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null path java error with all qc preprocessing skipping options enabled with revision 3.15.0 #1387

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jos4uke opened this issue Sep 17, 2024 · 1 comment · Fixed by #1410
Closed

null path java error with all qc preprocessing skipping options enabled with revision 3.15.0 #1387

jos4uke opened this issue Sep 17, 2024 · 1 comment · Fixed by #1410
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@jos4uke
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jos4uke commented Sep 17, 2024 •
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Description of the bug

Hi
I tried to skip all preprocessing qc steps using the following skipping options but I got a java null error on some path value:

nf-params.json:

{
    "input": "/home/me/work/DEG_RvsS_test_failed/samplesheet_test.csv",
    "outdir": "/home/me/work/DEG_RvsS_test_failed/results",
    "email": "[email protected]",
    "multiqc_title": "DEG_R_vs_S",
    "fasta": "/home/me/work/DEG_RvsS_test_failed/ref/KZ_150_8_H1_V2.fasta",
    "gtf": "/home/me/work/DEG_RvsS_test_failed/ref/KZ_150_H1V2_refGene.gtf",
    "save_reference": true,
    "star_ignore_sjdbgtf": true,
    "save_align_intermeds": false,
    "skip_pseudo_alignment": true,
    "skip_bbsplit": true,
    "skip_umi_extract": true,
    "skip_fastqc": true,
    "skip_trimming": true,
    "skip_qc": true
}

And here the error lines from stdout

...
Plus 27 more processes waiting for tasks…
ERROR ~ Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null

 -- Check script '/home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf' at line: 105 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/rnaseq] Sent summary e-mail to [email protected] (sendmail)-
-[nf-core/rnaseq] Pipeline completed with errors-

But when I downgrade to revision 3.14.0, this error did not occur.

Can you help fixing this bug with the latest revision please?

Thanks in advance

Command used and terminal output

# not working
nextflow run nf-core/rnaseq -r 3.15.0 \
        -name deg_r_vs_s_test_failed \
        -profile genotoul \
        -work-dir /home/me/work/DEG_RvsS_test_failed \
        -params-file nf-params.json

# working
nextflow run nf-core/rnaseq -r 3.14.0 \
        -name deg_r_vs_s_test_ok \
        -profile genotoul \
        -work-dir /home/me/work/DEG_RvsS_test_ok \
        -params-file nf-params.json

