May-03 22:25:40.663 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -profile test,docker --outdir test_run -r 3.14.0 May-03 22:25:40.695 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 May-03 22:25:40.703 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/arriyaz/.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 May-03 22:25:40.706 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-03 22:25:40.707 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-03 22:25:40.708 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-03 22:25:40.711 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-03 22:25:40.717 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/arriyaz/.nextflow/scm May-03 22:25:41.088 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git May-03 22:25:41.096 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] May-03 22:25:41.099 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git May-03 22:25:41.589 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/nextflow.config May-03 22:25:41.589 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/nextflow.config May-03 22:25:41.594 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` May-03 22:25:42.160 [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, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, test_full_gcp, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, test_full_aws, ebi_codon_slurm, ebc, 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, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, test_full_azure, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, test_cache, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] May-03 22:25:42.187 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion May-03 22:25:42.187 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/rnaseq` [berserk_curie] DSL2 - revision: b89fac3265 [3.14.0] May-03 22:25:42.187 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3] May-03 22:25:42.187 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-03 22:25:42.187 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3] May-03 22:25:42.187 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3 May-03 22:25:42.190 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved May-03 22:25:42.190 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3' May-03 22:25:42.193 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3 May-03 22:25:42.195 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/arriyaz/.nextflow/secrets/store.json May-03 22:25:42.196 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@26270b77] - activable => nextflow.secret.LocalSecretsProvider@26270b77 May-03 22:25:42.217 [main] DEBUG nextflow.Session - Session UUID: b32e4ed8-a816-496c-8c79-d7c3ec5f758c May-03 22:25:42.217 [main] DEBUG nextflow.Session - Run name: berserk_curie May-03 22:25:42.218 [main] DEBUG nextflow.Session - Executor pool size: 32 May-03 22:25:42.220 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null May-03 22:25:42.228 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.1 build 5891 Created: 12-01-2024 22:01 UTC (17:01 EDT) System: Linux 5.15.0-105-generic Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 21-internal-adhoc.conda.src Encoding: UTF-8 (ANSI_X3.4-1968) Process: 67423@Precision-3660 [127.0.1.1] CPUs: 32 - Mem: 31 GB (12.2 GB) - Swap: 30.5 GB (30.5 GB) - Virtual threads ON May-03 22:25:42.233 [main] DEBUG nextflow.Session - Work-dir: /home/arriyaz/temp/nextflow-practice/work [ext2/ext3] May-03 22:25:42.240 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-03 22:25:42.245 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-03 22:25:42.277 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-03 22:25:42.281 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool May-03 22:25:42.319 [main] DEBUG nextflow.Session - Session start May-03 22:25:42.321 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/arriyaz/temp/nextflow-practice/test_run/pipeline_info/execution_trace_2024-05-03_22-25-41.txt May-03 22:25:42.325 [main] DEBUG nextflow.Session - Using default localLib path: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/lib May-03 22:25:42.326 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/lib May-03 22:25:42.326 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/lib/nfcore_external_java_deps.jar May-03 22:25:42.514 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-03 22:25:42.520 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp]; plugin Id: nf-validation May-03 22:25:42.528 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation May-03 22:25:42.959 [main] DEBUG n.validation.DirectoryPathValidator - S3 paths are not supported by 'DirectoryPathValidator': 's3://ngi-igenomes/igenomes' May-03 22:25:43.040 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' with '/home/arriyaz/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json' May-03 22:25:44.563 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' with '/home/arriyaz/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json' May-03 22:25:44.564 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation May-03 22:25:44.871 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap, fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation May-03 22:25:44.879 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/rnaseq v3.14.0-gb89fac3 ------------------------------------------------------ Core Nextflow options revision : 3.14.0 runName : berserk_curie containerEngine : docker launchDir : /home/arriyaz/temp/nextflow-practice workDir : /home/arriyaz/temp/nextflow-practice/work projectDir : /home/arriyaz/.nextflow/assets/nf-core/rnaseq userName : arriyaz profile : test,docker configFiles :  Input/output options input : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv outdir : test_run Reference genome options fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genome.fasta gtf : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz gff : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes.gff.gz transcript_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/transcriptome.fasta additional_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz hisat2_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/hisat2.tar.gz rsem_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/rsem.tar.gz salmon_index : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz Read filtering options bbsplit_fasta_list : https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/bbsplit_fasta_list.txt UMI options umitools_bc_pattern : NNNN Alignment options pseudo_aligner : salmon min_mapped_reads : 5 Process skipping options skip_bbsplit : false Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function Max job request options max_cpus : 2 max_memory : 6.GB max_time : 6.h !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/rnaseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.1400710 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md May-03 22:25:44.881 [main] WARN nextflow.Nextflow - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Both '--gtf' and '--gff' parameters have been provided. Using GTF file as priority. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ May-03 22:25:44.881 [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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ May-03 22:25:47.436 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF May-03 22:25:47.