anikethjr
commented
2 years ago It took a few hours but it looks like the pipeline does make progress!
Closed anikethjr closed 2 years ago
anikethjr
commented
2 years ago It took a few hours but it looks like the pipeline does make progress!
l0ka
commented
2 years ago I'm experiencing a similar issue. It is affecting only 2 out of 412 RNA-seq samples. I run the pipeline on a HPC, using both qsub and an interactive node. It always quit after 7 steps. I tried to wait to see if the missing steps run successfully but there's no way, unfortunately. I'm using version 3.8:
nextflow run nf-core/rnaseq \
-r 3.8 \
-profile singularity \
--input ${samplesheet} \
--outdir ${out_dir} \
--genome GRCh38 \
-c $cfgexecutor > pbs (6), local (1)
[c8/d68284] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) [100%] 1 of 1 ✔
[5d/d8adc8] process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -
[f4/32d79b] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (GBM041) [100%] 1 of 1 ✔
[35/4d7c38] process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (GBM041) [100%] 1 of 1 ✔
[4e/eee04c] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED [100%] 1 of 1 ✔
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT -
[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED -
[- ] process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP -
[- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES -
[- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX -
[- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[- ] process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
[- ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP -
[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ -
[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION -
[- ] process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION -
[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED -
[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT -
[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON -
[d5/d201bf] process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔
[ff/9dabab] process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1) [100%] 1 of 1 ✔
-[nf-core/rnaseq] Pipeline completed successfully-
Completed at: 26-Aug-2022 10:05:46
Duration : 12m 3s
CPU hours : 0.2
Succeeded : 7Aug-26 09:53:38.044 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -r 3.8 -profile singularity --input /test/SAMPLE/samplesheet.csv --outdir /test/SAMPLE --genome GRCh38 -c rnaseq_GRCh38.conf
Aug-26 09:53:38.127 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.5
Aug-26 09:53:39.444 [main] DEBUG nextflow.scm.AssetManager - Git config: /test/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Aug-26 09:53:39.462 [main] DEBUG nextflow.scm.AssetManager - Git config: /test/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Aug-26 09:53:41.267 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /test/.nextflow/assets/nf-core/rnaseq/nextflow.config
Aug-26 09:53:41.296 [main] DEBUG nextflow.config.ConfigBuilder - User config file: rnaseq_GRCh38.conf
Aug-26 09:53:41.297 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /test/.nextflow/assets/nf-core/rnaseq/nextflow.config
Aug-26 09:53:41.297 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: rnaseq_GRCh38.conf
Aug-26 09:53:41.318 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Aug-26 09:53:41.705 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Aug-26 09:53:41.724 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-26 09:53:41.725 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-26 09:53:41.728 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-26 09:53:41.737 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Aug-26 09:53:42.192 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Aug-26 09:53:42.192 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager
Aug-26 09:53:43.383 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
Aug-26 09:53:43.454 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, mjolnir_globe, uppmax, abims, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, vsc_ugent, sage, cambridge, unibe_ibu, vai, podman, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, test_full, eddie, medair, azurebatch, bi, bigpurple, cedars, docker, gis, eva, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, imperial, maestro, aws_tower, binac]
