.267 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.270 [main] INFO  nextflow.executor.Executor - [warm up] executor > local
Nov-14 17:05:44.277 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=755.9 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
Nov-14 17:05:44.283 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
Nov-14 17:05:44.284 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Nov-14 17:05:44.288 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
Nov-14 17:05:44.340 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions)
Nov-14 17:05:44.344 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 64
Nov-14 17:05:44.414 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.415 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.415 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.417 [main] DEBUG nextflow.Session - >>> barrier register (process: makeBWAIndex)
Nov-14 17:05:44.419 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeBWAIndex -- maxForks: 64
Nov-14 17:05:44.432 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.433 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.436 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.440 [main] DEBUG nextflow.Session - >>> barrier register (process: makeFastaIndex)
Nov-14 17:05:44.442 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeFastaIndex -- maxForks: 64
Nov-14 17:05:44.454 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.454 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.455 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.457 [main] DEBUG nextflow.Session - >>> barrier register (process: makeSeqDict)
Nov-14 17:05:44.459 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeSeqDict -- maxForks: 64
Nov-14 17:05:44.492 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.493 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.493 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.496 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc)
Nov-14 17:05:44.496 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 64
Nov-14 17:05:44.547 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.547 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.547 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.549 [main] DEBUG nextflow.Session - >>> barrier register (process: fastp)
Nov-14 17:05:44.549 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastp -- maxForks: 64
Nov-14 17:05:44.580 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.581 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.581 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.584 [main] DEBUG nextflow.Session - >>> barrier register (process: adapter_removal)
Nov-14 17:05:44.585 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > adapter_removal -- maxForks: 64
Nov-14 17:05:44.597 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: fastp)
Nov-14 17:05:44.602 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.602 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.602 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.605 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc_after_clipping)
Nov-14 17:05:44.606 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc_after_clipping -- maxForks: 64
Nov-14 17:05:44.617 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.619 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.619 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.624 [main] DEBUG nextflow.Session - >>> barrier register (process: bwa)
Nov-14 17:05:44.627 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwa -- maxForks: 64
Nov-14 17:05:44.644 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.644 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.644 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.646 [main] DEBUG nextflow.Session - >>> barrier register (process: circulargenerator)
Nov-14 17:05:44.646 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > circulargenerator -- maxForks: 64
Nov-14 17:05:44.658 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.659 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.659 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.663 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: circulargenerator)
Nov-14 17:05:44.665 [main] DEBUG nextflow.Session - >>> barrier register (process: circularmapper)
Nov-14 17:05:44.666 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > circularmapper -- maxForks: 64
Nov-14 17:05:44.672 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: circularmapper)
Nov-14 17:05:44.679 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.680 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.680 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.682 [main] DEBUG nextflow.Session - >>> barrier register (process: bwamem)
Nov-14 17:05:44.682 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwamem -- maxForks: 64
Nov-14 17:05:44.685 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.701 [Task submitter] INFO  nextflow.Session - [91/bfd09f] Submitted process > fastqc (ABM006.A0101_S0_L003)
Nov-14 17:05:44.704 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.705 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.706 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.707 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_idxstats)
Nov-14 17:05:44.708 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_idxstats -- maxForks: 64
Nov-14 17:05:44.719 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.719 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.720 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.722 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_filter)
Nov-14 17:05:44.722 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_filter -- maxForks: 64
Nov-14 17:05:44.738 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.738 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.738 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.739 [main] DEBUG nextflow.Session - >>> barrier register (process: dedup)