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF May-03 22:25:47.440 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.440 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.442 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-03 22:25:47.446 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=31 GB; capacity=32; pollInterval=100ms; dumpInterval=5m May-03 22:25:47.447 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) May-03 22:25:47.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF_FILTER` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER May-03 22:25:47.483 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.483 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA May-03 22:25:47.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA May-03 22:25:47.485 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.485 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA May-03 22:25:47.488 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.488 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED May-03 22:25:47.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF2BED` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED May-03 22:25:47.491 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.491 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES May-03 22:25:47.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES May-03 22:25:47.494 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.494 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.505 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high,error_retry` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-03 22:25:47.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_high,error_retry` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-03 22:25:47.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_BBSPLIT` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-03 22:25:47.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:PREPARE_GENOME:BBMAP_BBSPLIT` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-03 22:25:47.507 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.507 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.510 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE May-03 22:25:47.510 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE May-03 22:25:47.510 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.510 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-03 22:25:47.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-03 22:25:47.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD` matches process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-03 22:25:47.514 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:47.514 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:47.518 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' with '/home/arriyaz/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json' May-03 22:25:48.116 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' with '/home/arriyaz/.nextflow/assets/nf-core/rnaseq/assets/schema_input.json' May-03 22:25:48.158 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:CAT_FASTQ May-03 22:25:48.158 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_RNASEQ:RNASEQ:CAT_FASTQ May-03 22:25:48.158 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.158 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC May-03 22:25:48.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC May-03 22:25:48.164 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.164 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.166 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE May-03 22:25:48.166 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE May-03 22:25:48.167 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.167 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.174 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high,error_retry` for process with name NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-03 22:25:48.174 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_high,error_retry` for process with name NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-03 22:25:48.174 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_BBSPLIT` matches process NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-03 22:25:48.175 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.175 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.182 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE May-03 22:25:48.182 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_SUBSAMPLE` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE May-03 22:25:48.182 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.182 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT May-03 22:25:48.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT May-03 22:25:48.185 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.185 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.191 [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 May-03 22:25:48.191 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN May-03 22:25:48.192 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.192 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.195 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT May-03 22:25:48.195 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT May-03 22:25:48.195 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.195 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.197 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX May-03 22:25:48.198 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX May-03 22:25:48.198 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.198 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.201 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-03 22:25:48.201 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-03 22:25:48.202 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.202 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.203 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-03 22:25:48.204 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-03 22:25:48.204 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.204 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.205 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-03 22:25:48.206 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-03 22:25:48.206 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.206 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.209 [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 May-03 22:25:48.209 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT May-03 22:25:48.209 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.209 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE May-03 22:25:48.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:TX2GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE May-03 22:25:48.212 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.212 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.214 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT May-03 22:25:48.214 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:TXIMPORT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT May-03 22:25:48.214 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.214 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.216 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE May-03 22:25:48.