Aug-26 09:53:43.512 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Aug-26 09:53:43.513 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/rnaseq` [zen_lovelace] DSL2 - revision: 6995330476 [3.8]
Aug-26 09:53:43.514 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/test/.nextflow/plugins; core-plugins: nf-amazon@1.7.2,nf-azure@0.13.2,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0
Aug-26 09:53:43.516 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-26 09:53:43.529 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-26 09:53:43.530 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-26 09:53:43.531 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-26 09:53:43.543 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Aug-26 09:53:43.632 [main] DEBUG nextflow.Session - Session uuid: 1ee7c3e7-69f7-4083-8a7e-5a54b5d6d828
Aug-26 09:53:43.632 [main] DEBUG nextflow.Session - Run name: zen_lovelace
Aug-26 09:53:43.632 [main] DEBUG nextflow.Session - Executor pool size: 20
Aug-26 09:53:43.674 [main] DEBUG nextflow.cli.CmdRun -
Version: 22.04.5 build 5708
Created: 15-07-2022 16:09 UTC (18:09 CEST)
System: Linux 3.10.0-1062.4.1.el7.x86_64
Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 18.0.1+10-24
Encoding: UTF-8 (UTF-8)
Process: 21461@g-04-c0249 [10.45.17.42]
CPUs: 20 - Mem: 80 GB (79.5 GB) - Swap: 16 GB (12.8 GB)
Aug-26 09:53:43.713 [main] DEBUG nextflow.Session - Work-dir: /test/SAMPLE/work [nfs]
Aug-26 09:53:43.743 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-26 09:53:43.759 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-26 09:53:43.878 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-26 09:53:43.903 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 21; maxThreads: 1000
Aug-26 09:53:44.046 [main] DEBUG nextflow.Session - Session start invoked
Aug-26 09:53:44.050 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /test/SAMPLE/pipeline_info/execution_trace_2022-08-26_09-53-42.txt
Aug-26 09:53:44.081 [main] DEBUG nextflow.Session - Using default localLib path: /test/.nextflow/assets/nf-core/rnaseq/lib
Aug-26 09:53:44.086 [main] DEBUG nextflow.Session - Adding to the classpath library: /test/.nextflow/assets/nf-core/rnaseq/lib
Aug-26 09:53:44.087 [main] DEBUG nextflow.Session - Adding to the classpath library: /test/.nextflow/assets/nf-core/rnaseq/lib/nfcore_external_java_deps.jar
Aug-26 09:53:45.006 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-26 09:53:45.302 [main] INFO nextflow.Nextflow -
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq v3.8[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
[0;34mrevision : [0;32m3.8[0m
[0;34mrunName : [0;32mzen_lovelace[0m
[0;34mcontainerEngine : [0;32msingularity[0m
[0;34mlaunchDir : [0;32m/test/SAMPLE[0m
[0;34mworkDir : [0;32m/test/SAMPLE/work[0m
[0;34mprojectDir : [0;32m/test/.nextflow/assets/nf-core/rnaseq[0m
[0;34muserName : [0;32maluloc[0m
[0;34mprofile : [0;32msingularity[0m
[0;34mconfigFiles : [0;32m/test/.nextflow/assets/nf-core/rnaseq/nextflow.config, rnaseq_GRCh38.conf[0m
[1mInput/output options[0m
[0;34minput : [0;32m/test/SAMPLE/samplesheet.csv[0m
[0;34moutdir : [0;32m/test/SAMPLE[0m
[1mRead filtering options[0m
[0;34mribo_database_manifest: [0;32m/GRCh38/rRNA_db.txt[0m
[1mReference genome options[0m
[0;34mgenome : [0;32mGRCh38[0m
[0;34mfasta : [0;32m/GRCh38/references/WholeGenomeFasta/genome.fa[0m
[0;34mgtf : [0;32m/GRCh38/references/genes.gtf[0m
[0;34mgene_bed : [0;32m/GRCh38/references/genes.bed[0m
[0;34mtranscript_fasta : [0;32m/GRCh38/transcripts.fa[0m
[0;34mstar_index : [0;32m/GRCh38/STARIndex/[0m
[0;34msalmon_index : [0;32m/GRCh38/salmon_index/[0m
[0;34mhisat2_build_memory : [0;32m180.GB[0m
[0;34mgencode : [0;32mtrue[0m
[0;34migenomes_base : [0;32m/GRCh38/igenomes/Homo_sapiens/NCBI/GRCh38/[0m
[0;34migenomes_ignore : [0;32mtrue[0m
[1mAlignment options[0m
[0;34mpseudo_aligner : [0;32msalmon[0m
[1mProcess skipping options[0m
[0;34mskip_biotype_qc : [0;32mtrue[0m
[1mMax job request options[0m
[0;34mmax_cpus : [0;32m10[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
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
-[2m----------------------------------------------------[0m-
Aug-26 09:53:46.356 [main] WARN nextflow.Nextflow - =============================================================================
'--transcript_fasta' parameter has been provided.
Make sure transcript names in this file match those in the GFF/GTF file.