Nov-14 17:05:44.740 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dedup -- maxForks: 64
Nov-14 17:05:44.750 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.751 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.752 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.753 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.754 [Task submitter] INFO  nextflow.Session - [da/e6a4de] Submitted process > makeBWAIndex (hg19_MT.fasta)
Nov-14 17:05:44.756 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq)
Nov-14 17:05:44.756 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 64
Nov-14 17:05:44.764 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.765 [Task submitter] INFO  nextflow.Session - [bb/01af32] Submitted process > get_software_versions
Nov-14 17:05:44.771 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.772 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.772 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.774 [main] DEBUG nextflow.Session - >>> barrier register (process: damageprofiler)
Nov-14 17:05:44.774 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > damageprofiler -- maxForks: 64
Nov-14 17:05:44.779 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.947 [Task submitter] INFO  nextflow.Session - [ce/8041f5] Submitted process > fastqc (ABM006.A0101_S0_L002)
Nov-14 17:05:44.949 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.950 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.958 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.959 [main] DEBUG nextflow.Session - >>> barrier register (process: qualimap)
Nov-14 17:05:44.959 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > qualimap -- maxForks: 64
Nov-14 17:05:44.968 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.969 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.969 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.970 [main] DEBUG nextflow.Session - >>> barrier register (process: markDup)
Nov-14 17:05:44.970 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDup -- maxForks: 64
Nov-14 17:05:44.974 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.975 [Task submitter] INFO  nextflow.Session - [75/c9fb9d] Submitted process > fastqc (ABM006.A0101_S0_L001)
Nov-14 17:05:44.982 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.982 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.983 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.983 [main] DEBUG nextflow.Session - >>> barrier register (process: pmdtools)
Nov-14 17:05:44.984 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > pmdtools -- maxForks: 64
Nov-14 17:05:44.986 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.987 [Task submitter] INFO  nextflow.Session - [50/4ffdd1] Submitted process > makeSeqDict (hg19_MT.fasta)
Nov-14 17:05:44.989 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:44.989 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:44.989 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:44.990 [main] DEBUG nextflow.Session - >>> barrier register (process: bam_trim)
Nov-14 17:05:44.990 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bam_trim -- maxForks: 64
Nov-14 17:05:44.994 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:44.994 [Task submitter] INFO  nextflow.Session - [1b/b417ff] Submitted process > fastqc (ABM006.A0101_S0_L004)
Nov-14 17:05:45.004 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:45.005 [Task submitter] INFO  nextflow.Session - [89/b9d708] Submitted process > makeFastaIndex (hg19_MT.fasta)
Nov-14 17:05:45.013 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:45.014 [Task submitter] INFO  nextflow.Session - [16/a08639] Submitted process > adapter_removal (ABM006.A0101_S0_L001)
Nov-14 17:05:45.022 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:45.023 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:45.023 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:45.024 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:45.025 [Task submitter] INFO  nextflow.Session - [c7/a27ea7] Submitted process > adapter_removal (ABM006.A0101_S0_L002)
Nov-14 17:05:45.025 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc)
Nov-14 17:05:45.025 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 64
Nov-14 17:05:45.032 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
Nov-14 17:05:45.033 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
Nov-14 17:05:45.033 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
Nov-14 17:05:45.034 [main] DEBUG nextflow.Session - >>> barrier register (process: output_documentation)
Nov-14 17:05:45.034 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 64
Nov-14 17:05:45.038 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:45.038 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
Nov-14 17:05:45.038 [main] DEBUG nextflow.Session - Session await
Nov-14 17:05:45.039 [Task submitter] INFO  nextflow.Session - [71/32a235] Submitted process > adapter_removal (ABM006.A0101_S0_L003)
Nov-14 17:05:45.048 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:45.049 [Task submitter] INFO  nextflow.Session - [e2/ed2b4f] Submitted process > adapter_removal (ABM006.A0101_S0_L004)
Nov-14 17:05:45.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: makeBWAIndex (hg19_MT.fasta); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/da/e6a4deeb54e90afa02c0784a161cb2]
Nov-14 17:05:45.060 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:05:45.061 [Task submitter] INFO  nextflow.Session - [d5/7c2c27] Submitted process > output_documentation
Nov-14 17:05:45.113 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: makeBWAIndex)
Nov-14 17:05:45.336 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: makeFastaIndex (hg19_MT.fasta); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/89/b9d7082c939763b360fe9d60b8658f]
Nov-14 17:05:45.342 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: makeFastaIndex)