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE May-03 22:25:48.217 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.218 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED May-03 22:25:48.218 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED May-03 22:25:48.219 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.219 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.219 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED May-03 22:25:48.220 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED May-03 22:25:48.220 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.220 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.221 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT May-03 22:25:48.221 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT May-03 22:25:48.221 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.221 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.223 [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 May-03 22:25:48.223 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DESEQ2_QC_STAR_SALMON` matches process NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON May-03 22:25:48.223 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.223 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.230 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES May-03 22:25:48.230 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES May-03 22:25:48.231 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.231 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.233 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX May-03 22:25:48.233 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX May-03 22:25:48.234 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.234 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.237 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-03 22:25:48.237 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-03 22:25:48.237 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.237 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.239 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-03 22:25:48.239 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-03 22:25:48.239 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.239 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.241 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-03 22:25:48.241 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-03 22:25:48.241 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.241 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.244 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE May-03 22:25:48.244 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:STRINGTIE_STRINGTIE` matches process NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE May-03 22:25:48.244 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.254 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS May-03 22:25:48.254 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SUBREAD_FEATURECOUNTS` matches process NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS May-03 22:25:48.254 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.255 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.257 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_CUSTOM_BIOTYPE` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE May-03 22:25:48.257 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.257 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.259 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV May-03 22:25:48.259 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV` matches process NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV May-03 22:25:48.260 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.260 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.262 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP May-03 22:25:48.262 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP May-03 22:25:48.262 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.262 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG May-03 22:25:48.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG May-03 22:25:48.264 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.264 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.266 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP May-03 22:25:48.266 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP May-03 22:25:48.266 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.266 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.267 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG May-03 22:25:48.268 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG May-03 22:25:48.268 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.268 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.271 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ May-03 22:25:48.271 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:QUALIMAP_RNASEQ` matches process NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ May-03 22:25:48.271 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.271 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.273 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_RNASEQ:RNASEQ:DUPRADAR May-03 22:25:48.273 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DUPRADAR` matches process NFCORE_RNASEQ:RNASEQ:DUPRADAR May-03 22:25:48.273 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.273 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.276 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT May-03 22:25:48.276 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_BAMSTAT` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT May-03 22:25:48.277 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.277 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.279 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE May-03 22:25:48.279 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_INNERDISTANCE` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE May-03 22:25:48.279 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.279 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.281 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT May-03 22:25:48.282 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT May-03 22:25:48.282 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.282 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.284 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION May-03 22:25:48.284 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION May-03 22:25:48.285 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.285 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.287 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION May-03 22:25:48.287 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION May-03 22:25:48.287 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.287 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.289 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION May-03 22:25:48.289 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_READDISTRIBUTION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION May-03 22:25:48.290 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.290 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION May-03 22:25:48.