Relevant files

Sep-17 13:30:23.361 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -r 3.15.0 -name deg_r_vs_s -profile genotoul -work-dir /home/me/work/DEG_RvsS_test_failed -params-file nf-params.json -resume
Sep-17 13:30:23.608 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Sep-17 13:30:23.691 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/me/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Sep-17 13:30:23.726 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Sep-17 13:30:23.728 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Sep-17 13:30:23.732 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Sep-17 13:30:23.776 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Sep-17 13:30:23.813 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/me/.nextflow/scm
Sep-17 13:30:26.685 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/me/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Sep-17 13:30:26.777 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Sep-17 13:30:26.814 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/me/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Sep-17 13:30:28.248 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/me/.nextflow/assets/nf-core/rnaseq/nextflow.config
Sep-17 13:30:28.250 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/me/.nextflow/assets/nf-core/rnaseq/nextflow.config
Sep-17 13:30:28.282 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/me/.nextflow/secrets/store.json
Sep-17 13:30:28.288 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@70997a94] - activable => nextflow.secret.LocalSecretsProvider@70997a94
Sep-17 13:30:28.347 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `genotoul`
Sep-17 13:30:33.763 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, test_full_gcp, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, test_full_aws, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, test_full_azure, eva, nygc, fgcz, conda, crg, singularity, mpcdf_viper, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Sep-17 13:30:33.781 [main] WARN  nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option `-resume` is ignored
Sep-17 13:30:33.924 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Sep-17 13:30:33.926 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/rnaseq` [deg_r_vs_s] DSL2 - revision: 4e34945f6c [3.15.0]
Sep-17 13:30:33.927 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[[email protected]]
Sep-17 13:30:33.928 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Sep-17 13:30:33.928 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[[email protected]]
Sep-17 13:30:33.929 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3
Sep-17 13:30:33.961 [main] INFO  org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
Sep-17 13:30:33.961 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin '[email protected]'
Sep-17 13:30:33.982 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected]
Sep-17 13:30:34.110 [main] DEBUG nextflow.Session - Session UUID: e28e9c39-5826-4772-bc64-32b7192cd4d4
Sep-17 13:30:34.110 [main] DEBUG nextflow.Session - Run name: deg_r_vs_s
Sep-17 13:30:34.111 [main] DEBUG nextflow.Session - Executor pool size: 2
Sep-17 13:30:34.132 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Sep-17 13:30:34.151 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Sep-17 13:30:34.194 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC (08:19 CEST)
  System: Linux 4.18.0-477.13.1.el8_8.x86_64
  Runtime: Groovy 4.0.21 on Java HotSpot(TM) 64-Bit Server VM 17.0.6+9-LTS-190
  Encoding: UTF-8 (UTF-8)
  Process: 3981810@n002 [192.168.2.2]
  CPUs: 1 - Mem: 4 GB (3.8 GB) - Swap: 0 (0)
Sep-17 13:30:34.250 [main] DEBUG nextflow.Session - Work-dir: /home/me/work/DEG_RvsS_test_failed [gpfs]
Sep-17 13:30:34.335 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Sep-17 13:30:34.360 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Sep-17 13:30:34.572 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Sep-17 13:30:34.597 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 2; maxThreads: 1000
Sep-17 13:30:34.911 [main] DEBUG nextflow.Session - Session start
Sep-17 13:30:34.914 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/me/work/DEG_RvsS_test_failed/results/pipeline_info/execution_trace_2024-09-17_13-30-30.txt
Sep-17 13:30:35.540 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Sep-17 13:30:43.911 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation
Sep-17 13:30:43.943 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation
Sep-17 13:30:43.957 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation
Sep-17 13:30:43.962 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Sep-17 13:30:52.898 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Sep-17 13:30:52.900 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation
Sep-17 13:31:01.931 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation
Sep-17 13:31:01.932 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation
Sep-17 13:31:01.932 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation
Sep-17 13:31:01.935 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Sep-17 13:31:05.059 [main] DEBUG nextflow.Nextflow - Using schema file: nextflow_schema.json
Sep-17 13:31:05.063 [main] WARN  nextflow.script.ScriptBinding - Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
Sep-17 13:31:05.099 [main] INFO  nextflow.Nextflow -

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v3.15.0-g4e34945
------------------------------------------------------
Core Nextflow options
  revision                  : 3.15.0
  runName                   : deg_r_vs_s
  containerEngine           : singularity
  launchDir                 : /work/user/me/DEG_RvsS_test_failed
  workDir                   : /home/me/work/DEG_RvsS_test_failed
  projectDir                : /home/me/.nextflow/assets/nf-core/rnaseq
  userName                  : me
  profile                   : genotoul
  configFiles               :

Input/output options
  input                     : /home/me/work/DEG_RvsS_test_failed/samplesheet_test.csv
  outdir                    : /home/me/work/DEG_RvsS_test_failed/results
  email                     : [email protected]
  multiqc_title             : DEG_R_vs_S_test_failed

Reference genome options
  fasta                     : /home/me/work/DEG_RvsS_test_failed/ref/KZ_150_8_H1_V2.fasta
  gtf                       : /home/me/work/DEG_RvsS_test_failed/ref/KZ_150_H1V2_refGene.gtf
  igenomes_ignore           : true

Alignment options
  star_ignore_sjdbgtf       : true
  min_mapped_reads          : 5

Optional outputs
  save_reference            : true

Process skipping options
  skip_umi_extract          : true
  skip_trimming             : true
  skip_pseudo_alignment     : true
  skip_fastqc               : true
  skip_qc                   : true

Institutional config options
  config_profile_description: The Genotoul cluster profile
  config_profile_contact    : [email protected]
  config_profile_url        : http://bioinfo.genotoul.fr/

Max job request options
  max_cpus                  : 48
  max_memory                : 120 GB
  max_time                  : 4d

!! 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
------------------------------------------------------
Sep-17 13:31:05.121 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation
Sep-17 13:31:05.423 [main] WARN  nextflow.validation.SchemaValidator - The following invalid input values have been detected:

* --igenomesIgnore: true
* --igenomes-ignore: true


Sep-17 13:31:05.443 [main] DEBUG n.validation.DirectoryPathValidator - S3 paths are not supported by 'DirectoryPathValidator': 's3://ngi-igenomes/igenomes/'
Sep-17 13:31:05.459 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/home/me/work/DEG_RvsS_test_failed/samplesheet_test.csv' with '/home/me/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json'
Sep-17 13:31:05.533 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/home/me/work/DEG_RvsS_test_failed/samplesheet_test.csv' with '/home/me/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json'
Sep-17 13:31:05.535 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation
Sep-17 13:31:05.749 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF_FILTER` matches process NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER
Sep-17 13:31:05.793 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:05.794 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:05.821 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
Sep-17 13:31:05.842 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
Sep-17 13:31:05.847 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
Sep-17 13:31:05.877 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Sep-17 13:31:06.060 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED
Sep-17 13:31:06.063 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF2BED` matches process NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED
Sep-17 13:31:06.070 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.099 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
Sep-17 13:31:06.121 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
Sep-17 13:31:06.146 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.146 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.214 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Sep-17 13:31:06.215 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Sep-17 13:31:06.236 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.238 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.297 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE
Sep-17 13:31:06.298 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD` matches process NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE
Sep-17 13:31:06.326 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.326 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.414 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/home/me/work/DEG_RvsS_test_failed/samplesheet_test.csv' with '/home/me/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json'
Sep-17 13:31:06.423 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/home/me/work/DEG_RvsS_test_failed/samplesheet_test.csv' with '/home/me/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json'
Sep-17 13:31:06.561 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ
Sep-17 13:31:06.565 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ
Sep-17 13:31:06.570 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.583 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.844 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
Sep-17 13:31:06.848 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SALMON_INDEX` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
Sep-17 13:31:06.872 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.873 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.890 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE
Sep-17 13:31:06.912 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE
Sep-17 13:31:06.915 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.916 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:06.952 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
Sep-17 13:31:06.953 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
Sep-17 13:31:06.972 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:06.972 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.198 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Sep-17 13:31:07.199 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Sep-17 13:31:07.212 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.213 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.293 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Sep-17 13:31:07.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Sep-17 13:31:07.297 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.298 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.342 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Sep-17 13:31:07.344 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Sep-17 13:31:07.348 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Sep-17 13:31:07.416 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Sep-17 13:31:07.433 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.433 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.465 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Sep-17 13:31:07.467 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Sep-17 13:31:07.470 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.471 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Sep-17 13:31:07.502 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Sep-17 13:31:07.506 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.506 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.652 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Sep-17 13:31:07.655 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Sep-17 13:31:07.659 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.661 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE
Sep-17 13:31:07.724 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE
Sep-17 13:31:07.727 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.727 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
Sep-17 13:31:07.796 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
Sep-17 13:31:07.814 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.815 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE
Sep-17 13:31:07.883 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE
Sep-17 13:31:07.884 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE
Sep-17 13:31:07.887 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.887 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.939 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED
Sep-17 13:31:07.941 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED
Sep-17 13:31:07.942 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED
Sep-17 13:31:07.944 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:07.944 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:07.991 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED
Sep-17 13:31:07.993 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED
Sep-17 13:31:07.994 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_GENE_SCALED` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED
Sep-17 13:31:08.002 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.003 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.033 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT
Sep-17 13:31:08.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT
Sep-17 13:31:08.036 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT
Sep-17 13:31:08.038 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.038 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.206 [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
Sep-17 13:31:08.208 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES
Sep-17 13:31:08.226 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.226 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.282 [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
Sep-17 13:31:08.283 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX
Sep-17 13:31:08.286 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.287 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.361 [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
Sep-17 13:31:08.367 [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
Sep-17 13:31:08.370 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.370 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.423 [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
Sep-17 13:31:08.426 [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
Sep-17 13:31:08.430 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.430 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.465 [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
Sep-17 13:31:08.474 [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
Sep-17 13:31:08.477 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.477 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.618 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Sep-17 13:31:08.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:STRINGTIE_STRINGTIE` matches process NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Sep-17 13:31:08.637 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.637 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.677 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW
Sep-17 13:31:08.679 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV_FW` matches process NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW
Sep-17 13:31:08.697 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.698 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.724 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV
Sep-17 13:31:08.727 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV_REV` matches process NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV
Sep-17 13:31:08.731 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.731 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.769 [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
Sep-17 13:31:08.771 [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
Sep-17 13:31:08.788 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.788 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.813 [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
Sep-17 13:31:08.833 [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
Sep-17 13:31:08.836 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.837 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.889 [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
Sep-17 13:31:08.891 [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
Sep-17 13:31:08.895 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.895 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:08.929 [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
Sep-17 13:31:08.931 [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
Sep-17 13:31:08.933 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:08.933 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:09.194 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:MULTIQC
Sep-17 13:31:09.195 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC
Sep-17 13:31:09.210 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Sep-17 13:31:09.210 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Sep-17 13:31:09.342 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Sep-17 13:31:09.347 [main] DEBUG nextflow.Session - Igniting dataflow network (94)
Sep-17 13:31:09.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER
Sep-17 13:31:09.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED
Sep-17 13:31:09.395 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
Sep-17 13:31:09.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Sep-17 13:31:09.400 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE
Sep-17 13:31:09.457 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ
Sep-17 13:31:09.487 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
Sep-17 13:31:09.499 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE
Sep-17 13:31:09.499 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
Sep-17 13:31:09.556 [Actor Thread 12] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Sep-17 13:31:09.569 [Actor Thread 12] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.9--1; path=/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/depot.galaxyproject.org-singularity-python-3.9--1.img
Sep-17 13:31:09.569 [Actor Thread 22] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0; path=/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/depot.galaxyproject.org-singularity-samtools-1.20--h50ea8bc_0.img
Sep-17 13:31:09.587 [Actor Thread 18] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Sep-17 13:31:09.594 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE
Sep-17 13:31:09.595 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
Sep-17 13:31:09.595 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE
Sep-17 13:31:09.595 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED
Sep-17 13:31:09.595 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED
Sep-17 13:31:09.595 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT
Sep-17 13:31:09.595 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES
Sep-17 13:31:09.606 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX
Sep-17 13:31:09.606 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Sep-17 13:31:09.606 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Sep-17 13:31:09.606 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Sep-17 13:31:09.606 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Sep-17 13:31:09.607 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW
Sep-17 13:31:09.607 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV
Sep-17 13:31:09.607 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP
Sep-17 13:31:09.607 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Sep-17 13:31:09.607 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP
Sep-17 13:31:09.607 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Sep-17 13:31:09.667 [Actor Thread 1] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/me/.nextflow/assets/nf-core/rnaseq/bin/filter_gtf.py
Sep-17 13:31:09.695 [Actor Thread 18] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files
Sep-17 13:31:09.696 [Actor Thread 21] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files
Sep-17 13:31:09.698 [Actor Thread 12] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0; path=/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/depot.galaxyproject.org-singularity-fq-0.9.1--h9ee0642_0.img
Sep-17 13:31:09.739 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC
Sep-17 13:31:09.740 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_db1de4232c4cc4b7: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
  Script_56c7c9e8363ee20a: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/custom/tx2gene/main.nf
  Script_f289bdfe26d7f1cf: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/fastqc/main.nf
  Script_4fb9e5798185138e: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_align_hisat2/main.nf
  Script_cdbce3e23a8f89e8: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/quantify_rsem/../../nf-core/bam_sort_stats_samtools/../bam_stats_samtools/main.nf
  Script_bf81af2b96de0168: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/../../../modules/nf-core/ucsc/bedgraphtobigwig/main.nf
  Script_271870af059e4192: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/kallisto/index/main.nf
  Script_a702034016a53c43: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_subsample_fq_salmon/../../../modules/nf-core/salmon/quant/main.nf
  Script_274aad67990f7b6d: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/local/deseq2_qc/main.nf
  Script_69e14f38e32bc194: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_markduplicates_picard/../bam_stats_samtools/../../../modules/nf-core/samtools/flagstat/main.nf
  Script_a4ac0ea044c720d7: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/quantify_rsem/main.nf
  Script_223ca400878df5b0: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/untar/main.nf
  Script_7cae7a5555a00165: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/quantify_rsem/../../../modules/nf-core/rsem/calculateexpression/main.nf
  Script_7bbd1ec48b03ff67: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
  Script_c3146a026d768f52: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/bedtools/genomecov/main.nf
  Script_b924201e33aa1599: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/hisat2/extractsplicesites/main.nf
  Script_a6b84a8d8db37c9d: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/gunzip/main.nf
  Script_f9581eb244f08763: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/quantify_rsem/../../nf-core/bam_sort_stats_samtools/../../../modules/nf-core/samtools/sort/main.nf
  Script_81a2876a059155a7: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/local/gtf_filter/main.nf
  Script_cc2a9c8ba5b8cc15: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/tin/main.nf
  Script_6012db1a2adb3e63: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/summarizedexperiment/summarizedexperiment/main.nf
  Script_17a330eff9da7d9b: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_markduplicates_picard/../bam_stats_samtools/../../../modules/nf-core/samtools/idxstats/main.nf
  Script_967ea477ddb06272: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/quantify_rsem/../../nf-core/bam_sort_stats_samtools/../../../modules/nf-core/samtools/index/main.nf
  Script_b23445b93c86c515: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_align_hisat2/../../../modules/nf-core/hisat2/align/main.nf
  Script_1e545e1c37680b0d: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf
  Script_e10a0e7467f0b3e9: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_markduplicates_picard/../../../modules/nf-core/picard/markduplicates/main.nf
  Script_00f15dacb1370c16: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/junctionannotation/main.nf
  Script_b043057988626cf5: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/local/gtf2bed/main.nf
  Script_2882453b74be5692: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/local/multiqc_custom_biotype/main.nf
  Script_da05a45d4fc5617e: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/../../../modules/nf-core/sortmerna/main.nf
  Script_5d261b30ca6cdcdb: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/custom/getchromsizes/main.nf
  Script_bf5c4db2e13898ce: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/main.nf
  Script_5f794e9468aa1f6f: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/main.nf
  Script_54e0c3dce4d8c049: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/dupradar/main.nf
  Script_fe6f9a2d2d32c34f: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/innerdistance/main.nf
  Script_d34500cd85bfd0d5: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/main.nf
  Script_e927852b807f691d: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/inferexperiment/main.nf
  Script_031dd6cf330b7909: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_fastp/main.nf
  Script_4240a2dab247dd20: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_subsample_fq_salmon/../../../modules/nf-core/fq/subsample/main.nf
  Script_18089a64b4672be8: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/main.nf
  Script_2fa3c1f588d620ba: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/subread/featurecounts/main.nf
  Script_a7d371fe23db7aab: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf
  Script_8703d5c7d48af3ab: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/local/star_genomegenerate_igenomes/main.nf
  Script_59101990e865c327: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/../../../modules/nf-core/umitools/dedup/main.nf
  Script_b4163cee6a6b2681: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/umitools/extract/main.nf
  Script_200ea493670cb6c3: /home/me/.nextflow/assets/nf-core/rnaseq/main.nf
  Script_58ab0c288a51eacd: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/quantify_rsem/../../../modules/local/rsem_merge_counts/main.nf
  Script_1adca4cb4e6fb5ea: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
  Script_bac6d352d496d867: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/rsem/preparereference/main.nf
  Script_cf1e17a1e4a14232: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/bamstat/main.nf
  Script_89479fc8fff50057: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/local/preprocess_transcripts_fasta_gencode/main.nf
  Script_b666edf0129ec7fc: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/gffread/main.nf
  Script_f3cf076a526d2485: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_markduplicates_picard/main.nf
  Script_f0c9be7d13f120a6: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/../../../modules/nf-core/cat/fastq/main.nf
  Script_f84ac7d7414849ca: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/qualimap/rnaseq/main.nf
  Script_23e9bb1f954772b0: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/../../../modules/nf-core/ucsc/bedclip/main.nf
  Script_495548ce4a6ba5f4: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/../bam_stats_samtools/../../../modules/nf-core/samtools/stats/main.nf
  Script_9f6ce129b29ed4a5: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_fastp/../../../modules/nf-core/fastp/main.nf
  Script_f7557425db44c1bf: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
  Script_3ba0967a93b6148f: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/fastq_qc_trim_filter_setstrandedness/../../../modules/nf-core/bbmap/bbsplit/main.nf
  Script_7d7cfc0ec284a12d: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_subsample_fq_salmon/../../../modules/nf-core/salmon/index/main.nf
  Script_196bdeb58a32d123: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf
  Script_210bd6478ac003f9: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/align_star/../../../modules/local/star_align_igenomes/main.nf
  Script_dbe8fbfa975cebf1: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/junctionsaturation/main.nf
  Script_8a63e8328f1e932a: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/kallisto/quant/main.nf
  Script_7acb62b9e60b283e: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/readduplication/main.nf
  Script_8b4cd5023b0747bc: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/star/genomegenerate/main.nf
  Script_95a2ba62b36bc275: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/multiqc/main.nf
  Script_c3f4bd3b3e600606: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/main.nf
  Script_997cce4b25cc363d: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/preseq/lcextrap/main.nf
  Script_1a18572a60f1dc55: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/align_star/main.nf
  Script_a3c6aef209ebf998: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/custom/catadditionalfasta/main.nf
  Script_2b72a5be5c8fe209: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/tximeta/tximport/main.nf
  Script_1abd298cf97eebd1: /home/me/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/hisat2/build/main.nf
  Script_8c5ab2a06c1905d8: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/trimgalore/main.nf
  Script_e76b9210f32f34ec: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/umitools/prepareforrsem/main.nf
  Script_a71a24a4c2f30a37: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/local/align_star/../../../modules/nf-core/star/align/main.nf
  Script_f1f53abfc1403f76: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_subsample_fq_salmon/main.nf
  Script_bd8537eec78d4f82: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/readdistribution/main.nf