Nov-14 17:05:45.693 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/d5/7c2c276deb95f9032859d610a93d92]
Nov-14 17:05:45.698 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: output_documentation)
Nov-14 17:05:50.552 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: get_software_versions; status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/bb/01af3254665a48f38d7a8990932cb6]
Nov-14 17:05:50.554 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: get_software_versions)
Nov-14 17:05:50.851 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: makeSeqDict (hg19_MT.fasta); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/50/4ffdd1631049bf5c7457bacb5a3bec]
Nov-14 17:05:50.858 [Actor Thread 19] DEBUG nextflow.Session - <<< barrier arrive (process: makeSeqDict)
Nov-14 17:06:26.687 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: fastqc (ABM006.A0101_S0_L004); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/1b/b417ff7e5399a18e8a20a8ca0356d2]
Nov-14 17:06:27.765 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: fastqc (ABM006.A0101_S0_L001); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/75/c9fb9d10f8f6382a47b5a8953513a7]
Nov-14 17:06:28.823 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: fastqc (ABM006.A0101_S0_L002); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/ce/8041f503b02440bf92078c66e3c427]
Nov-14 17:06:30.936 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: fastqc (ABM006.A0101_S0_L003); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/91/bfd09f16842aeed76fb13e2b0c3ec2]
Nov-14 17:06:30.942 [Actor Thread 19] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc)
Nov-14 17:08:04.140 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: adapter_removal (ABM006.A0101_S0_L002); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/c7/a27ea7eb290a47c50b2d37ab0ff1cc]
Nov-14 17:08:04.158 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: bwamem)
Nov-14 17:08:04.163 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:08:04.163 [Task submitter] INFO  nextflow.Session - [87/15fe16] Submitted process > fastqc_after_clipping (ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq)
Nov-14 17:08:04.197 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:08:04.198 [Task submitter] INFO  nextflow.Session - [09/867e24] Submitted process > bwa (ABM006.A0101_S0_L002_R1_001)
Nov-14 17:08:09.307 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: adapter_removal (ABM006.A0101_S0_L004); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/e2/ed2b4f835a69fcd974503d0332b4ad]
Nov-14 17:08:09.355 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:08:09.357 [Task submitter] INFO  nextflow.Session - [cf/ba6ed3] Submitted process > fastqc_after_clipping (ABM006.A0101_S0_L004_R1_001.combined.prefixed.fq)
Nov-14 17:08:09.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: adapter_removal (ABM006.A0101_S0_L001); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/16/a08639887353e1c0b878e5d99693df]
Nov-14 17:08:09.423 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: adapter_removal (ABM006.A0101_S0_L003); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/71/32a235fbc141f590657466cd9f6614]
Nov-14 17:08:09.431 [Actor Thread 27] DEBUG nextflow.Session - <<< barrier arrive (process: adapter_removal)
Nov-14 17:08:09.438 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:08:09.439 [Task submitter] INFO  nextflow.Session - [45/b04c02] Submitted process > fastqc_after_clipping (ABM006.A0101_S0_L001_R1_001.combined.prefixed.fq)
Nov-14 17:08:09.444 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-14 17:08:09.444 [Task submitter] INFO  nextflow.Session - [02/104778] Submitted process > fastqc_after_clipping (ABM006.A0101_S0_L003_R1_001.combined.prefixed.fq)
Nov-14 17:08:20.013 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: fastqc_after_clipping (ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/87/15fe16f19bb22323f758ab31c53862]
Nov-14 17:08:25.225 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: fastqc_after_clipping (ABM006.A0101_S0_L004_R1_001.combined.prefixed.fq); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/cf/ba6ed3a793c5173a4610f7a2421d3b]
Nov-14 17:08:25.324 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: fastqc_after_clipping (ABM006.A0101_S0_L001_R1_001.combined.prefixed.fq); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/45/b04c02dad64844f34b766aa23515b3]
Nov-14 17:08:30.490 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: fastqc_after_clipping (ABM006.A0101_S0_L003_R1_001.combined.prefixed.fq); status: COMPLETED; exit: 0; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/02/10477841b6597458caa554e1bad1e8]
Nov-14 17:08:30.497 [Actor Thread 29] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc_after_clipping)
Nov-14 17:08:40.709 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: bwa (ABM006.A0101_S0_L002_R1_001); status: COMPLETED; exit: 1; error: -; workDir: /projects1/users/fellows/nextflow/eager2/my_test/work/09/867e241abeeb78307c9fc618980ca2]
Nov-14 17:08:40.790 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'bwa (ABM006.A0101_S0_L002_R1_001)'

Caused by:
  Process `bwa (ABM006.A0101_S0_L002_R1_001)` terminated with an error exit status (1)

Command executed:

  bwa aln -t 1 hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz -n 0.04 -l 32 -k 2 -f "ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai"
  bwa samse -r "@RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina" hg19_MT.fasta "ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq".sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz | samtools sort -@ 1 -O bam - > "ABM006.A0101_S0_L002_R1_001".sorted.bam
  samtools index -@ 1 "ABM006.A0101_S0_L002_R1_001".sorted.bam

Command exit status:
  1

Command output:
  (empty)

Command error:
  [bwa_aln_core] calculate SA coordinate... 1.14 sec
  [bwa_aln_core] write to the disk... 0.01 sec
  [bwa_aln_core] 1835008 sequences have been processed.