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_READDUPLICATION` matches process NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION May-03 22:25:48.292 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.292 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.296 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT May-03 22:25:48.297 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT May-03 22:25:48.297 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.297 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.299 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE May-03 22:25:48.299 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE May-03 22:25:48.299 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.299 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.301 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT May-03 22:25:48.301 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT May-03 22:25:48.301 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.301 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.303 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE May-03 22:25:48.303 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE May-03 22:25:48.304 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.304 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.305 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED May-03 22:25:48.305 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED May-03 22:25:48.305 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.305 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED May-03 22:25:48.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED May-03 22:25:48.307 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.307 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.308 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT May-03 22:25:48.309 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*` matches process NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT May-03 22:25:48.309 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.309 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.310 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO May-03 22:25:48.311 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DESEQ2_QC_PSEUDO` matches process NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO May-03 22:25:48.311 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.311 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.321 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-03 22:25:48.321 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-03 22:25:48.321 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.321 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.351 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNASEQ:RNASEQ:MULTIQC May-03 22:25:48.351 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_RNASEQ:RNASEQ:MULTIQC May-03 22:25:48.351 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-03 22:25:48.352 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-03 22:25:48.357 [main] DEBUG nextflow.Session - Config process names validation disabled as requested May-03 22:25:48.359 [main] DEBUG nextflow.Session - Igniting dataflow network (163) May-03 22:25:48.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF May-03 22:25:48.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_FILTER May-03 22:25:48.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA May-03 22:25:48.361 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA May-03 22:25:48.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF2BED May-03 22:25:48.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES May-03 22:25:48.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT May-03 22:25:48.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE May-03 22:25:48.362 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX May-03 22:25:48.363 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ May-03 22:25:48.363 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC May-03 22:25:48.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE May-03 22:25:48.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT May-03 22:25:48.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE May-03 22:25:48.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT May-03 22:25:48.364 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TX2GENE May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMPORT May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE May-03 22:25:48.365 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED May-03 22:25:48.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED May-03 22:25:48.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT May-03 22:25:48.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON May-03 22:25:48.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES May-03 22:25:48.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX May-03 22:25:48.366 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP May-03 22:25:48.367 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DUPRADAR May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION May-03 22:25:48.368 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMPORT May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-03 22:25:48.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNASEQ:RNASEQ:MULTIQC May-03 22:25:48.370 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_6b19e24a26493d52: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/sortmerna/main.nf Script_e2630658c898fe40: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/local/deseq2_qc/main.nf Script_34ba2812f30702a7: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/local/umitools_prepareforrsem/main.nf Script_673026636b2831f5: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/../../../modules/nf-core/umitools/dedup/main.nf Script_d796aa85128d1482: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/trimgalore/main.nf Script_a6d1af179eafaaba: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/bbmap/bbsplit/main.nf Script_cdbce3e23a8f89e8: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_rsem/../../nf-core/bam_sort_stats_samtools/../bam_stats_samtools/main.nf Script_61c3ce7fada41b46: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/local/multiqc_custom_biotype/main.nf Script_547b2784134e812e: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/bamstat/main.nf Script_01be85e6c9570169: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/local/multiqc/main.nf Script_58e794dbd977701f: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/../../../modules/nf-core/samtools/index/main.nf Script_d1a9b70e0dfbb833: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/main.nf Script_a4ac0ea044c720d7: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_rsem/main.nf Script_f41a20a3a562e689: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/local/bedtools_genomecov/main.nf Script_48287a9e4162d8a9: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/junctionsaturation/main.nf Script_9768c067a05f91e9: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_pseudo/../../../modules/local/tximport/main.nf