Please see:
https://github.com/nf-core/rnaseq/issues/753
===================================================================================
Aug-26 09:53:54.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Aug-26 09:53:54.461 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Aug-26 09:53:54.482 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.482 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.490 [main] DEBUG nextflow.executor.Executor - [warm up] executor > pbs
Aug-26 09:53:54.501 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'pbs' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
Aug-26 09:53:54.510 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'pbs' > queue-stat-interval: 1m
Aug-26 09:53:54.631 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLESHEET_CHECK` matches process NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Aug-26 09:53:54.635 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.635 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Aug-26 09:53:54.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Aug-26 09:53:54.693 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.693 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.710 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Aug-26 09:53:54.711 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQC_UMITOOLS_TRIMGALORE:FASTQC` matches process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Aug-26 09:53:54.712 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.713 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Aug-26 09:53:54.723 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` matches process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Aug-26 09:53:54.726 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.726 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.754 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_TSV_FAIL_TRIMMED` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED
Aug-26 09:53:54.755 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-26 09:53:54.755 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-26 09:53:54.760 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Aug-26 09:53:54.765 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=20; memory=80 GB; capacity=20; pollInterval=100ms; dumpInterval=5m
Aug-26 09:53:54.780 [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
Aug-26 09:53:54.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ALIGN_STAR:STAR_ALIGN` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Aug-26 09:53:54.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Aug-26 09:53:54.782 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.782 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.794 [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_SAMTOOLS:SAMTOOLS_SORT
Aug-26 09:53:54.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
Aug-26 09:53:54.796 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.796 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.802 [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_SAMTOOLS:SAMTOOLS_INDEX
Aug-26 09:53:54.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
Aug-26 09:53:54.803 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.803 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.819 [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_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Aug-26 09:53:54.820 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Aug-26 09:53:54.820 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.821 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.835 [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_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Aug-26 09:53:54.836 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Aug-26 09:53:54.837 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.837 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.842 [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_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Aug-26 09:53:54.843 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Aug-26 09:53:54.843 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.843 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.857 [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
Aug-26 09:53:54.858 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Aug-26 09:53:54.859 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.859 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
Aug-26 09:53:54.872 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
Aug-26 09:53:54.873 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.873 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.880 [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_TXIMPORT
Aug-26 09:53:54.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
Aug-26 09:53:54.882 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.882 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.888 [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_SE_GENE
Aug-26 09:53:54.888 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE
Aug-26 09:53:54.889 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.889 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.894 [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_SE_GENE_LENGTH_SCALED
Aug-26 09:53:54.895 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Aug-26 09:53:54.895 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.895 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.899 [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_SE_GENE_SCALED
Aug-26 09:53:54.899 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED
Aug-26 09:53:54.900 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.900 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.903 [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_SE_TRANSCRIPT
Aug-26 09:53:54.903 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT
Aug-26 09:53:54.904 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.904 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
Aug-26 09:53:54.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DESEQ2_QC_STAR_SALMON` matches process NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
Aug-26 09:53:54.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.931 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_TSV_FAIL_MAPPED` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED
Aug-26 09:53:54.938 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-26 09:53:54.938 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-26 09:53:54.944 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,error_ignore` for process with name NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Aug-26 09:53:54.944 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches labels `process_medium,error_ignore` for process with name NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Aug-26 09:53:54.944 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PRESEQ_LCEXTRAP` matches process NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Aug-26 09:53:54.946 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.946 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.956 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
Aug-26 09:53:54.956 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
Aug-26 09:53:54.957 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.957 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.973 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
Aug-26 09:53:54.974 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
Aug-26 09:53:54.974 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.975 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Aug-26 09:53:54.991 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Aug-26 09:53:54.991 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.991 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:54.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Aug-26 09:53:54.999 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Aug-26 09:53:54.999 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:54.999 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Aug-26 09:53:55.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Aug-26 09:53:55.010 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.010 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.023 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Aug-26 09:53:55.023 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:STRINGTIE_STRINGTIE` matches process NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Aug-26 09:53:55.024 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.024 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.032 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Aug-26 09:53:55.032 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV` matches process NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Aug-26 09:53:55.033 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.033 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.043 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP
Aug-26 09:53:55.043 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP
Aug-26 09:53:55.044 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.044 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.052 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Aug-26 09:53:55.052 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Aug-26 09:53:55.053 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.053 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP
Aug-26 09:53:55.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP
Aug-26 09:53:55.063 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.063 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Aug-26 09:53:55.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Aug-26 09:53:55.070 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.081 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ
Aug-26 09:53:55.082 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:QUALIMAP_RNASEQ` matches process NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ
Aug-26 09:53:55.082 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.082 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.092 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_RNASEQ:RNASEQ:DUPRADAR
Aug-26 09:53:55.093 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUPRADAR` matches process NFCORE_RNASEQ:RNASEQ:DUPRADAR
Aug-26 09:53:55.094 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.094 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.103 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT
Aug-26 09:53:55.109 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_BAMSTAT` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT
Aug-26 09:53:55.110 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.110 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.131 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE
Aug-26 09:53:55.132 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_INNERDISTANCE` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE
Aug-26 09:53:55.135 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.135 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.142 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT
Aug-26 09:53:55.145 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_INFEREXPERIMENT` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT
Aug-26 09:53:55.145 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.145 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.156 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION
Aug-26 09:53:55.157 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_JUNCTIONANNOTATION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION
Aug-26 09:53:55.158 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.158 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.167 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION
Aug-26 09:53:55.168 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_JUNCTIONSATURATION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION
Aug-26 09:53:55.169 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.169 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
Aug-26 09:53:55.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_READDISTRIBUTION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
Aug-26 09:53:55.177 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.177 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.187 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION
Aug-26 09:53:55.187 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:RSEQC:RSEQC_READDUPLICATION` matches process NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION
Aug-26 09:53:55.188 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.201 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_TSV_STRAND_CHECK` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK
Aug-26 09:53:55.208 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: local
Aug-26 09:53:55.208 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Aug-26 09:53:55.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT
Aug-26 09:53:55.213 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.213 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.218 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE
Aug-26 09:53:55.219 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.219 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.227 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT
Aug-26 09:53:55.228 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.228 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.235 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE
Aug-26 09:53:55.236 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.236 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.240 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Aug-26 09:53:55.241 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.241 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.247 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED
Aug-26 09:53:55.248 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.248 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.251 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT
Aug-26 09:53:55.252 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.252 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.256 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON
Aug-26 09:53:55.256 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.257 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.291 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Aug-26 09:53:55.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Aug-26 09:53:55.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.353 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MULTIQC
Aug-26 09:53:55.353 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC
Aug-26 09:53:55.354 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: pbs
Aug-26 09:53:55.354 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'pbs'
Aug-26 09:53:55.373 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: DUPRADAR, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION, RSEM_PREPAREREFERENCE, CAT_ADDITIONAL_FASTA, NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON, DESEQ2_QC_SALMON, RSEQC_READDISTRIBUTION, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX, NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS, GFFREAD, RSEQC_JUNCTIONSATURATION, RSEQC_READDUPLICATION, NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK, NFCORE_RNASEQ:RNASEQ:CAT_FASTQ, CAT_FASTQ, GUNZIP, NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES, SAMTOOLS_STATS, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT, GUNZIP_GFF, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG, HISAT2_BUILD, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT, TRIMGALORE, BEDTOOLS_GENOMECOV, SALMON_TX2GENE, SORTMERNA, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP, NFCORE_RNASEQ:RNASEQ:DUPRADAR, UMITOOLS_PREPAREFORRSEM, SAMTOOLS_INDEX, NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV, PRESEQ_LCEXTRAP, FASTQC, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG, UCSC_BEDCLIP, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT, UCSC_BEDGRAPHTOBIGWIG, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, MULTIQC, GTF2BED, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE, GUNZIP_GTF, SALMON_INDEX, UMITOOLS_EXTRACT, UNTAR_HISAT2_INDEX, NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE, UNTAR_BBSPLIT_INDEX, SAMTOOLS_FLAGSTAT, SAMPLESHEET_CHECK, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED, DESEQ2_QC_RSEM, GUNZIP_FASTA, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES, RSEM_PREPAREREFERENCE_GENOME, UNTAR_RSEM_INDEX, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION, SALMON_SE_GENE_SCALED, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT, SALMON_QUANT, MULTIQC_CUSTOM_BIOTYPE, DESEQ2_QC_STAR_SALMON, RSEM_CALCULATEEXPRESSION, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT, GUNZIP_TRANSCRIPT_FASTA, MAKE_TRANSCRIPTS_FASTA, NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC, MULTIQC_TSV_FAIL_MAPPED, SALMON_SE_GENE_LENGTH_SCALED, DESEQ2_QC, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX, PICARD_MARKDUPLICATES, RSEM_MERGE_COUNTS, SALMON_SE_GENE, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE, UNTAR, NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED, SALMON_SUMMARIZEDEXPERIMENT, RSEQC_INNERDISTANCE, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE, GTF_GENE_FILTER, RSEQC_BAMSTAT, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT, NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON, QUALIMAP_RNASEQ, RSEQC_INFEREXPERIMENT, NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE, STAR_ALIGN, MULTIQC_TSV_STRAND_CHECK, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, RSEQC_JUNCTIONANNOTATION, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT, SALMON_TXIMPORT, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE, CUSTOM_GETCHROMSIZES, NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP, SAMTOOLS_SORT, MULTIQC_TSV_FAIL_TRIMMED, SUBREAD_FEATURECOUNTS, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, GUNZIP_GENE_BED, UNTAR_STAR_INDEX, UNTAR_SALMON_INDEX, HISAT2_ALIGN, NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT, BBMAP_BBSPLIT, NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED, RSEQC_TIN, MULTIQC_TSV_FROM_LIST, NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ, UMITOOLS_DEDUP, STRINGTIE_STRINGTIE, HISAT2_EXTRACTSPLICESITES, SALMON_SE_TRANSCRIPT, NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE, NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED, NFCORE_RNASEQ:RNASEQ:MULTIQC, SAMTOOLS_IDXSTATS, NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP, CUSTOM_DUMPSOFTWAREVERSIONS, STAR_GENOMEGENERATE, GUNZIP_ADDITIONAL_FASTA, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION, NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED, NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
Aug-26 09:53:55.382 [main] DEBUG nextflow.Session - Ignite dataflow network (133)
Aug-26 09:53:55.382 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES
Aug-26 09:53:55.384 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
Aug-26 09:53:55.384 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ
Aug-26 09:53:55.384 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC
Aug-26 09:53:55.384 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE
Aug-26 09:53:55.384 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED
Aug-26 09:53:55.384 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
Aug-26 09:53:55.388 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
Aug-26 09:53:55.389 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED
Aug-26 09:53:55.390 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
Aug-26 09:53:55.391 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
Aug-26 09:53:55.391 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
Aug-26 09:53:55.393 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
Aug-26 09:53:55.393 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DUPRADAR
Aug-26 09:53:55.394 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT
Aug-26 09:53:55.395 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE
Aug-26 09:53:55.395 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT
Aug-26 09:53:55.395 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION
Aug-26 09:53:55.395 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION
Aug-26 09:53:55.398 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
Aug-26 09:53:55.399 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC
Aug-26 09:53:55.399 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Aug-26 09:53:55.399 [main] DEBUG nextflow.Session - Session await
Aug-26 09:53:55.527 [Actor Thread 2] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.9--1; path=/dbs/singularity_cachedir/3.8.1/depot.galaxyproject.org-singularity-python-3.9--1.img
Aug-26 09:53:55.528 [Actor Thread 24] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0; path=/dbs/singularity_cachedir/3.8.1/depot.galaxyproject.org-singularity-samtools-1.15.1--h1170115_0.img
Aug-26 09:53:55.546 [Actor Thread 23] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.024 s; total time: 0.024 s
Aug-26 09:53:55.555 [Actor Thread 10] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /test/.nextflow/assets/nf-core/rnaseq/bin/check_samplesheet.py
Aug-26 09:53:55.557 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /scratch/37451830/329b062983f07cb1e1c82cf625cbcf86.collect-file
Aug-26 09:53:55.573 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/37451830/nxf-506801252056431605
Aug-26 09:53:55.752 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) > jobId: 37451872; workDir: /test/SAMPLE/work/5d/d8adc8e9214030243ff2c7b9fddf41
Aug-26 09:53:55.752 [Task submitter] INFO nextflow.Session - [5d/d8adc8] Submitted process > NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)
Aug-26 09:53:55.804 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) > jobId: 37451873; workDir: /test/SAMPLE/work/c8/d682846b11912d1242f5db6d9d8859
Aug-26 09:53:55.805 [Task submitter] INFO nextflow.Session - [c8/d68284] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa)
Aug-26 09:56:29.557 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 37451872; id: 2; name: NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /test/SAMPLE/work/5d/d8adc8e9214030243ff2c7b9fddf41 started: 1661500589545; exited: 2022-08-26T07:56:14.016725Z; ]
Aug-26 09:56:29.597 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=4; maxSize=4; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-26 09:56:29.613 [Actor Thread 19] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0; path=/dbs/singularity_cachedir/3.8.1/depot.galaxyproject.org-singularity-trim-galore-0.6.7--hdfd78af_0.img
Aug-26 09:56:29.615 [Actor Thread 4] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0; path=/dbs/singularity_cachedir/3.8.1/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img
Aug-26 09:56:29.879 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAMPLE) > jobId: 37451900; workDir: /test/SAMPLE/work/f4/32d79b3d1d8d37c44448f42ca55297
Aug-26 09:56:29.879 [Task submitter] INFO nextflow.Session - [f4/32d79b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAMPLE)
Aug-26 09:56:29.930 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAMPLE) > jobId: 37451901; workDir: /test/SAMPLE/work/35/4d7c3841f8733288bbe121c66586e7
Aug-26 09:56:29.930 [Task submitter] INFO nextflow.Session - [35/4d7c38] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAMPLE)
Aug-26 09:56:59.549 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 37451873; id: 1; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /test/SAMPLE/work/c8/d682846b11912d1242f5db6d9d8859 started: 1661500619541; exited: 2022-08-26T07:56:23.756097Z; ]
Aug-26 09:58:54.972 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED
status=ACTIVE
port 0: (value) OPEN ; channel: tsv_data
port 1: (value) bound ; channel: header
port 2: (value) bound ; channel: out_prefix
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: index
port 2: (value) bound ; channel: gtf
port 3: (value) bound ; channel: star_ignore_sjdbgtf
port 4: (value) bound ; channel: seq_platform
port 5: (value) bound ; channel: seq_center
port 6: (value) bound ; channel: is_aws_igenome
port 7: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: fasta
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_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_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) bound ; channel: gtf
port 3: (value) bound ; 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:SALMON_TX2GENE
status=ACTIVE
port 0: (value) OPEN ; channel: salmon/*
port 1: (value) bound ; channel: gtf
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT
status=ACTIVE
port 0: (value) OPEN ; channel: salmon/*
port 1: (value) OPEN ; channel: tx2gene
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) bound ; channel: pca_header_multiqc
port 2: (value) bound ; channel: clustering_header_multiqc
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED
status=ACTIVE
port 0: (value) OPEN ; channel: tsv_data
port 1: (value) bound ; channel: header
port 2: (value) bound ; channel: out_prefix
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: fasta
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_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) bound ; channel: gtf
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: sizes
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: sizes
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: sizes
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: sizes
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: gtf
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:DUPRADAR
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: gtf
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: bed
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: bed
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: bed
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: bed
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: bed
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK
status=ACTIVE
port 0: (value) OPEN ; channel: tsv_data
port 1: (value) bound ; channel: header
port 2: (value) bound ; channel: out_prefix
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: index
port 2: (value) bound ; channel: gtf
port 3: (value) bound ; 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_SALMON:SALMON_TX2GENE
status=ACTIVE
port 0: (value) OPEN ; channel: salmon/*
port 1: (value) bound ; channel: gtf
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT
status=ACTIVE
port 0: (value) OPEN ; channel: salmon/*
port 1: (value) OPEN ; channel: tx2gene
port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) OPEN ; channel: tpm
port 2: (value) OPEN ; channel: tx2gene
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON
status=ACTIVE
port 0: (value) OPEN ; channel: counts
port 1: (value) bound ; channel: pca_header_multiqc
port 2: (value) bound ; channel: clustering_header_multiqc
port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS
status=ACTIVE
port 0: (queue) OPEN ; channel: versions
port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC
status=ACTIVE
port 0: (value) bound ; channel: multiqc_config
port 1: (value) bound ; channel: multiqc_custom_config
port 2: (value) OPEN ; channel: software_versions
port 3: (queue) OPEN ; channel: workflow_summary
port 4: (value) OPEN ; channel: fail_trimming_summary
port 5: (value) OPEN ; channel: fail_mapping_summary