  [bwa_aln_core] calculate SA coordinate... 0.93 sec
  [bwa_aln_core] write to the disk... 0.01 sec
  [bwa_aln_core] 2027689 sequences have been processed.
  [main] Version: 0.7.12-r1039
  [main] CMD: bwa aln -t 1 -n 0.04 -l 32 -k 2 -f ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 13.003 sec; CPU: 12.988 sec
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 262144 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.04 sec
  [bwa_aln_core] refine gapped alignments... 0.05 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 524288 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.06 sec
  [bwa_aln_core] refine gapped alignments... 0.04 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 786432 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1048576 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1310720 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1572864 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.03 sec
  [bwa_aln_core] refine gapped alignments... 0.05 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 1835008 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.04 sec
  [bwa_aln_core] print alignments... 0.15 sec
  [bwa_aln_core] 2027689 sequences have been processed.
  [main] Version: 0.7.12-r1039
  [main] CMD: bwa samse -r @RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 7.227 sec; CPU: 6.184 sec
  index: invalid option -- '@'
  Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
  Options:
    -b       Generate BAI-format index for BAM files [default]
    -c       Generate CSI-format index for BAM files
    -m INT   Set minimum interval size for CSI indices to 2^INT [14]

Work dir:
  /projects1/users/fellows/nextflow/eager2/my_test/work/09/867e241abeeb78307c9fc618980ca2

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Nov-14 17:08:40.801 [Actor Thread 29] DEBUG nextflow.Session - <<< barrier arrive (process: bwa)
Nov-14 17:08:40.802 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `bwa (ABM006.A0101_S0_L002_R1_001)` terminated with an error exit status (1)
Nov-14 17:08:40.803 [Actor Thread 29] DEBUG nextflow.Session - <<< barrier arrive (process: damageprofiler)
Nov-14 17:08:40.803 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_idxstats)
Nov-14 17:08:40.811 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_filter)
Nov-14 17:08:40.811 [Actor Thread 29] DEBUG nextflow.Session - <<< barrier arrive (process: markDup)
Nov-14 17:08:40.811 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: qualimap)
Nov-14 17:08:40.812 [Actor Thread 35] DEBUG nextflow.Session - <<< barrier arrive (process: dedup)
Nov-14 17:08:40.813 [Actor Thread 35] DEBUG nextflow.Session - <<< barrier arrive (process: pmdtools)
Nov-14 17:08:40.814 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: bam_trim)
Nov-14 17:08:40.815 [Actor Thread 39] DEBUG nextflow.Session - <<< barrier arrive (process: preseq)
Nov-14 17:08:40.895 [main] DEBUG nextflow.Session - Session await > all process finished
Nov-14 17:08:40.908 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
Nov-14 17:08:40.909 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-14 17:08:41.003 [main] INFO  nextflow.Nextflow - [nf-core/eager] Pipeline Complete
