search

nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
904 stars 705 forks source link

Command exit status: 127 Command error: .command.run: line 262: docker: command not found #714

Closed ghost closed 2 years ago

ghost commented 3 years ago

Check Documentation

Description of the bug

I am trying to run rnaseq pipeline with singularity on HPC and it fails stright after running. I am not sure why it tries to run docker if I specify the engine in the command as shown below:

Steps to reproduce

nextflow run nf-core/rnaseq --input /path/to/samplesheet.csv --genome GRCh38 -profile singularity -w /path/to/work

Log files

Below

System

Nextflow Installation

Container engine

Additional context

The log file is below:


Oct-12 13:17:10.115 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -profile test,docker
Oct-12 13:17:10.189 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 21.04.3
Oct-12 13:17:10.222 [main] INFO  nextflow.cli.CmdRun - Pulling nf-core/rnaseq ...
Oct-12 13:17:10.224 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/rnaseq/contents/nextflow.config
Oct-12 13:17:11.884 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/rnaseq/contents/main.nf
Oct-12 13:17:12.060 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/rnaseq
Oct-12 13:17:12.242 [main] DEBUG nextflow.scm.AssetManager - Pulling nf-core/rnaseq -- Using remote clone url: https://github.com/nf-core/rnaseq.git
Oct-12 13:17:17.159 [main] INFO  nextflow.cli.CmdRun -  downloaded from https://github.com/nf-core/rnaseq.git
Oct-12 13:17:17.193 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/rnaseq` [marvelous_monod] - revision: 964425e3fd [master]
Oct-12 13:17:17.204 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/simonova/.nextflow/assets/nf-core/rnaseq/nextflow.config
Oct-12 13:17:17.205 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/simonova/.nextflow/assets/nf-core/rnaseq/nextflow.config
Oct-12 13:17:17.211 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker`
Oct-12 13:17:17.621 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-12 13:17:17.622 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-12 13:17:17.626 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-12 13:17:18.656 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, uppmax, abims, nu_genomics, imperial_mb, oist, mpcdf, lugh, cambridge, podman, czbiohub_aws, jax, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, test_full, eddie, bi, bigpurple, docker, gis, eva, utd_ganymede, charliecloud, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac]
Oct-12 13:17:18.667 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/simonova/.nextflow/plugins
Oct-12 13:17:18.669 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-12 13:17:18.670 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty
Oct-12 13:17:18.673 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-12 13:17:18.673 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-12 13:17:18.716 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-12 13:17:18.729 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Oct-12 13:17:18.798 [main] DEBUG nextflow.Session - Session uuid: 65c07c22-374f-40a5-9361-cfe6c50eb6f2
Oct-12 13:17:18.799 [main] DEBUG nextflow.Session - Run name: marvelous_monod
Oct-12 13:17:18.799 [main] DEBUG nextflow.Session - Executor pool size: 72
Oct-12 13:17:18.823 [main] DEBUG nextflow.cli.CmdRun -
  Version: 21.04.3 build 5560
  Created: 21-07-2021 15:09 UTC (17:09 CEST)
  System: Linux 3.10.0-1160.6.1.el7.x86_64
  Runtime: Groovy 3.0.7 on Java HotSpot(TM) 64-Bit Server VM 13.0.1+9
  Encoding: UTF-8 (UTF-8)
  Process: 156558@login1.barbora.it4i.cz [10.32.2.1]
  CPUs: 72 - Mem: 187.4 GB (40.9 GB) - Swap: 4 GB (1.9 GB)
Oct-12 13:17:18.851 [main] DEBUG nextflow.Session - Work-dir: /home/simonova/work [nfs]
Oct-12 13:17:18.879 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-12 13:17:18.895 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-12 13:17:19.120 [main] DEBUG nextflow.Session - Session start invoked
Oct-12 13:17:19.124 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/simonova/results/pipeline_info/execution_trace_2021-10-12_13-17-18.txt
Oct-12 13:17:19.140 [main] DEBUG nextflow.Session - Using default localLib path: /home/simonova/.nextflow/assets/nf-core/rnaseq/lib
Oct-12 13:17:19.145 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/simonova/.nextflow/assets/nf-core/rnaseq/lib
Oct-12 13:17:19.145 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/simonova/.nextflow/assets/nf-core/rnaseq/lib/nfcore_external_java_deps.jar
Oct-12 13:17:20.196 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-12 13:17:20.466 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v3.4
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : marvelous_monod
  containerEngine           : docker
  launchDir                 : /home/simonova
  workDir                   : /home/simonova/work
  projectDir                : /home/simonova/.nextflow/assets/nf-core/rnaseq
  userName                  : simonova
  profile                   : test,docker
  configFiles               : /home/simonova/.nextflow/assets/nf-core/rnaseq/nextflow.config

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv

UMI options
  umitools_bc_pattern       : NNNN

Read filtering options
  bbsplit_fasta_list        : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/bbsplit_fasta_list.txt
  skip_bbsplit              : false

Reference genome options
  fasta                     : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa
  gtf                       : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz
  gff                       : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz
  transcript_fasta          : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta
  additional_fasta          : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz
  star_index                : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/star.tar.gz
  hisat2_index              : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz
  rsem_index                : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz
  salmon_index              : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz

Alignment options
  pseudo_aligner            : salmon

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 6h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/rnaseq for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.1400710

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
------------------------------------------------------
Oct-12 13:17:22.656 [main] WARN  nextflow.Nextflow - =============================================================================
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
===================================================================================
Oct-12 13:17:22.657 [main] WARN  nextflow.Nextflow - =============================================================================
  When using '--additional_fasta <FASTA_FILE>' the aligner index will not
  be re-built with the transgenes incorporated by default since you have
  already provided an index via '--star_index <INDEX>'.

  Set '--additional_fasta <FASTA_FILE> --star_index false --save_reference' to
  re-build the index with transgenes included and the index will be saved in
  'results/genome/index/star/' for re-use with '--star_index'.

  Ignore this warning if you know that the index already contains transgenes.

  Please see:
  https://github.com/nf-core/rnaseq/issues/556
===================================================================================
Oct-12 13:17:48.007 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: DUPRADAR, GUNZIP_TRANSCRIPT_FASTA, MULTIQC_TSV_FAIL_MAPPED, RSEM_PREPAREREFERENCE, CAT_ADDITIONAL_FASTA, SALMON_SE_GENE_LENGTH_SCALED, DESEQ2_QC_SALMON, RSEQC_READDISTRIBUTION, DESEQ2_QC, GFFREAD, RSEQC_JUNCTIONSATURATION, RSEQC_READDUPLICATION, PICARD_MARKDUPLICATES, RSEM_MERGE_COUNTS, SALMON_SE_GENE, CAT_FASTQ, GUNZIP, SAMTOOLS_STATS, UNTAR, SALMON_SUMMARIZEDEXPERIMENT, GUNZIP_GFF, HISAT2_BUILD, RSEQC_INNERDISTANCE, TRIMGALORE, BEDTOOLS_GENOMECOV, GTF_GENE_FILTER, SALMON_TX2GENE, RSEQC_BAMSTAT, SORTMERNA, QUALIMAP_RNASEQ, RSEQC_INFEREXPERIMENT, STAR_ALIGN, MULTIQC_TSV_STRAND_CHECK, SAMTOOLS_INDEX, PRESEQ_LCEXTRAP, FASTQC, RSEQC_JUNCTIONANNOTATION, UCSC_BEDCLIP, SALMON_TXIMPORT, UCSC_BEDGRAPHTOBIGWIG, MULTIQC, GTF2BED, SAMTOOLS_SORT, SUBREAD_FEATURECOUNTS, GET_CHROM_SIZES, GUNZIP_GTF, SALMON_INDEX, GUNZIP_GENE_BED, UNTAR_STAR_INDEX, UMITOOLS_EXTRACT, UNTAR_SALMON_INDEX, HISAT2_ALIGN, UNTAR_HISAT2_INDEX, UNTAR_BBSPLIT_INDEX, BBMAP_BBSPLIT, SAMTOOLS_FLAGSTAT, MULTIQC_TSV_FROM_LIST, SAMPLESHEET_CHECK, DESEQ2_QC_RSEM, GUNZIP_FASTA, UMITOOLS_DEDUP, SALMON_SE_TRANSCRIPT, HISAT2_EXTRACTSPLICESITES, UNTAR_RSEM_INDEX, STRINGTIE, SALMON_SE_GENE_SCALED, RSEM_PREPAREREFERENCE_TRANSCRIPTS, SALMON_MERGE_COUNTS, SAMTOOLS_IDXSTATS, STAR_GENOMEGENERATE, CUSTOM_DUMPSOFTWAREVERSIONS, SALMON_QUANT, GUNZIP_ADDITIONAL_FASTA, MULTIQC_CUSTOM_BIOTYPE, DESEQ2_QC_STAR_SALMON, RSEM_CALCULATEEXPRESSION
Oct-12 13:17:48.201 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF
Oct-12 13:17:48.227 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.227 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.235 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Oct-12 13:17:48.244 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=72; memory=187.4 GB; capacity=72; pollInterval=100ms; dumpInterval=5m
Oct-12 13:17:48.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA
Oct-12 13:17:48.359 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.359 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.379 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.379 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.388 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED
Oct-12 13:17:48.388 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.388 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.397 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.397 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT
Oct-12 13:17:48.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.464 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.474 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_STAR_INDEX
Oct-12 13:17:48.474 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.474 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.482 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX
Oct-12 13:17:48.482 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.482 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.493 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.493 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.508 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Oct-12 13:17:48.509 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.509 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.521 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Oct-12 13:17:48.521 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.521 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.531 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Oct-12 13:17:48.531 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.531 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.540 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT
Oct-12 13:17:48.541 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.541 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.553 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches label `process_high` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Oct-12 13:17:48.554 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.554 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.562 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
Oct-12 13:17:48.562 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.562 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.567 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
Oct-12 13:17:48.568 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.568 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Oct-12 13:17:48.586 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.592 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Oct-12 13:17:48.592 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.592 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.599 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Oct-12 13:17:48.600 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.601 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Oct-12 13:17:48.609 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.609 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.614 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
Oct-12 13:17:48.615 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.615 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.620 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
Oct-12 13:17:48.620 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.620 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.625 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE
Oct-12 13:17:48.625 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.625 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.628 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Oct-12 13:17:48.628 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.628 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.630 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED
Oct-12 13:17:48.631 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.631 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.633 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT
Oct-12 13:17:48.633 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.633 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.638 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
Oct-12 13:17:48.638 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.638 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.650 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.650 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.654 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Oct-12 13:17:48.654 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches label `error_ignore` for process with name NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Oct-12 13:17:48.654 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.654 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.661 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
Oct-12 13:17:48.661 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.662 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.667 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
Oct-12 13:17:48.667 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.667 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.675 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Oct-12 13:17:48.676 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.676 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.680 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Oct-12 13:17:48.680 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.681 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.685 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Oct-12 13:17:48.685 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.685 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:STRINGTIE
Oct-12 13:17:48.692 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.692 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.708 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS
Oct-12 13:17:48.708 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.708 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.713 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.713 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.718 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Oct-12 13:17:48.718 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.718 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.724 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP
Oct-12 13:17:48.724 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.724 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.729 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Oct-12 13:17:48.730 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.730 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.735 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP
Oct-12 13:17:48.736 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.736 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Oct-12 13:17:48.741 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.741 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.749 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ
Oct-12 13:17:48.749 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.749 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.754 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches label `process_long` for process with name NFCORE_RNASEQ:RNASEQ:DUPRADAR
Oct-12 13:17:48.755 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.755 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.761 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT
Oct-12 13:17:48.761 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.761 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.767 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE
Oct-12 13:17:48.768 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.768 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.775 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT
Oct-12 13:17:48.775 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.775 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.782 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION
Oct-12 13:17:48.783 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.783 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.791 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION
Oct-12 13:17:48.791 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.791 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.796 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
Oct-12 13:17:48.797 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.797 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION
Oct-12 13:17:48.803 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.803 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.812 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.812 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.819 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT
Oct-12 13:17:48.819 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.819 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.825 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE
Oct-12 13:17:48.825 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.825 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.830 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT
Oct-12 13:17:48.831 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.831 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE
Oct-12 13:17:48.837 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.837 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Oct-12 13:17:48.842 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.842 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.846 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED
Oct-12 13:17:48.846 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.846 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.849 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT
Oct-12 13:17:48.849 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.849 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.854 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON
Oct-12 13:17:48.854 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.854 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.880 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches label `process_low` for process with name NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Oct-12 13:17:48.880 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Oct-12 13:17:48.880 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.880 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.924 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches label `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MULTIQC
Oct-12 13:17:48.924 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Oct-12 13:17:48.924 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Oct-12 13:17:48.939 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.940 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Oct-12 13:17:48.941 [main] DEBUG nextflow.Session - Ignite dataflow network (139)
Oct-12 13:17:48.942 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_STAR_INDEX
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX
Oct-12 13:17:48.944 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Oct-12 13:17:48.945 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Oct-12 13:17:48.945 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Oct-12 13:17:48.945 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Oct-12 13:17:48.946 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT
Oct-12 13:17:48.948 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Oct-12 13:17:48.950 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
Oct-12 13:17:48.951 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
Oct-12 13:17:48.951 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Oct-12 13:17:48.952 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED
Oct-12 13:17:48.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT
Oct-12 13:17:48.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
Oct-12 13:17:48.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED
Oct-12 13:17:48.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Oct-12 13:17:48.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
Oct-12 13:17:48.954 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
Oct-12 13:17:48.954 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:STRINGTIE
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Oct-12 13:17:48.955 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DUPRADAR
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Oct-12 13:17:48.956 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC
Oct-12 13:17:48.956 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Oct-12 13:17:48.956 [main] DEBUG nextflow.Session - Session await
Oct-12 13:17:49.109 [Actor Thread 3] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.013 s; total time: 0.014 s
Oct-12 13:17:49.116 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/9f4e53edd30094e47fd846780710b8ea.collect-file
Oct-12 13:17:49.124 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-16959062972457650669
Oct-12 13:17:49.174 [Actor Thread 24] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=216; maxQueueSize=648; keepAlive=1m
Oct-12 13:17:49.182 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.4/samplesheet_test.csv to work dir: /home/simonova/work/stage/75/18f0e9d50753f339dc1e7a60eb2c16/samplesheet_test.csv
Oct-12 13:17:49.286 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz to work dir: /home/simonova/work/stage/6d/5f5c5afadeaf16c02fb0d9e15135b4/salmon.tar.gz
Oct-12 13:17:49.349 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz to work dir: /home/simonova/work/stage/88/b807534a397f4c7ce6181f9e6da70a/gfp.fa.gz
Oct-12 13:17:49.444 [FileTransfer-thread-4] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz to work dir: /home/simonova/work/stage/ab/dfb19b3416f316bd57968917c675b4/genes.gtf.gz
Oct-12 13:17:49.534 [FileTransfer-thread-5] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/nf-core/test-datasets/raw/rnaseq/reference/star.tar.gz to work dir: /home/simonova/work/stage/46/907cd2d9b6ce3c8b9f5184ff9142f6/star.tar.gz
Oct-12 13:17:49.579 [Actor Thread 24] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/simonova/.nextflow/assets/nf-core/rnaseq/bin/check_samplesheet.py
Oct-12 13:17:49.674 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-12 13:17:49.679 [Task submitter] INFO  nextflow.Session - [d4/3d8539] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
Oct-12 13:17:49.697 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-12 13:17:49.698 [Task submitter] INFO  nextflow.Session - [59/c2091e] Submitted process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)
Oct-12 13:17:49.707 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-12 13:17:49.707 [Task submitter] INFO  nextflow.Session - [ea/4e652e] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
Oct-12 13:17:49.717 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Oct-12 13:17:49.718 [Task submitter] INFO  nextflow.Session - [ec/bed300] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)
Oct-12 13:17:49.737 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz); status: COMPLETED; exit: 127; error: -; workDir: /home/simonova/work/d4/3d8539dd75980d02eef766997e0f41]
Oct-12 13:17:49.943 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (127)