port 6: (value) OPEN ; channel: fail_strand_check
port 7: (value) OPEN ; channel: fastqc/*
port 8: (value) OPEN ; channel: trimgalore/fastqc/*
port 9: (value) OPEN ; channel: trimgalore/*
port 10: (value) bound ; channel: sortmerna/*
port 11: (value) OPEN ; channel: star/*
port 12: (value) bound ; channel: hisat2/*
port 13: (value) bound ; channel: rsem/*
port 14: (value) OPEN ; channel: salmon/*
port 15: (value) OPEN ; channel: samtools/stats/*
port 16: (value) OPEN ; channel: samtools/flagstat/*
port 17: (value) OPEN ; channel: samtools/idxstats/*
port 18: (value) OPEN ; channel: picard/markduplicates/*
port 19: (value) bound ; channel: featurecounts/*
port 20: (value) OPEN ; channel: deseq2/aligner/*
port 21: (value) OPEN ; channel: deseq2/aligner/*
port 22: (value) OPEN ; channel: deseq2/pseudoaligner/*
port 23: (value) OPEN ; channel: deseq2/pseudoaligner/*
port 24: (value) OPEN ; channel: preseq/*
port 25: (value) OPEN ; channel: qualimap/*
port 26: (value) OPEN ; channel: dupradar/*
port 27: (value) OPEN ; channel: rseqc/bam_stat/*
port 28: (value) OPEN ; channel: rseqc/infer_experiment/*
port 29: (value) OPEN ; channel: rseqc/inner_distance/*
port 30: (value) OPEN ; channel: rseqc/junction_annotation/*
port 31: (value) OPEN ; channel: rseqc/junction_saturation/*
port 32: (value) OPEN ; channel: rseqc/read_distribution/*
port 33: (value) OPEN ; channel: rseqc/read_duplication/*
port 34: (value) bound ; channel: rseqc/tin/*
port 35: (cntrl) - ; channel: $
Aug-26 09:58:59.565 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[jobId: 37451900; id: 4; name: NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAMPLE); status: SUBMITTED; exit: -; error: -; workDir: /test/SAMPLE/work/f4/32d79b3d1d8d37c44448f42ca55297 started: -; exited: -; ]
~> TaskHandler[jobId: 37451901; id: 3; name: NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAMPLE); status: SUBMITTED; exit: -; error: -; workDir: /test/SAMPLE/work/35/4d7c3841f8733288bbe121c66586e7 started: -; exited: -; ]
Aug-26 09:59:29.577 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 37451900; id: 4; name: NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAMPLE); status: COMPLETED; exit: 0; error: -; workDir: /test/SAMPLE/work/f4/32d79b3d1d8d37c44448f42ca55297 started: 1661500739566; exited: 2022-08-26T07:59:08.716672Z; ]
Aug-26 09:59:29.607 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 37451901; id: 3; name: NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAMPLE); status: COMPLETED; exit: 0; error: -; workDir: /test/SAMPLE/work/35/4d7c3841f8733288bbe121c66586e7 started: 1661500739580; exited: 2022-08-26T07:59:11.26673Z; ]
Aug-26 09:59:29.747 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Aug-26 09:59:29.779 [Actor Thread 40] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 4; slices: 1; internal sort time: 0.009 s; external sort time: 0.001 s; total time: 0.01 s
Aug-26 09:59:29.783 [Task submitter] INFO nextflow.Session - [4e/eee04c] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED
Aug-26 09:59:29.790 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_TRIMMED; status: COMPLETED; exit: -; error: -; workDir: /test/SAMPLE/work/4e/eee04c7de2d9064333ac902203fe1a]
Aug-26 09:59:29.800 [Actor Thread 40] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /scratch/37451830/046b6ca717a9b8c0a7126d980b08b6e0.collect-file
Aug-26 09:59:29.801 [Actor Thread 40] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/37451830/nxf-6759088701034148847
Aug-26 09:59:29.858 [Actor Thread 35] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0; path=/dbs/singularity_cachedir/3.8.1/depot.galaxyproject.org-singularity-multiqc-1.11--pyhdfd78af_0.img
Aug-26 09:59:29.935 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1) > jobId: 37451994; workDir: /test/SAMPLE/work/d5/d201bf64babc5cf4a948edf4bf4037
Aug-26 09:59:29.935 [Task submitter] INFO nextflow.Session - [d5/d201bf] Submitted process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1)
Aug-26 10:03:09.598 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 37451994; id: 6; name: NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS (1); status: COMPLETED; exit: 0; error: -; workDir: /test/SAMPLE/work/d5/d201bf64babc5cf4a948edf4bf4037 started: 1661500989588; exited: 2022-08-26T08:02:53.567749Z; ]
Aug-26 10:03:09.652 [Actor Thread 24] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /test/.nextflow/assets/nf-core/rnaseq/assets/multiqc_config.yml
Aug-26 10:03:09.721 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [PBS] submitted process NFCORE_RNASEQ:RNASEQ:MULTIQC (1) > jobId: 37452165; workDir: /test/SAMPLE/work/ff/9dabab6e2ee78c0aa70c443bd139a8
Aug-26 10:03:09.721 [Task submitter] INFO nextflow.Session - [ff/9dabab] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
Aug-26 10:03:55.032 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
[operator] toList
Aug-26 10:03:59.594 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor pbs > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[jobId: 37452165; id: 7; name: NFCORE_RNASEQ:RNASEQ:MULTIQC (1); status: SUBMITTED; exit: -; error: -; workDir: /test/SAMPLE/work/ff/9dabab6e2ee78c0aa70c443bd139a8 started: -; exited: -; ]
Aug-26 10:05:44.614 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 37452165; id: 7; name: NFCORE_RNASEQ:RNASEQ:MULTIQC (1); status: COMPLETED; exit: 0; error: -; workDir: /test/SAMPLE/work/ff/9dabab6e2ee78c0aa70c443bd139a8 started: 1661501114763; exited: 2022-08-26T08:05:30.657464Z; ]
Aug-26 10:05:44.648 [main] DEBUG nextflow.Session - Session await > all process finished
Aug-26 10:05:44.748 [main] DEBUG nextflow.Session - Session await > all barriers passed
Aug-26 10:05:44.754 [main] INFO nextflow.Nextflow - -[0;35m[nf-core/rnaseq][0;32m Pipeline completed successfully[0m-
Aug-26 10:05:45.606 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=7; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=11m 3s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=16; peakMemory=108 GB; ]
Aug-26 10:05:45.606 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file
Aug-26 10:05:45.608 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report
Aug-26 10:05:45.638 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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Aug-26 10:05:46.285 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline
Aug-26 10:05:46.760 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Aug-26 10:05:46.798 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- GoodbyeNextflow version: 22.04.5
Hardware: HPC
Executor: pbs
Container engine: Singularity
OS: CentOS Linux release 7.8.2003 (Core)
Version of nf-core/rnaseq: 3.8Trying to re-run the pipeline with the -resume option doesn't do anything.
l0ka
commented
2 years ago Within the work dir I found a file called fail_trimmed_samples_mqc.tsv. Here's the content:
Sample Reads after trimming
SAMPLE 0Can this be the source of the issue?
l0ka
commented
2 years ago So, the FASTQs are the issue: after trimming there's nothing left.
drpatelh
commented
2 years ago Oooof 🤦🏽 Thanks for de-bugging @l0ka. I have created an issue for this so we can add the functionality to automatically exclude these samples in future releases https://github.com/nf-core/rnaseq/issues/862#issue-1352053147
l0ka
commented
2 years ago Thank you :)
Description of the bug
I am trying to process a dataset that consists of about 100 fastq files using the pipeline. I am running the pipeline on a HPC which is managed using Slurm. The first few stages of the pipeline finish successfully. However, once the
NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQCandNFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALOREstages are completed, none of the other stages spawn Slurm jobs.When I look at the
.nextflow.logfile, I see that the script is polling to see if the other stages are done but there seem to be no actual jobs running them. This problem is similar to https://github.com/nextflow-io/nextflow/issues/981. I would greatly appreciate your help with this!Command used and terminal output
Relevant files
Apr-30 03:51:27.473 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active: [process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: index port 2: (value) bound ; channel: gtf port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: fasta port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_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_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) bound ; channel: gtf port 3: (value) bound ; 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:SALMON_TX2GENE status=ACTIVE port 0: (value) OPEN ; channel: salmon/* port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT status=ACTIVE port 0: (value) OPEN ; channel: salmon/* port 1: (value) OPEN ; channel: tx2gene port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (value) OPEN ; channel: tpm port 2: (value) OPEN ; channel: tx2gene port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (value) OPEN ; channel: tpm port 2: (value) OPEN ; channel: tx2gene port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (value) OPEN ; channel: tpm port 2: (value) OPEN ; channel: tx2gene port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (value) OPEN ; channel: tpm port 2: (value) OPEN ; channel: tx2gene port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (value) bound ; channel: pca_header_multiqc port 2: (value) bound ; channel: clustering_header_multiqc port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_FAIL_MAPPED status=ACTIVE port 0: (value) OPEN ; channel: tsv_data port 1: (value) bound ; channel: header port 2: (value) bound ; channel: out_prefix port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:PRESEQ_LCEXTRAP status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: fasta port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:STRINGTIE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: header port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDCLIP status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: sizes port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: sizes port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDCLIP status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: sizes port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:BEDGRAPH_TO_BIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: sizes port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:DUPRADAR status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: gtf port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_BAMSTAT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INNERDISTANCE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: bed port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: bed port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: bed port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: bed port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDISTRIBUTION status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: bed port 2: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:RSEQC:RSEQC_READDUPLICATION status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC_TSV_STRAND_CHECK status=ACTIVE port 0: (value) OPEN ; channel: tsv_data port 1: (value) bound ; channel: header port 2: (value) bound ; channel: out_prefix port 3: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS status=ACTIVE port 0: (queue) OPEN ; channel: versions port 1: (cntrl) - ; channel: $
[process] NFCORE_RNASEQ:RNASEQ:MULTIQC status=ACTIVE port 0: (value) bound ; channel: multiqc_config port 1: (value) bound ; channel: multiqc_custom_config port 2: (value) OPEN ; channel: software_versions port 3: (queue) OPEN ; channel: workflow_summary port 4: (value) OPEN ; channel: fail_mapping_summary port 5: (value) OPEN ; channel: fail_strand_check port 6: (value) bound ; channel: fastqc/ port 7: (value) bound ; channel: trimgalore/fastqc/ port 8: (value) bound ; channel: trimgalore/ port 9: (value) bound ; channel: sortmerna/ port 10: (value) OPEN ; channel: star/ port 11: (value) bound ; channel: hisat2/ port 12: (value) bound ; channel: rsem/ port 13: (value) bound ; channel: salmon/ port 14: (value) OPEN ; channel: samtools/stats/ port 15: (value) OPEN ; channel: samtools/flagstat/ port 16: (value) OPEN ; channel: samtools/idxstats/ port 17: (value) OPEN ; channel: picard/markduplicates/ port 18: (value) OPEN ; channel: featurecounts/ port 19: (value) OPEN ; channel: deseq2/aligner/ port 20: (value) OPEN ; channel: deseq2/aligner/ port 21: (value) bound ; channel: deseq2/pseudoaligner/ port 22: (value) bound ; channel: deseq2/pseudoaligner/ port 23: (value) OPEN ; channel: preseq/ port 24: (value) OPEN ; channel: qualimap/ port 25: (value) OPEN ; channel: dupradar/ port 26: (value) OPEN ; channel: rseqc/bam_stat/ port 27: (value) OPEN ; channel: rseqc/infer_experiment/ port 28: (value) OPEN ; channel: rseqc/inner_distance/ port 29: (value) OPEN ; channel: rseqc/junction_annotation/ port 30: (value) OPEN ; channel: rseqc/junction_saturation/ port 31: (value) OPEN ; channel: rseqc/read_distribution/ port 32: (value) OPEN ; channel: rseqc/read_duplication/ port 33: (value) bound ; channel: rseqc/tin/ port 34: (cntrl) - ; channel: $
System information
Nextflow version: 22.04.0 Hardware: HPC Executor: slurm Container engine: Singularity OS: CentOS Linux Version of nf-core/rnaseq: 3.6