Nov-14 17:08:41.019 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=17; failedCount=1; ignoredCount=0; cachedCount=0; succeedDuration=13m 24s; failedDuration=36.3s; cachedDuration=0ms]
Nov-14 17:08:41.020 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Nov-14 17:08:41.024 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Nov-14 17:08:41.144 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  {"makeFastaIndex":{"cpu":null,"mem":null,"time":{"mean":15,"min":15,"q1":15,"q2":15,"q3":15,"max":15,"minLabel":"makeFastaIndex (hg19_MT.fasta)","maxLabel":"makeFastaIndex (hg19_MT.fasta)","q1Label":"makeFastaIndex (hg19_MT.fasta)","q2Label":"makeFastaIndex (hg19_MT.fasta)","q3Label":"makeFastaIndex (hg19_MT.fasta)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"output_documentation":{"cpu":null,"mem":{"mean":2743349248,"min":2743349248,"q1":2743349248,"q2":2743349248,"q3":2743349248,"max":2743349248,"minLabel":"output_documentation","maxLabel":"output_documentation","q1Label":"output_documentation","q2Label":"output_documentation","q3Label":"output_documentation"},"time":{"mean":400,"min":400,"q1":400,"q2":400,"q3":400,"max":400,"minLabel":"output_documentation","maxLabel":"output_documentation","q1Label":"output_documentation","q2Label":"output_documentation","q3Label":"output_documentation"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"fastqc":{"cpu":{"mean":372.38,"min":303.4,"q1":362.95,"q2":383.45,"q3":392.88,"max":419.2,"minLabel":"fastqc (ABM006.A0101_S0_L003)","maxLabel":"fastqc (ABM006.A0101_S0_L002)","q1Label":"fastqc (ABM006.A0101_S0_L003)","q2Label":"fastqc (ABM006.A0101_S0_L001)","q3Label":"fastqc (ABM006.A0101_S0_L004)"},"mem":{"mean":3695329280,"min":3695329280,"q1":3695329280,"q2":3695329280,"q3":3695329280,"max":3695329280,"minLabel":"fastqc (ABM006.A0101_S0_L004)","maxLabel":"fastqc (ABM006.A0101_S0_L003)","q1Label":"fastqc (ABM006.A0101_S0_L004)","q2Label":"fastqc (ABM006.A0101_S0_L001)","q3Label":"fastqc (ABM006.A0101_S0_L002)"},"time":{"mean":43221.5,"min":41480,"q1":42245,"q2":42982.5,"q3":43959,"max":45441,"minLabel":"fastqc (ABM006.A0101_S0_L004)","maxLabel":"fastqc (ABM006.A0101_S0_L003)","q1Label":"fastqc (ABM006.A0101_S0_L004)","q2Label":"fastqc (ABM006.A0101_S0_L001)","q3Label":"fastqc (ABM006.A0101_S0_L002)"},"reads":null,"writes":{"mean":1164288,"min":737280,"q1":1096704,"q2":1275904,"q3":1343488,"max":1368064,"minLabel":"fastqc (ABM006.A0101_S0_L004)","maxLabel":"fastqc (ABM006.A0101_S0_L002)","q1Label":"fastqc (ABM006.A0101_S0_L004)","q2Label":"fastqc (ABM006.A0101_S0_L001)","q3Label":"fastqc (ABM006.A0101_S0_L003)"},"cpuUsage":{"mean":372.38,"min":303.4,"q1":362.95,"q2":383.45,"q3":392.88,"max":419.2,"minLabel":"fastqc (ABM006.A0101_S0_L003)","maxLabel":"fastqc (ABM006.A0101_S0_L002)","q1Label":"fastqc (ABM006.A0101_S0_L003)","q2Label":"fastqc (ABM006.A0101_S0_L001)","q3Label":"fastqc (ABM006.A0101_S0_L004)"},"memUsage":null,"timeUsage":null},"adapter_removal":{"cpu":{"mean":122.15,"min":117.3,"q1":119.85,"q2":122.4,"q3":124.7,"max":126.5,"minLabel":"adapter_removal (ABM006.A0101_S0_L002)","maxLabel":"adapter_removal (ABM006.A0101_S0_L003)","q1Label":"adapter_removal (ABM006.A0101_S0_L002)","q2Label":"adapter_removal (ABM006.A0101_S0_L004)","q3Label":"adapter_removal (ABM006.A0101_S0_L001)"},"mem":{"mean":39592308736,"min":39592308736,"q1":39592308736,"q2":39592308736,"q3":39592308736,"max":39592308736,"minLabel":"adapter_removal (ABM006.A0101_S0_L002)","maxLabel":"adapter_removal (ABM006.A0101_S0_L003)","q1Label":"adapter_removal (ABM006.A0101_S0_L002)","q2Label":"adapter_removal (ABM006.A0101_S0_L004)","q3Label":"adapter_removal (ABM006.A0101_S0_L001)"},"time":{"mean":140570,"min":138877,"q1":139076.5,"q2":140133,"q3":141626.5,"max":143137,"minLabel":"adapter_removal (ABM006.A0101_S0_L002)","maxLabel":"adapter_removal (ABM006.A0101_S0_L003)","q1Label":"adapter_removal (ABM006.A0101_S0_L002)","q2Label":"adapter_removal (ABM006.A0101_S0_L004)","q3Label":"adapter_removal (ABM006.A0101_S0_L001)"},"reads":null,"writes":{"mean":53248,"min":49152,"q1":49152,"q2":53248,"q3":57344,"max":57344,"minLabel":"adapter_removal (ABM006.A0101_S0_L002)","maxLabel":"adapter_removal (ABM006.A0101_S0_L003)","q1Label":"adapter_removal (ABM006.A0101_S0_L002)","q2Label":"adapter_removal (ABM006.A0101_S0_L004)","q3Label":"adapter_removal (ABM006.A0101_S0_L001)"},"cpuUsage":{"mean":122.15,"min":117.3,"q1":119.85,"q2":122.4,"q3":124.7,"max":126.5,"minLabel":"adapter_removal (ABM006.A0101_S0_L002)","maxLabel":"adapter_removal (ABM006.A0101_S0_L003)","q1Label":"adapter_removal (ABM006.A0101_S0_L002)","q2Label":"adapter_removal (ABM006.A0101_S0_L004)","q3Label":"adapter_removal (ABM006.A0101_S0_L001)"},"memUsage":null,"timeUsage":null},"makeBWAIndex":{"cpu":null,"mem":null,"time":{"mean":54,"min":54,"q1":54,"q2":54,"q3":54,"max":54,"minLabel":"makeBWAIndex (hg19_MT.fasta)","maxLabel":"makeBWAIndex (hg19_MT.fasta)","q1Label":"makeBWAIndex (hg19_MT.fasta)","q2Label":"makeBWAIndex (hg19_MT.fasta)","q3Label":"makeBWAIndex (hg19_MT.fasta)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"get_software_versions":{"cpu":{"mean":81.3,"min":81.3,"q1":81.3,"q2":81.3,"q3":81.3,"max":81.3,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"},"mem":{"mean":5037150208,"min":5037150208,"q1":5037150208,"q2":5037150208,"q3":5037150208,"max":5037150208,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"},"time":{"mean":5149,"min":5149,"q1":5149,"q2":5149,"q3":5149,"max":5149,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"},"reads":null,"writes":{"mean":32768,"min":32768,"q1":32768,"q2":32768,"q3":32768,"max":32768,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"},"cpuUsage":{"mean":81.3,"min":81.3,"q1":81.3,"q2":81.3,"q3":81.3,"max":81.3,"minLabel":"get_software_versions","maxLabel":"get_software_versions","q1Label":"get_software_versions","q2Label":"get_software_versions","q3Label":"get_software_versions"},"memUsage":null,"timeUsage":null},"makeSeqDict":{"cpu":{"mean":142.1,"min":142.1,"q1":142.1,"q2":142.1,"q3":142.1,"max":142.1,"minLabel":"makeSeqDict 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Nov-14 17:08:42.052 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Nov-14 17:08:42.186 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Nov-14 17:08:42.200 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye