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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
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The following error occurs during operation, and I don't know how to solve it #1055

Closed WangDong-ls closed 1 year ago

WangDong-ls commented 1 year ago

Description of the bug

Command error:
  Singularity 1.0b1 (commit: b0d3406e311f4ac3aa6f4d0187f32926b3808fef)
  Running under Python 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]
  pygame 1.9.6
  Hello from the pygame community. https://www.pygame.org/contribute.html
  Traceback (most recent call last):
    File "/usr/games/singularity", line 11, in <module>
      load_entry_point('Endgame-Singularity==1.0b1', 'gui_scripts', 'singularity')()
    File "/usr/lib/python3/dist-packages/singularity/__init__.py", line 106, in main
      g.logfile = dirs.get_writable_file_in_dirs("error.log", "log")
    File "/usr/lib/python3/dist-packages/singularity/code/dirs.py", line 220, in get_writable_file_in_dirs
      write_dir = write_dirs[dir_name]
  KeyError: 'log'

Work dir:
  /mnt/e/nextflow/work/f4/b1e5f04d8d3637e378a709567dab99

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Command used and terminal output

No response

Relevant files

Jul-02 23:22:53.905 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow --input /mnt/e/nextflow/rnaseqtest/samplesheet.csv --fasta /mnt/e/nextflow/rnaseqtest/PN40024v4.fa --gtf /mnt/e/nextflow/rnaseqtest/PN40024v4.gtf --aligner hisat2 --skip_qualimap -profile singularity --outdir rnaseqtest/
Jul-02 23:22:53.967 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.1
Jul-02 23:22:53.984 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/xianhang/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2
Jul-02 23:22:53.995 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-02 23:22:53.997 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-02 23:22:54.000 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jul-02 23:22:54.014 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jul-02 23:22:54.798 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/nextflow.config
Jul-02 23:22:54.799 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/nextflow.config
Jul-02 23:22:54.808 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Jul-02 23:22:55.679 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, eddie, medair, bi, bigpurple, sbc_sharc, test_full_gcp, adcra, cedars, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, test_full_aws, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, genotoul, abims, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, cambridge, podman, cheaha, xanadu, test, computerome, seg_globe, sanger, dkfz, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, psmn, test_full_azure, eva, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac]
Jul-02 23:22:55.733 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jul-02 23:22:55.752 [main] INFO  nextflow.cli.CmdRun - Launching `/mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/main.nf` [stoic_lamarck] DSL2 - revision: f421ddc35d
Jul-02 23:22:55.753 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-02 23:22:55.753 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-02 23:22:55.761 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/xianhang/.nextflow/secrets/store.json
Jul-02 23:22:55.763 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6e00837f] - activable => nextflow.secret.LocalSecretsProvider@6e00837f
Jul-02 23:22:55.807 [main] DEBUG nextflow.Session - Session UUID: e41a90f3-2978-4139-89c0-445488a03d5f
Jul-02 23:22:55.808 [main] DEBUG nextflow.Session - Run name: stoic_lamarck
Jul-02 23:22:55.808 [main] DEBUG nextflow.Session - Executor pool size: 16
Jul-02 23:22:55.817 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=48; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jul-02 23:22:55.843 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.1 build 5866
  Created: 15-04-2023 06:51 UTC (14:51 CDT)
  System: Linux 5.10.16.3-microsoft-standard-WSL2
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.15-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 102@LAPTOP-A1TBJN4F [127.0.1.1]
  CPUs: 16 - Mem: 24.9 GB (24.1 GB) - Swap: 7 GB (7 GB)
Jul-02 23:22:55.873 [main] DEBUG nextflow.Session - Work-dir: /mnt/e/nextflow/work [v9fs]
Jul-02 23:22:55.906 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-02 23:22:55.914 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-02 23:22:55.995 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-02 23:22:56.010 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Jul-02 23:22:56.125 [main] DEBUG nextflow.Session - Session start
Jul-02 23:22:56.128 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/e/nextflow/rnaseqtest/pipeline_info/execution_trace_2023-07-02_23-22-55.txt
Jul-02 23:22:56.141 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/lib
Jul-02 23:22:56.155 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/lib
Jul-02 23:22:56.173 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/lib/nfcore_external_java_deps.jar
Jul-02 23:22:56.886 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-02 23:22:56.959 [main] INFO  nextflow.Nextflow - 

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v3.11.1
------------------------------------------------------
Core Nextflow options
  runName           : stoic_lamarck
  containerEngine   : singularity
  launchDir         : /mnt/e/nextflow
  workDir           : /mnt/e/nextflow/work
  projectDir        : /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow
  userName          : xianhang
  profile           : singularity
  configFiles       : /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/nextflow.config

Input/output options
  input             : /mnt/e/nextflow/rnaseqtest/samplesheet.csv
  outdir            : rnaseqtest/

Reference genome options
  fasta             : /mnt/e/nextflow/rnaseqtest/PN40024v4.fa
  gtf               : /mnt/e/nextflow/rnaseqtest/PN40024v4.gtf

Alignment options
  aligner           : hisat2

Process skipping options
  skip_qualimap     : true

Institutional config options
  custom_config_base: /mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/../configs/

Max job request options
  max_cpus          : 4
  max_memory        : 20.GB

!! 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
------------------------------------------------------
Jul-02 23:23:07.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED
Jul-02 23:23:07.478 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF2BED` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED
Jul-02 23:23:07.494 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.495 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.499 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-02 23:23:07.504 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=16; memory=24.9 GB; capacity=16; pollInterval=100ms; dumpInterval=5m
Jul-02 23:23:07.579 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF_GENE_FILTER` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER
Jul-02 23:23:07.580 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.580 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
Jul-02 23:23:07.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
Jul-02 23:23:07.586 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.586 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.604 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Jul-02 23:23:07.605 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Jul-02 23:23:07.606 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.606 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.618 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES
Jul-02 23:23:07.618 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HISAT2_EXTRACTSPLICESITES` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES
Jul-02 23:23:07.619 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.619 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.624 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high,process_high_memory` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_BUILD
Jul-02 23:23:07.624 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high_memory` matches labels `process_high,process_high_memory` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_BUILD
Jul-02 23:23:07.624 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_BUILD
Jul-02 23:23:07.625 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.626 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.637 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Jul-02 23:23:07.637 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLESHEET_CHECK` matches process NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Jul-02 23:23:07.639 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.639 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Jul-02 23:23:07.670 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Jul-02 23:23:07.672 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.672 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
Jul-02 23:23:07.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SALMON_INDEX` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
Jul-02 23:23:07.693 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.693 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.699 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE
Jul-02 23:23:07.699 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_SUBSAMPLE` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE
Jul-02 23:23:07.700 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.700 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.706 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
Jul-02 23:23:07.707 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
Jul-02 23:23:07.708 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.708 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.725 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Jul-02 23:23:07.726 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Jul-02 23:23:07.726 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.727 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.734 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Jul-02 23:23:07.735 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Jul-02 23:23:07.736 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.737 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.773 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN
Jul-02 23:23:07.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN
Jul-02 23:23:07.775 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.776 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Jul-02 23:23:07.787 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Jul-02 23:23:07.788 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.789 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Jul-02 23:23:07.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Jul-02 23:23:07.797 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.797 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.808 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jul-02 23:23:07.809 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jul-02 23:23:07.810 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.810 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jul-02 23:23:07.817 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jul-02 23:23:07.818 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.818 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.825 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jul-02 23:23:07.826 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jul-02 23:23:07.827 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.827 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.834 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES
Jul-02 23:23:07.835 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES
Jul-02 23:23:07.836 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.836 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX
Jul-02 23:23:07.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX
Jul-02 23:23:07.842 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.843 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.849 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jul-02 23:23:07.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jul-02 23:23:07.851 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.851 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.855 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jul-02 23:23:07.856 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jul-02 23:23:07.857 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.857 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.862 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jul-02 23:23:07.862 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jul-02 23:23:07.863 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.863 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.869 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Jul-02 23:23:07.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:STRINGTIE_STRINGTIE` matches process NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Jul-02 23:23:07.871 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.871 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS
Jul-02 23:23:07.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SUBREAD_FEATURECOUNTS` matches process NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS
Jul-02 23:23:07.883 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.883 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.888 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_CUSTOM_BIOTYPE` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE
Jul-02 23:23:07.889 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.889 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.895 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Jul-02 23:23:07.896 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV` matches process NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Jul-02 23:23:07.897 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.897 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP
Jul-02 23:23:07.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP
Jul-02 23:23:07.904 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.904 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.909 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Jul-02 23:23:07.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Jul-02 23:23:07.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.915 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP
Jul-02 23:23:07.916 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP
Jul-02 23:23:07.917 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.917 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.921 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Jul-02 23:23:07.922 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Jul-02 23:23:07.923 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.923 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.931 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_RNASEQ:RNASEQ:DUPRADAR
Jul-02 23:23:07.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUPRADAR` matches process NFCORE_RNASEQ:RNASEQ:DUPRADAR
Jul-02 23:23:07.933 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.933 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.939 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT
Jul-02 23:23:07.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_BAMSTAT` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT
Jul-02 23:23:07.940 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.941 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.945 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE
Jul-02 23:23:07.946 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_INNERDISTANCE` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE
Jul-02 23:23:07.947 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.947 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.951 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT
Jul-02 23:23:07.952 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT
Jul-02 23:23:07.952 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.952 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.958 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
Jul-02 23:23:07.958 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
Jul-02 23:23:07.959 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.959 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION
Jul-02 23:23:07.964 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION
Jul-02 23:23:07.965 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.965 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.969 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION
Jul-02 23:23:07.970 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_READDISTRIBUTION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION
Jul-02 23:23:07.971 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.971 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:07.976 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION
Jul-02 23:23:07.976 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_READDUPLICATION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION
Jul-02 23:23:07.977 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:07.977 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:08.015 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-02 23:23:08.015 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-02 23:23:08.016 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:08.016 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:08.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MULTIQC
Jul-02 23:23:08.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC
Jul-02 23:23:08.085 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-02 23:23:08.085 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-02 23:23:08.092 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: DUPRADAR, NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC, RSEM_PREPAREREFERENCE, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP, NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, CAT_ADDITIONAL_FASTA, DESEQ2_QC_SALMON, NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE, RSEQC_READDISTRIBUTION, NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS, NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, GFFREAD, RSEQC_READDUPLICATION, RSEQC_JUNCTIONSATURATION, NFCORE_RNASEQ:RNASEQ:CAT_FASTQ, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION, CAT_FASTQ, GUNZIP, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES, SAMTOOLS_STATS, GUNZIP_GFF, HISAT2_BUILD, TRIMGALORE, BEDTOOLS_GENOMECOV, SALMON_TX2GENE, SORTMERNA, NFCORE_RNASEQ:RNASEQ:DUPRADAR, UMITOOLS_PREPAREFORRSEM, NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_BUILD, NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT, NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS, SAMTOOLS_INDEX, NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV, PRESEQ_LCEXTRAP, FASTQC, UCSC_BEDCLIP, UCSC_BEDGRAPHTOBIGWIG, MULTIQC, GTF2BED, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION, GUNZIP_GTF, SALMON_INDEX, UMITOOLS_EXTRACT, UNTAR_HISAT2_INDEX, NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK, UNTAR_BBSPLIT_INDEX, NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER, SAMTOOLS_FLAGSTAT, SAMPLESHEET_CHECK, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION, DESEQ2_QC_RSEM, GUNZIP_FASTA, RSEM_PREPAREREFERENCE_GENOME, UNTAR_RSEM_INDEX, SALMON_SE_GENE_SCALED, STAR_GENOMEGENERATE_IGENOMES, SALMON_QUANT, MULTIQC_CUSTOM_BIOTYPE, RSEM_CALCULATEEXPRESSION, DESEQ2_QC_STAR_SALMON, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG, GUNZIP_TRANSCRIPT_FASTA, MAKE_TRANSCRIPTS_FASTA, FASTQC_TRIM, SALMON_SE_GENE_LENGTH_SCALED, FQ_SUBSAMPLE, FASTP, DESEQ2_QC, NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE, PICARD_MARKDUPLICATES, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG, RSEM_MERGE_COUNTS, SALMON_SE_GENE, NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX, UNTAR, SALMON_SUMMARIZEDEXPERIMENT, FASTQC_RAW, NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP, RSEQC_INNERDISTANCE, NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX, GTF_GENE_FILTER, RSEQC_BAMSTAT, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION, QUALIMAP_RNASEQ, RSEQC_INFEREXPERIMENT, NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE, NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES, STAR_ALIGN, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE, RSEQC_JUNCTIONANNOTATION, NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, SALMON_TXIMPORT, CUSTOM_GETCHROMSIZES, STAR_ALIGN_IGENOMES, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT, SAMTOOLS_SORT, SUBREAD_FEATURECOUNTS, NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, GUNZIP_GENE_BED, UNTAR_STAR_INDEX, UNTAR_SALMON_INDEX, HISAT2_ALIGN, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES, NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN, BBMAP_BBSPLIT, RSEQC_TIN, UMITOOLS_PREPAREFORSALMON, UMITOOLS_DEDUP, STRINGTIE_STRINGTIE, HISAT2_EXTRACTSPLICESITES, SALMON_SE_TRANSCRIPT, NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA, NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT, NFCORE_RNASEQ:RNASEQ:MULTIQC, SAMTOOLS_IDXSTATS, STAR_GENOMEGENERATE, CUSTOM_DUMPSOFTWAREVERSIONS, PREPROCESS_TRANSCRIPTS_FASTA_GENCODE, GUNZIP_ADDITIONAL_FASTA
Jul-02 23:23:08.097 [main] DEBUG nextflow.Session - Igniting dataflow network (131)
Jul-02 23:23:08.113 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED
Jul-02 23:23:08.115 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER
Jul-02 23:23:08.115 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
Jul-02 23:23:08.115 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Jul-02 23:23:08.117 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES
Jul-02 23:23:08.118 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_BUILD
Jul-02 23:23:08.118 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Jul-02 23:23:08.119 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Jul-02 23:23:08.119 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
Jul-02 23:23:08.119 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE
Jul-02 23:23:08.119 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
Jul-02 23:23:08.120 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Jul-02 23:23:08.121 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Jul-02 23:23:08.122 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN
Jul-02 23:23:08.122 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Jul-02 23:23:08.123 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Jul-02 23:23:08.123 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jul-02 23:23:08.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jul-02 23:23:08.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jul-02 23:23:08.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES
Jul-02 23:23:08.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX
Jul-02 23:23:08.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Jul-02 23:23:08.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Jul-02 23:23:08.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Jul-02 23:23:08.126 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Jul-02 23:23:08.126 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS
Jul-02 23:23:08.126 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE
Jul-02 23:23:08.127 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Jul-02 23:23:08.127 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP
Jul-02 23:23:08.127 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Jul-02 23:23:08.127 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP
Jul-02 23:23:08.129 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Jul-02 23:23:08.129 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DUPRADAR
Jul-02 23:23:08.129 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT
Jul-02 23:23:08.129 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE
Jul-02 23:23:08.129 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT
Jul-02 23:23:08.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION
Jul-02 23:23:08.130 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION
Jul-02 23:23:08.131 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION
Jul-02 23:23:08.131 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION
Jul-02 23:23:08.132 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Jul-02 23:23:08.132 [Actor Thread 6] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-02 23:23:08.133 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC
Jul-02 23:23:08.134 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jul-02 23:23:08.134 [main] DEBUG nextflow.Session - Session await
Jul-02 23:23:08.226 [Actor Thread 1] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/perl:5.26.2; path=/mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/../singularity-images/depot.galaxyproject.org-singularity-perl-5.26.2.img
Jul-02 23:23:08.225 [Actor Thread 18] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1; path=/mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/../singularity-images/depot.galaxyproject.org-singularity-samtools-1.16.1--h6899075_1.img
Jul-02 23:23:08.225 [Actor Thread 9] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.9--1; path=/mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/../singularity-images/depot.galaxyproject.org-singularity-python-3.9--1.img
Jul-02 23:23:08.225 [Actor Thread 6] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3; path=/mnt/e/nextflow/nf-core-rnaseq-3.11.1/workflow/../singularity-images/depot.galaxyproject.org-singularity-hisat2-2.2.1--h1b792b2_3.img
Jul-02 23:23:08.307 [Actor Thread 19] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.004 s; external sort time: 0.009 s; total time: 0.013 s
Jul-02 23:23:08.307 [Actor Thread 13] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.004 s; external sort time: 0.009 s; total time: 0.013 s
Jul-02 23:23:08.323 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/e/nextflow/work/collect-file/e98095d31f0ec80a776aa8010a080f0f
Jul-02 23:23:08.323 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/e/nextflow/work/collect-file/fab0c9753b4adade05597255a8ea3297
Jul-02 23:23:08.327 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-564124403292568449
Jul-02 23:23:08.327 [Actor Thread 19] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-9560648664428425437
Jul-02 23:23:08.342 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-02 23:23:08.345 [Task submitter] INFO  nextflow.Session - [f4/b1e5f0] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)
Jul-02 23:23:08.355 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-02 23:23:08.355 [Task submitter] INFO  nextflow.Session - [3a/04d3aa] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)
Jul-02 23:23:08.364 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-02 23:23:08.365 [Task submitter] INFO  nextflow.Session - [09/6768fe] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)
Jul-02 23:23:08.928 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa); status: COMPLETED; exit: 1; error: -; workDir: /mnt/e/nextflow/work/f4/b1e5f04d8d3637e378a709567dab99]
Jul-02 23:23:08.930 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa); work-dir=/mnt/e/nextflow/work/f4/b1e5f04d8d3637e378a709567dab99
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)` terminated with an error exit status (1)
Jul-02 23:23:08.935 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-02 23:23:08.936 [Task submitter] INFO  nextflow.Session - [10/1523a4] Submitted process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)
Jul-02 23:23:08.941 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)` terminated with an error exit status (1)

Command executed:

  samtools faidx PN40024v4.fa
  cut -f 1,2 PN40024v4.fa.fai > PN40024v4.fa.sizes

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES":
      getchromsizes: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  Singularity 1.0b1 (commit: b0d3406e311f4ac3aa6f4d0187f32926b3808fef)
  Running under Python 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]
  pygame 1.9.6
  Hello from the pygame community. https://www.pygame.org/contribute.html

Command error:
  Singularity 1.0b1 (commit: b0d3406e311f4ac3aa6f4d0187f32926b3808fef)
  Running under Python 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]
  pygame 1.9.6
  Hello from the pygame community. https://www.pygame.org/contribute.html
  Traceback (most recent call last):
    File "/usr/games/singularity", line 11, in <module>
      load_entry_point('Endgame-Singularity==1.0b1', 'gui_scripts', 'singularity')()
    File "/usr/lib/python3/dist-packages/singularity/__init__.py", line 106, in main
      g.logfile = dirs.get_writable_file_in_dirs("error.log", "log")
    File "/usr/lib/python3/dist-packages/singularity/code/dirs.py", line 220, in get_writable_file_in_dirs
      write_dir = write_dirs[dir_name]
  KeyError: 'log'

Work dir:
  /mnt/e/nextflow/work/f4/b1e5f04d8d3637e378a709567dab99

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jul-02 23:23:08.952 [Actor Thread 1] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-02 23:23:08.961 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Jul-02 23:23:08.965 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-02 23:23:08.981 [Actor Thread 23] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-02 23:23:08.981 [Actor Thread 13] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-02 23:23:08.984 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa); status: COMPLETED; exit: 1; error: -; workDir: /mnt/e/nextflow/work/3a/04d3aa049452eb23e15eb65100e27f]
Jul-02 23:23:08.984 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa); work-dir=/mnt/e/nextflow/work/3a/04d3aa049452eb23e15eb65100e27f
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)` terminated with an error exit status (1)
Jul-02 23:23:08.990 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf); status: COMPLETED; exit: 1; error: -; workDir: /mnt/e/nextflow/work/09/6768fef48948ec7cc60e7319e94233]
Jul-02 23:23:08.990 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf); work-dir=/mnt/e/nextflow/work/09/6768fef48948ec7cc60e7319e94233
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)` terminated with an error exit status (1)
Jul-02 23:23:09.267 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv); status: COMPLETED; exit: 1; error: -; workDir: /mnt/e/nextflow/work/10/1523a42c1a1b1b9068fa44d8dc040c]
Jul-02 23:23:09.268 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv); work-dir=/mnt/e/nextflow/work/10/1523a42c1a1b1b9068fa44d8dc040c
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)` terminated with an error exit status (1)
Jul-02 23:23:09.271 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-02 23:23:09.673 [Actor Thread 11] WARN  nextflow.Nextflow - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Biotype attribute 'gene_biotype' not found in the last column of the GTF file!

  Biotype QC will be skipped to circumvent the issue below:
  https://github.com/nf-core/rnaseq/issues/460

  Amend '--featurecounts_group_type' to change this behaviour.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Jul-02 23:23:09.676 [main] INFO  nextflow.Nextflow - -[nf-core/rnaseq] Pipeline completed with errors-
Jul-02 23:23:09.679 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=4; ignoredCount=0; cachedCount=0; pendingCount=1; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=2.4s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=4; peakMemory=24 GB; ]
Jul-02 23:23:09.679 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-02 23:23:09.681 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-02 23:23:09.698 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":null,"process":"CUSTOM_GETCHROMSIZES","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":506,"min":506,"q1":506,"q2":506,"q3":506,"max":506,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (PN40024v4.fa)"},"writes":null},{"cpuUsage":null,"process":"GTF_GENE_FILTER","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":560,"min":560,"q1":560,"q2":560,"q3":560,"max":560,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (PN40024v4.fa)"},"writes":null},{"cpuUsage":null,"process":"GTF2BED","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":565,"min":565,"q1":565,"q2":565,"q3":565,"max":565,"minLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)","maxLabel":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)","q1Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)","q2Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)","q3Label":"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED (PN40024v4.gtf)"},"writes":null},{"cpuUsage":null,"process":"SAMPLESHEET_CHECK","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":null,"cpu":null,"time":{"mean":251,"min":251,"q1":251,"q2":251,"q3":251,"max":251,"minLabel":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","maxLabel":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q1Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q2Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q3Label":"NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)"},"writes":null}]
Jul-02 23:23:10.090 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-02 23:23:10.181 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-02 23:23:10.202 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jul-02 23:23:10.205 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

No response

MatthiasZepper commented 1 year ago

Well, the problem is that you have another application (a game?) installed that is also called Singularity. So when Nextflow tries to use the container system Singularity (Apptainer), it instead launches the other application.

You need to make sure, that Singularity does not point to the other application when you execute Nextflow. You can check with which singularity on the terminal and ideally should install your applications within virtual environments. Then you can have a gaming environment where Singularity points to the game and a Nextflow environment, where it points to the container executor. 

Running under Python 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]
pygame 1.9.6
Hello from the pygame community. https://www.pygame.org/contribute.html
Traceback (most recent call last):
File "/usr/games/singularity", line 11, in
load_entry_point('Endgame-Singularity==1.0b1', 'gui_scripts', 'singularity')()
File "/usr/lib/python3/dist-packages/singularity/init.py", line 106, in main
g.logfile = dirs.get_writable_file_in_dirs("error.log", "log")
File "/usr/lib/python3/dist-packages/singularity/code/dirs.py", line 220, in get_writable_file_in_dirs
write_dir = write_dirs[dir_name]
KeyError: 'log'
drpatelh commented 1 year ago

Yep, agree. This looks like some sort of install issue with Singularity. Closing this for now as it doesn't appear to be a pipeline issue. I would recommend running the pipeline with the test profile to ensure you can get it working; see point 4 here

Please feel free to join the nf-core Slack Workspace for any future questions/issues. We have an #rnaseq channel where you can get more real-time help.