  Script_2ebe1d1a775a7432: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/bam_sort_stats_samtools/main.nf
  Script_70d113e39d74f54c: /home/me/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../modules/nf-core/stringtie/stringtie/main.nf
Sep-17 13:31:09.741 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Sep-17 13:31:09.741 [main] DEBUG nextflow.Session - Session await
Sep-17 13:31:09.859 [Actor Thread 15] ERROR nextflow.extension.OperatorImpl - @unknown
java.lang.NullPointerException: Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null
        at java.base/java.nio.file.Files.provider(Files.java:105)
        at java.base/java.nio.file.Files.newInputStream(Files.java:160)
        at nextflow.file.SlurperEx.load(SlurperEx.groovy:67)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at Script_1e545e1c37680b0d.processVersionsFromYAML(Script_1e545e1c37680b0d:105)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:342)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at Script_1e545e1c37680b0d$_softwareVersionsToYAML_closure3.doCall(Script_1e545e1c37680b0d:126)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
        at jdk.internal.reflect.GeneratedMethodAccessor124.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at groovy.lang.Closure.call(Closure.java:433)
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
        at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
        at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
        at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
        at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
        at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)
Sep-17 13:31:09.923 [Actor Thread 15] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null
Sep-17 13:31:09.949 [Actor Thread 13] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.011 s; external sort time: 0.056 s; total time: 0.067 s
Sep-17 13:31:09.955 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/me/work/DEG_RvsS_test_failed/collect-file/70263c81dc22033b8b7ca3c385b9a010
Sep-17 13:31:09.981 [Actor Thread 21] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files
Sep-17 13:31:09.952 [Actor Thread 12] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.065 s; total time: 0.065 s
Sep-17 13:31:09.996 [Actor Thread 6] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files
Sep-17 13:31:10.027 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/me/work/DEG_RvsS_test_failed/collect-file/3db016d8c7a980fd408819fc3c4ba768
Sep-17 13:31:10.029 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-11879696529069352671
Sep-17 13:31:10.030 [Actor Thread 21] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files
Sep-17 13:31:10.033 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-18308412332747759995
Sep-17 13:31:10.041 [Actor Thread 1] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 2 FASTQ files
Sep-17 13:31:10.101 [Actor Thread 24] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 24; slices: 1; internal sort time: 0.174 s; external sort time: 0.019 s; total time: 0.193 s
Sep-17 13:31:10.125 [Actor Thread 24] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/me/work/DEG_RvsS_test_failed/collect-file/558c5086fb6d4c5015bdc8a879589d4e
Sep-17 13:31:10.127 [Actor Thread 24] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13315228042059668753
Sep-17 13:31:10.176 [Actor Thread 15] DEBUG nextflow.Session - The following nodes are still active:
[process] NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED
  status=ACTIVE
  port 0: (value) OPEN  ; channel: gtf
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA
  status=ACTIVE
  port 0: (value) bound ; channel: fasta
  port 1: (value) OPEN  ; channel: gtf
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE
  status=ACTIVE
  port 0: (value) bound ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX
  status=ACTIVE
  port 0: (value) bound ; channel: genome_fasta
  port 1: (value) OPEN  ; channel: transcript_fasta
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: index
  port 2: (value) OPEN  ; channel: gtf
  port 3: (value) OPEN  ; channel: transcript_fasta
  port 4: (value) bound ; channel: alignment_mode
  port 5: (value) bound ; channel: lib_type
  port 6: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) OPEN  ; channel: -
  port 3: (value) bound ; channel: star_ignore_sjdbgtf
  port 4: (value) bound ; channel: seq_platform
  port 5: (value) bound ; channel: seq_center
  port 6: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: index
  port 2: (value) OPEN  ; channel: gtf
  port 3: (value) OPEN  ; channel: transcript_fasta
  port 4: (value) bound ; channel: alignment_mode
  port 5: (value) bound ; channel: lib_type
  port 6: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE
  status=ACTIVE
  port 0: (value) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) bound ; channel: quant_type
  port 3: (value) bound ; channel: id
  port 4: (value) bound ; channel: extra
  port 5: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
  status=ACTIVE
  port 0: (value) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) bound ; channel: quant_type
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: -
  port 2: (value) bound ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (value) OPEN  ; channel: -
  port 3: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: -
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: annotation_gtf
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: sizes
  port 2: (value) bound ; channel: extension
  port 3: (value) bound ; channel: sort
  port 4: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) bound ; channel: sizes
  port 2: (value) bound ; channel: extension
  port 3: (value) bound ; channel: sort
  port 4: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: sizes
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: sizes
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: sizes
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (value) OPEN  ; channel: sizes
  port 2: (cntrl) -     ; channel: $

[process] NFCORE_RNASEQ:RNASEQ:MULTIQC
  status=ACTIVE
  port 0: (value) OPEN  ; channel: multiqc_files
  port 1: (value) bound ; channel: multiqc_config
  port 2: (value) bound ; channel: extra_multiqc_config
  port 3: (value) bound ; channel: multiqc_logo
  port 4: (queue) OPEN  ; channel: replace_names
  port 5: (value) bound ; channel: sample_names
  port 6: (cntrl) -     ; channel: $

Sep-17 13:31:10.189 [Actor Thread 15] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
Sep-17 13:31:10.195 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop
Sep-17 13:31:10.196 [main] DEBUG nextflow.Session - Session await > all processes finished
Sep-17 13:31:10.196 [main] DEBUG nextflow.Session - Session await > all barriers passed
Sep-17 13:31:10.263 [Actor Thread 18] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Sep-17 13:31:10.266 [Actor Thread 22] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.001 s; total time: 0.002 s
Sep-17 13:31:10.278 [Actor Thread 17] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0; path=/usr/local/bioinfo/src/NextflowWorkflows/singularity-img/depot.galaxyproject.org-singularity-multiqc-1.24.1--pyhdfd78af_0.img
Sep-17 13:31:10.280 [Actor Thread 4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:MULTIQC; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Sep-17 13:31:10.282 [Actor Thread 22] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/me/work/DEG_RvsS_test_failed/collect-file/90de61e675c250f6d04d1902b590d2bf
Sep-17 13:31:10.284 [Actor Thread 22] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8300871830237149890
Sep-17 13:31:10.291 [Actor Thread 24] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/me/.nextflow/assets/nf-core/rnaseq/workflows/rnaseq/assets/multiqc/multiqc_config.yml
Sep-17 13:31:10.305 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Sep-17 13:31:10.787 [main] INFO  nextflow.Nextflow - -[nf-core/rnaseq] Sent summary e-mail to [email protected] (sendmail)-
Sep-17 13:31:10.796 [main] INFO  nextflow.Nextflow - -[nf-core/rnaseq] Pipeline completed with errors-
Sep-17 13:31:10.801 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=9; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Sep-17 13:31:10.802 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Sep-17 13:31:10.803 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Sep-17 13:31:11.698 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Sep-17 13:31:12.027 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Sep-17 13:31:12.101 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Sep-17 13:31:12.103 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Sep-17 13:31:12.108 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

  • Nextflow version: 24.04.2
  • Version of nf-core/rnaseq: 3.15.0
  • Hardware: HPC
  • Executor: slurm
  • config profile: genotoul
  • Container engine: Singularity
  • OS:
NAME="Red Hat Enterprise Linux"
VERSION="8.8 (Ootpa)"
ID="rhel"
ID_LIKE="fedora"
VERSION_ID="8.8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Red Hat Enterprise Linux 8.8 (Ootpa)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:redhat:enterprise_linux:8::baseos"
HOME_URL="https://www.redhat.com/"
DOCUMENTATION_URL="https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8"
BUG_REPORT_URL="https://bugzilla.redhat.com/"

REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 8"
REDHAT_BUGZILLA_PRODUCT_VERSION=8.8
REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.8"
@jos4uke jos4uke added the bug Something isn't working label Sep 17, 2024
@pinin4fjords pinin4fjords mentioned this issue Oct 15, 2024
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@pinin4fjords pinin4fjords linked a pull request Oct 15, 2024 that will close this issue
Fix issues caused by empty versions from trimming subworkflows #1410
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Fixed in #1410

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Fix issues caused by empty versions from trimming subworkflows nf-core/rnaseq
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@jos4uke @pinin4fjords