Command executed:

  gunzip \
      -f \
       \
      gfp.fa.gz

  cat <<-END_VERSIONS > versions.yml
  GUNZIP_ADDITIONAL_FASTA:
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 262: docker: command not found

Work dir:
  /home/simonova/work/d4/3d8539dd75980d02eef766997e0f41

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Oct-12 13:17:49.983 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Oct-12 13:17:49.992 [main] DEBUG nextflow.Session - Session await > all process finished
Oct-12 13:17:50.038 [Actor Thread 8] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Oct-12 13:17:50.058 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv); status: COMPLETED; exit: 127; error: -; workDir: /home/simonova/work/59/c2091ecbc2d36aed358e1bf5525fce]
Oct-12 13:17:50.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz); status: COMPLETED; exit: 127; error: -; workDir: /home/simonova/work/ea/4e652e281a1d790fad9ad8d24a19f5]
Oct-12 13:17:50.069 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz); status: COMPLETED; exit: 127; error: -; workDir: /home/simonova/work/ec/bed300ce72956c1edfa0695601a84e]
Oct-12 13:17:50.071 [main] DEBUG nextflow.Session - Session await > all barriers passed
Oct-12 13:17:50.107 [main] INFO  nextflow.Nextflow - -[nf-core/rnaseq] Pipeline completed with errors-
Oct-12 13:17:50.143 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=4; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=23ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=2; peakMemory=6 GB; ]
Oct-12 13:17:50.144 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Oct-12 13:17:50.145 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Oct-12 13:17:50.177 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"GUNZIP_ADDITIONAL_FASTA","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":5,"min":5,"q1":5,"q2":5,"q3":5,"max":5,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)"},"writes":null},{"cpuUsage":null,"process":"SAMPLESHEET_CHECK","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":3,"min":3,"q1":3,"q2":3,"q3":3,"max":3,"minLabel":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","maxLabel":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","q1Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","q2Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)","q3Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_test.csv)"},"writes":null},{"cpuUsage":null,"process":"UNTAR_SALMON_INDEX","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":3,"min":3,"q1":3,"q2":3,"q3":3,"max":3,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)"},"writes":null},{"cpuUsage":null,"process":"GUNZIP_GTF","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":2,"min":2,"q1":2,"q2":2,"q3":2,"max":2,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz)"},"writes":null}]
Oct-12 13:17:50.737 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Oct-12 13:17:50.865 [main] WARN  nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Oct-12 13:17:51.000 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Oct-12 13:17:51.034 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
drpatelh commented 2 years ago

Hi @simonovae ! Apologies for the late response. Did you manage to figure out what was going on here?

Right at the top of the log it looks like you are running Docker?

Oct-12 13:17:10.115 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -profile test,docker

Please come and find us on the #rnaseq channel on the nf-core Slack Workspace. It will be much quicker to resolve these sorts of issues there. Will close this for now.