Open acpicornell opened 5 months ago
Hello, I think I've encountered the same GSEA issue, please see below. The workflow runs fine when GSEA is not invoked. Please note that the GTF is dog, but the GMT is human - I don't think this should cause issues though, as gene symbol is largely in common between the two species.
Thanks, and all the best. Aaron.
nextflow run nf-core/differentialabundance -r 1.4.0\
-profile rnaseq,singularity\
--input c2bbe1-samplesheet.csv\
--contrasts c2bbe1-contrasts.csv\
--matrix nf-core_rnaseq_canfam6/star_salmon/salmon.merged.gene_counts_length_scaled.tsv\
--gtf /projects/health_sciences/ric/ogf/ngs/refs/dog/canfam6/GCF_000002285.5_Dog10K_Boxer_Tasha_genomic.gtf\
--outdir nf-core_diffabun_gsea_hall\
--gsea_run\
--gsea_gene_sets h.all.v2023.2.Hs.symbols.gmt\
N E X T F L O W ~ version 23.10.1
Launching https://github.com/nf-core/differentialabundance
[pedantic_mirzakhani] DSL2 - revision: a3d664c12c [1.4.0]
,--./,-.
___ __ __ __ ___ /,-._.--~'
/ \ |__) |__ } { | \| | \__, \__/ | \ |___ \
-.,--,
.,._,'
nf-core/differentialabundance v1.4.0-ga3d664cCore Nextflow options revision : 1.4.0 runName : pedantic_mirzakhani containerEngine : singularity container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0] launchDir : /projects/health_sciences/ric/ogf/ngs/illumina/rna-seq/c2bbe1 workDir : /projects/health_sciences/ric/ogf/ngs/illumina/rna-seq/c2bbe1/work projectDir : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance userName : jefaa92p profile : rnaseq,singularity configFiles :
Input/output options input : c2bbe1-samplesheet.csv contrasts : c2bbe1-contrasts.csv outdir : nf-core_diffabun_gsea_hall
Abundance values matrix : nf-core_rnaseq_canfam6/star_salmon/salmon.merged.gene_counts_length_scaled.tsv affy_cel_files_archive : null querygse : null
Affy input options affy_cdfname : null
Proteus input options proteus_round_digits : -1
Filtering filtering_min_abundance : 1 filtering_min_samples : 1
Differential analysis differential_min_fold_change: 2 differential_max_pval : 1
Limma specific options (microarray only) limma_spacing : null limma_block : null limma_correlation : null limma_p_value : 1
GSEA gsea_run : true gsea_gene_sets : h.all.v2023.2.Hs.symbols.gmt
Shiny app settings shinyngs_shinyapps_account : null shinyngs_shinyapps_app_name : null
Reporting options report_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd logo_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png css_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css citations_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/CITATIONS.md report_title : null report_author : null report_description : null
Reference genome options gtf : /projects/health_sciences/ric/ogf/ngs/refs/dog/canfam6/GCF_000002285.5_Dog10K_Boxer_Tasha_genomic.gtf
Institutional config options config_profile_name : RNA-seq profile config_profile_description : Settings for RNA-seq analysis
If you use nf-core/differentialabundance for your analysis please cite:
The pipeline https://doi.org/10.5281/zenodo.7568000
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md
executor > slurm (5) [3b/8a7e65] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (GCF_000002285) [100%] 1 of 1 ✔ [50/f6a435] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (c2bbe1-samplesheet.csv) [100%] 1 of 1 ✔ [5c/8521c4] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) [ 0%] 0 of 1 [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT - [01/6d36ef] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (condition_control_treated) [ 0%] 0 of 1 [d7/3314d6] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) [ 0%] 0 of 1 [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'
Caused by: executor > slurm (5) [3b/8a7e65] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (GCF_000002285) [100%] 1 of 1 ✔ [50/f6a435] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (c2bbe1-samplesheet.csv) [100%] 1 of 1 ✔ [5c/8521c4] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) [100%] 1 of 1 ✔ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT - [01/6d36ef] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (condition_control_treated) [100%] 1 of 1 ✔ [d7/3314d6] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'
Caused by:
Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)
terminated with an error exit status (1)
executor > slurm (5) [3b/8a7e65] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (GCF_000002285) [100%] 1 of 1 ✔ [50/f6a435] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (c2bbe1-samplesheet.csv) [100%] 1 of 1 ✔ [5c/8521c4] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) [100%] 1 of 1 ✔ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT - [01/6d36ef] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (condition_control_treated) [100%] 1 of 1 ✔ [d7/3314d6] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'
Caused by:
Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)
terminated with an error exit status (1)
Command executed:
function find_column_number { file=$1 column=$2
head -n 1 $file | tr '\t' '\n' | grep -n "^${column}$" | awk -F':' '{print $1}'
}
id_col=$(find_column_number GCF_000002285.anno.feature_metadata.tsv gene_id) symbol_col=$(find_column_number GCF_000002285.anno.feature_metadata.tsv gene_name) outfile=$(echo GCF_000002285.anno.feature_metadata.tsv | sed 's/(.)../\1/').chip
echo -e "Probe Set ID\tGene Symbol\tGene Title" > ${outfile}.tmp tail -n +2 GCF_000002285.anno.feature_metadata.tsv | awk -F'\t' -v id=$id_col -v symbol=$symbol_col '{print $id"\t"$symbol"\tNA"}' >> ${outfile}.tmp mv ${outfile}.tmp ${outfile}
cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP": bash: $(echo $(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')) END_VERSIONS
Command exit status: 1
Command output: (empty)
Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Work dir: /projects/health_sciences/ric/ogf/ngs/illumina/rna-seq/c2bbe1/work/d7/3314d6616f60deb8356fcb2ca7ea6d
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
-- Check '.nextflow.log' file for details
Description of the bug
Hello,
I am trying to run GSEA but I get an error when trying to process the GMT file I obtained from MSigDB.
Previously, I have executed the pipeline without the GSEA part, and the differential expression analysis works without any issues.
Is anyone else encountering this problem?
Thank you very much.
Command used and terminal output
And I get:
Relevant files
Apr-09 13:16:47.240 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0 --study_type rnaseq --input /mnt/storage/acpicornell/thytreg/240405/samplesheet.csv --outdir /mnt/storage/acpicornell/thytreg/240405/output --matrix /mnt/storage/acpicornell/thytreg/240405/salmon.merged.gene_counts.tsv --transcript_length_matrix /mnt/storage/acpicornell/thytreg/240405/salmon.merged.gene_lengths.tsv --contrasts /mnt/storage/acpicornell/thytreg/240405/contrasts.csv --gtf /mnt/storage/data/ncbi/data/GCF_000001405.40/genomic.gtf --features_id_col gene_id --features_name_col gene_name --features_type gene --gsea_run TRUE --gsea_gene_sets /mnt/storage/data/gsea/c2.cp.v2023.2.Hs.symbols.gmt -profile rnaseq,singularity -c /home/acpicornell/configs/nextflow_slurm.config Apr-09 13:16:47.359 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 Apr-09 13:16:47.378 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/user1/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1 Apr-09 13:16:47.387 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-09 13:16:47.388 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-09 13:16:47.391 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-09 13:16:47.408 [main] INFO org.pf4j.AbstractPluginManager - No plugins Apr-09 13:16:49.107 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/nextflow.config Apr-09 13:16:49.110 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/user1/configs/nextflow_slurm.config Apr-09 13:16:49.111 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/nextflow.config Apr-09 13:16:49.111 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/user1/configs/nextflow_slurm.config Apr-09 13:16:49.132 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:
rnaseq,singularity
Apr-09 13:16:51.513 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:rnaseq,singularity
Apr-09 13:16:51.580 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, soft, test_soft, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, test_maxquant, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, rnaseq, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, utd_europa, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, affy, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, test_nogtf, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, test_affy, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] Apr-09 13:16:51.644 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Apr-09 13:16:51.665 [main] INFO nextflow.cli.CmdRun - Launching/mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/main.nf
[prickly_neumann] DSL2 - revision: 2a636b2a04 Apr-09 13:16:51.666 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation] Apr-09 13:16:51.667 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Apr-09 13:16:51.667 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation] Apr-09 13:16:51.667 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest Apr-09 13:16:52.415 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved Apr-09 13:16:52.416 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3' Apr-09 13:16:52.422 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3 Apr-09 13:16:52.433 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/user1/.nextflow/secrets/store.json Apr-09 13:16:52.436 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@79b8ecb] - activable => nextflow.secret.LocalSecretsProvider@79b8ecb Apr-09 13:16:52.502 [main] DEBUG nextflow.Session - Session UUID: 1c2cadfc-259f-4005-bf34-c1f7b1a9e852 Apr-09 13:16:52.503 [main] DEBUG nextflow.Session - Run name: prickly_neumann Apr-09 13:16:52.503 [main] DEBUG nextflow.Session - Executor pool size: 2 Apr-09 13:16:52.512 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Apr-09 13:16:52.517 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Apr-09 13:16:52.540 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.1 build 5891 Created: 12-01-2024 22:01 UTC (23:01 CEST) System: Linux 5.14.0-362.24.1.el9_3.x86_64 Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 17.0.6+10-LTS Encoding: UTF-8 (UTF-8) Process: 1235491@kraken.bioinfo.lan [192.168.224.6] CPUs: 2 - Mem: 125 GB (23 GB) - Swap: 4 GB (3.6 GB) Apr-09 13:16:52.564 [main] DEBUG nextflow.Session - Work-dir: /mnt/storage/scratch/hgugm_93947 [xfs] Apr-09 13:16:52.580 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Apr-09 13:16:52.590 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Apr-09 13:16:52.694 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Apr-09 13:16:52.705 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 Apr-09 13:16:52.889 [main] DEBUG nextflow.Session - Session start Apr-09 13:16:52.895 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/storage/user1/thytreg/240405/output/pipeline_info/execution_trace_2024-04-09_13-16-50.txt Apr-09 13:16:52.909 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/lib Apr-09 13:16:52.912 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/lib Apr-09 13:16:52.912 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/lib/nfcore_external_java_deps.jar Apr-09 13:16:53.672 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Apr-09 13:16:53.686 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp]; plugin Id: nf-validation Apr-09 13:16:53.703 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation Apr-09 13:16:54.023 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/mnt/storage/user1/thytreg/240405/samplesheet.csv' with '/mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/schema_input.json' Apr-09 13:16:54.050 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/mnt/storage/user1/thytreg/240405/samplesheet.csv' with '/mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/schema_input.json' Apr-09 13:16:54.052 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation Apr-09 13:16:55.333 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation Apr-09 13:16:55.358 [main] INFO nextflow.Nextflow -|\ | | /
/ \ |__) |__ } { | \| | \__, \__/ | \ |___ \
-.,--,
.,._,' nf-core/differentialabundance v1.4.0Core Nextflow options runName : prickly_neumann containerEngine : singularity container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0] launchDir : /mnt/storage/user1/thytreg/240405 workDir : /mnt/storage/scratch/hgugm_93947 projectDir : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0 userName : user1 profile : rnaseq,singularity configFiles :
Input/output options input : /mnt/storage/user1/thytreg/240405/samplesheet.csv contrasts : /mnt/storage/user1/thytreg/240405/contrasts.csv outdir : /mnt/storage/user1/thytreg/240405/output
Abundance values matrix : /mnt/storage/user1/thytreg/240405/salmon.merged.gene_counts.tsv transcript_length_matrix : /mnt/storage/user1/thytreg/240405/salmon.merged.gene_lengths.tsv affy_cel_files_archive : null querygse : null
Affy input options affy_cdfname : null
Proteus input options proteus_round_digits : -1
Filtering filtering_min_abundance : 1 filtering_min_samples : 1
Differential analysis differential_min_fold_change: 2 differential_max_pval : 1
Limma specific options (microarray only) limma_spacing : null limma_block : null limma_correlation : null limma_p_value : 1
GSEA gsea_run : true gsea_gene_sets : /mnt/storage/data/gsea/c2.cp.v2023.2.Hs.symbols.gmt
Shiny app settings shinyngs_shinyapps_account : null shinyngs_shinyapps_app_name : null
Reporting options report_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/differentialabundance_report.Rmd logo_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/docs/images/nf-core-differentialabundance_logo_light.png css_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/nf-core_style.css citations_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/CITATIONS.md report_title : null report_author : null report_description : null
Reference genome options gtf : /mnt/storage/data/ncbi/data/GCF_000001405.40/genomic.gtf
Institutional config options custom_config_base : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/../configs/ config_profile_name : RNA-seq profile config_profile_description : IiSGM SLURM profile in single nodes
Max job request options max_cpus : 32 max_memory : 100 GB max_time : 5d
!! Only displaying parameters that differ from the pipeline defaults !!
If you use nf-core/differentialabundance for your analysis please cite:
The pipeline https://doi.org/10.5281/zenodo.7568000
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md
Apr-09 13:16:58.334 [main] DEBUG nextflow.script.ProcessConfig - Config settings
withLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE Apr-09 13:16:58.337 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:GTF_TO_TABLE
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE Apr-09 13:16:58.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.349 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.358 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Apr-09 13:16:58.362 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 50; pollInterval: 15s; dumpInterval: 5m Apr-09 13:16:58.364 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Apr-09 13:16:58.366 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Apr-09 13:16:58.499 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR Apr-09 13:16:58.500 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:VALIDATOR
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR Apr-09 13:16:58.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.523 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER Apr-09 13:16:58.524 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:CUSTOM_MATRIXFILTER
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER Apr-09 13:16:58.527 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.527 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.546 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_medium
matches labelsprocess_medium
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.547 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DESEQ2_DIFFERENTIAL
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.547 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DESEQ2_NORM
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.553 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.566 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_medium
matches labelsprocess_medium
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL Apr-09 13:16:58.566 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:DESEQ2_DIFFERENTIAL
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL Apr-09 13:16:58.570 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.570 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.587 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT Apr-09 13:16:58.590 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:CUSTOM_TABULARTOGSEAGCT
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT Apr-09 13:16:58.606 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.608 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.628 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS Apr-09 13:16:58.628 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:CUSTOM_TABULARTOGSEACLS
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS Apr-09 13:16:58.633 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.633 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.638 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP Apr-09 13:16:58.639 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:TABULAR_TO_GSEA_CHIP
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP Apr-09 13:16:58.640 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.640 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.658 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA Apr-09 13:16:58.659 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:GSEA_GSEA
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA Apr-09 13:16:58.661 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.661 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.694 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY Apr-09 13:16:58.695 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:PLOT_EXPLORATORY
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY Apr-09 13:16:58.697 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.697 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.704 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.705 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:PLOT_DIFFERENTIAL
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.707 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.707 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.728 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS Apr-09 13:16:58.728 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:CUSTOM_DUMPSOFTWAREVERSIONS
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS Apr-09 13:16:58.729 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.729 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.784 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP Apr-09 13:16:58.785 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:SHINYNGS_APP
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP Apr-09 13:16:58.786 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.786 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.797 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_low
matches labelsprocess_low
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK Apr-09 13:16:58.798 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:RMARKDOWNNOTEBOOK
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK Apr-09 13:16:58.799 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.799 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.808 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithLabel:process_single
matches labelsprocess_single
for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE Apr-09 13:16:58.809 [main] DEBUG nextflow.script.ProcessConfig - Config settingswithName:MAKE_REPORT_BUNDLE
matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE Apr-09 13:16:58.809 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.809 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.812 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: VALIDATOR, ZIP, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER, CUSTOM_TABULARTOGSEAGCT, MAKE_REPORT_BUNDLE, ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA, PLOT_DIFFERENTIAL, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM, GSEA_GSEA, SHINYNGS_VALIDATEFOMCOMPONENTS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP, GUNZIP_GTF, AFFY_JUSTRMA, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS, TABULAR_TO_GSEA_CHIP, CUSTOM_TABULARTOGSEACLS, GUNZIP, SHINYNGS_STATICDIFFERENTIAL, UNTAR, AFFY_JUSTRMA_RAW, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK, GTF_TO_TABLE, GEOQUERY_GETGEO, PROTEUS_READPROTEINGROUPS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE, DESEQ2_DIFFERENTIAL, SHINYNGS_STATICEXPLORATORY, DESEQ2_NORM, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL, RMARKDOWNNOTEBOOK, LIMMA_DIFFERENTIAL, SHINYNGS_APP, CUSTOM_DUMPSOFTWAREVERSIONS, CUSTOM_MATRIXFILTER, PLOT_EXPLORATORY, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS, PROTEUS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY, AFFY_JUSTRMA_NORM, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.821 [main] DEBUG nextflow.Session - Igniting dataflow network (25) Apr-09 13:16:58.826 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.836 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS Apr-09 13:16:58.840 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP Apr-09 13:16:58.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK Apr-09 13:16:58.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE Apr-09 13:16:58.842 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_736359fe28427d7c: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf Script_0b2b547b5bd8d72f: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/deseq2/differential/main.nf Script_bd162165863945c5: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/validatefomcomponents/main.nf Script_8258fa18ec202f1e: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/geoquery/getgeo/main.nf Script_fd29bcfb844eda4d: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/limma/differential/main.nf Script_e11ffbac6afe36ec: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/gsea/gsea/main.nf Script_c3c7f0ae80cda0cc: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/staticexploratory/main.nf Script_66ffa6df5b55d922: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/main.nf Script_f291caf4f7573aca: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/tabulartogseagct/main.nf Script_af0fb319323fde68: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/affy/justrma/main.nf Script_61045595cd57fdfa: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/tabulartogseacls/main.nf Script_cb1a92e48950cb6f: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/app/main.nf Script_36fafb73beaa89a0: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/rmarkdownnotebook/main.nf Script_a9670c657bdfaa03: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/local/tabular_to_gsea_chip.nf Script_1a6661f1fced92e0: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/rmarkdownnotebook/./parametrize.nf Script_980ffca4de0b9bc8: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/staticdifferential/main.nf Script_c901260d3c3d641a: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/matrixfilter/main.nf Script_777604ec37a36f79: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf Script_66471300492dce16: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/differentialabundance.nf Script_7002cd4537b0f229: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/proteus/readproteingroups/main.nf Script_079385570c0cda9d: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/untar/main.nf Script_b4abc93ac1f4bba3: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/zip/main.nf Script_a71c717f63173976: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/gunzip/main.nf Apr-09 13:16:58.842 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Apr-09 13:16:58.842 [main] DEBUG nextflow.Session - Session await Apr-09 13:16:58.905 [Actor Thread 6] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0.img Apr-09 13:16:59.023 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genomic) > jobId: 93948; workDir: /mnt/storage/scratch/hgugm_93947/63/ef6582369bb192473c82f71d1aa553 Apr-09 13:16:59.023 [Task submitter] INFO nextflow.Session - [63/ef6582] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genomic) Apr-09 13:17:13.445 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93948; id: 1; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genomic); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/63/ef6582369bb192473c82f71d1aa553 started: 1712661433434; exited: 2024-04-09T11:17:13.341673264Z; ] Apr-09 13:17:13.610 [Actor Thread 1] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-r-shinyngs-1.8.4--r43hdfd78af_0.img Apr-09 13:17:13.625 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Apr-09 13:17:13.650 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samplesheet.csv) > jobId: 93949; workDir: /mnt/storage/scratch/hgugm_93947/58/750c316aef52caf4b6414f176971a0 Apr-09 13:17:13.651 [Task submitter] INFO nextflow.Session - [58/750c31] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samplesheet.csv) Apr-09 13:17:13.658 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Apr-09 13:17:43.434 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93949; id: 2; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/58/750c316aef52caf4b6414f176971a0 started: 1712661448432; exited: 2024-04-09T11:17:29.020728634Z; ] Apr-09 13:17:43.465 [Actor Thread 5] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/gawk:5.1.0; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-gawk-5.1.0.img Apr-09 13:17:43.521 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) > jobId: 93950; workDir: /mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca Apr-09 13:17:43.521 [Task submitter] INFO nextflow.Session - [bb/9d07fb] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) Apr-09 13:17:43.557 [Actor Thread 12] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/r-base:4.2.1; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-r-base-4.2.1.img Apr-09 13:17:43.564 [Actor Thread 16] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ubuntu:20.04; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-ubuntu-20.04.img Apr-09 13:17:43.611 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_THY) > jobId: 93951; workDir: /mnt/storage/scratch/hgugm_93947/9f/69878e624c65d509e991b42369590f Apr-09 13:17:43.612 [Task submitter] INFO nextflow.Session - [9f/69878e] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_THY) Apr-09 13:17:43.627 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_UCB) > jobId: 93952; workDir: /mnt/storage/scratch/hgugm_93947/a6/5e105b1fe42c43b373e3401cc10038 Apr-09 13:17:43.627 [Task submitter] INFO nextflow.Session - [a6/5e105b] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_UCB) Apr-09 13:17:43.643 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (UCB_THY) > jobId: 93953; workDir: /mnt/storage/scratch/hgugm_93947/21/0db74c4adfc8cf01b83e811c6cb162 Apr-09 13:17:43.643 [Task submitter] INFO nextflow.Session - [21/0db74c] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (UCB_THY) Apr-09 13:17:43.656 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) > jobId: 93954; workDir: /mnt/storage/scratch/hgugm_93947/c3/7880b13be409b600288e83ecd6e5c2 Apr-09 13:17:43.656 [Task submitter] INFO nextflow.Session - [c3/7880b1] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) Apr-09 13:17:58.440 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93950; id: 3; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca started: 1712661478434; exited: 2024-04-09T11:17:44.207782267Z; ] Apr-09 13:17:58.451 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1); work-dir=/mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca error [nextflow.exception.ProcessFailedException]: ProcessNFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)
terminated with an error exit status (1) Apr-09 13:17:58.474 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'Caused by: Process
NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)
terminated with an error exit status (1)Command executed:
function find_column_number { file=$1 column=$2
}
id_col=$(find_column_number genomic.anno.feature_metadata.tsv gene_id) symbol_col=$(find_column_number genomic.anno.feature_metadata.tsv gene_name) outfile=$(echo genomic.anno.feature_metadata.tsv | sed 's/(.)../\1/').chip
echo -e "Probe Set ID\tGene Symbol\tGene Title" > ${outfile}.tmp tail -n +2 genomic.anno.feature_metadata.tsv | awk -F'\t' -v id=$id_col -v symbol=$symbol_col '{print $id"\t"$symbol"\tNA"}' >> ${outfile}.tmp mv ${outfile}.tmp ${outfile}
cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP": bash: $(echo $(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')) END_VERSIONS
Command exit status: 1
Command output: (empty)
Work dir: /mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line Apr-09 13:17:58.491 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Apr-09 13:17:58.494 [main] DEBUG nextflow.Session - Session await > all processes finished Apr-09 13:17:58.506 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93951; id: 5; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_THY); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/9f/69878e624c65d509e991b42369590f started: 1712661478504; exited: 2024-04-09T11:17:44.326782687Z; ] Apr-09 13:17:58.519 [Actor Thread 3] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.017 s; external sort time: 0.001 s; total time: 0.018 s Apr-09 13:17:58.525 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93952; id: 6; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_UCB); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/a6/5e105b1fe42c43b373e3401cc10038 started: 1712661478525; exited: 2024-04-09T11:17:44.291782564Z; ] Apr-09 13:17:58.540 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/storage/scratch/hgugm_93947/collect-file/528b46773b4417d538eb709b5dafcdb3 Apr-09 13:17:58.544 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93953; id: 7; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (UCB_THY); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/21/0db74c4adfc8cf01b83e811c6cb162 started: 1712661478544; exited: 2024-04-09T11:17:44.291782564Z; ] Apr-09 13:17:58.552 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-10896104743810972899 Apr-09 13:17:58.554 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93954; id: 4; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/c3/7880b13be409b600288e83ecd6e5c2 started: 1712661478554; exited: 2024-04-09T11:17:45.329786229Z; ] Apr-09 13:17:58.574 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Apr-09 13:17:58.576 [main] DEBUG nextflow.Session - Session await > all barriers passed Apr-09 13:17:58.580 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Apr-09 13:17:58.615 [main] INFO nextflow.Nextflow - -[nf-core/differentialabundance] Pipeline completed with errors- Apr-09 13:17:58.619 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=6; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=27.1s; failedDuration=5ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=6 GB; ] Apr-09 13:17:58.619 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Apr-09 13:17:58.620 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Apr-09 13:17:59.237 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Apr-09 13:17:59.496 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Apr-09 13:17:59.496 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3' Apr-09 13:17:59.496 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation Apr-09 13:17:59.508 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Apr-09 13:17:59.509 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- GoodbyeSystem information
Nextflow: 23.10.1 Hardware: Workstation Executor: Slurm Container Image: singularity OS: RHEL 9.3 Version of nf-core/differentialabundance : 1.4.0