Script_28988da553552ea1: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/local/gtf2bed/main.nf Script_893ba4a8cb5dd8d4: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/untar/main.nf Script_4a8d3b4ff2edeb32: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/readduplication/main.nf Script_502b6aa3ba845e26: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf Script_50ac8c61b2d88259: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/align_star/../../../modules/local/star_align_igenomes/main.nf Script_2fa4b6601d9aa276: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/../bam_stats_samtools/../../../modules/nf-core/samtools/flagstat/main.nf Script_4f6739ae1680d27b: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_align_hisat2/../bam_sort_stats_samtools/main.nf Script_7bbd1ec48b03ff67: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf Script_ad119ddb6089cee6: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/local/star_genomegenerate_igenomes/main.nf Script_e2e56b17c72cf182: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/kallisto/index/main.nf Script_023d2c935be30472: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/main.nf Script_d8f4ff0ac99235df: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_pseudo/../../../modules/nf-core/kallisto/quant/main.nf Script_6bf902dd399b1bf6: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/fastqc/main.nf Script_dbfcd99b4643d9a2: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_markduplicates_picard/main.nf Script_b8de0c3b09f058c1: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/main.nf Script_36d4290842df373a: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/align_star/../../nf-core/bam_sort_stats_samtools/../../../modules/nf-core/samtools/sort/main.nf Script_cd6f3947962f62c4: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/gunzip/main.nf Script_0bcd59939d66b312: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/star/genomegenerate/main.nf Script_77e22a61eb1f2dd3: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_fastqc_umitools_fastp/../../../modules/nf-core/fastp/main.nf Script_86dc49bc95f589f5: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/align_star/../../../modules/nf-core/star/align/main.nf Script_8c2fb876e2407727: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/salmon/index/main.nf Script_0ece4f9f87f44994: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_align_hisat2/../../../modules/nf-core/hisat2/align/main.nf Script_5035106a6d4a4c78: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_rsem/../../../modules/nf-core/rsem/calculateexpression/main.nf Script_ef7f9d1ec8699697: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_fastqc_umitools_fastp/../../../modules/nf-core/umitools/extract/main.nf Script_d5246004cd2515da: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/readdistribution/main.nf Script_f6daae3b2f230e87: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_pseudo/../../../modules/local/summarizedexperiment/main.nf Script_d528242dc97acc08: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/local/cat_additional_fasta/main.nf Script_03e47f2ea1ad4bda: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/align_star/../../nf-core/bam_sort_stats_samtools/../bam_stats_samtools/../../../modules/nf-core/samtools/stats/main.nf Script_32be0b964abad83e: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/preseq/lcextrap/main.nf Script_59bebcfe6e6c5be7: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/../../../modules/nf-core/ucsc/bedgraphtobigwig/main.nf Script_962c2ce5d43568d5: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/stringtie/stringtie/main.nf Script_15aad8e3750532d8: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/inferexperiment/main.nf Script_9e89f1fdf9ced4f0: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/align_star/../../nf-core/bam_sort_stats_samtools/../bam_stats_samtools/../../../modules/nf-core/samtools/idxstats/main.nf Script_7329460fefebed16: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/align_star/main.nf Script_424e39626e3efddc: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/hisat2/build/main.nf Script_ce727ac81418a182: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/innerdistance/main.nf Script_560e11be19b372ad: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_rsem/../../../modules/local/rsem_merge_counts/main.nf Script_766f7e39f48e49dd: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/junctionannotation/main.nf Script_a8680b05987b83ce: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_subsample_fq_salmon/../../../modules/nf-core/fq/subsample/main.nf Script_a25682ea8940372b: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf Script_a6969db08b6a2fa3: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/rsem/preparereference/main.nf Script_4f4d47ffc2aec98f: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_rseqc/../../../modules/nf-core/rseqc/tin/main.nf Script_91b94b1b2c123e51: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_pseudo/main.nf Script_52a402eec631a008: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/subread/featurecounts/main.nf Script_e1744fc9afdc235e: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/local/gtf_filter/main.nf Script_40c85c154a33da2e: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/qualimap/rnaseq/main.nf Script_04d488c7ab8c434e: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/local/preprocess_transcripts_fasta_gencode/main.nf Script_3d373e9ea7e32c45: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf Script_69dcaec0b873a44f: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/local/dupradar/main.nf Script_aaa732d0dff599b5: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/../../../modules/nf-core/ucsc/bedclip/main.nf Script_01525ffa4dcd5952: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/bam_markduplicates_picard/../../../modules/nf-core/picard/markduplicates/main.nf Script_ee92193e093c17f9: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../modules/nf-core/cat/fastq/main.nf Script_f31f876704902403: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/quantify_pseudo/../../../modules/local/tx2gene/main.nf Script_5f794e9468aa1f6f: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf Script_c500707623393013: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/hisat2/extractsplicesites/main.nf Script_36edeae94666a272: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/custom/getchromsizes/main.nf Script_1d5ac5ca703fb43c: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome/../../../modules/nf-core/gffread/main.nf Script_4252288c0b8e38d5: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf Script_a1f1676a62a35970: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq.nf Script_fb75b7b95d3b5ff0: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_align_hisat2/main.nf Script_262fb08c188e9bfd: /home/arriyaz/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/nf-core/fastq_subsample_fq_salmon/../../../modules/nf-core/salmon/quant/main.nf May-03 22:25:48.370 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination May-03 22:25:48.370 [main] DEBUG nextflow.Session - Session await May-03 22:25:48.425 [Actor Thread 443] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.006 s; total time: 0.007 s May-03 22:25:48.425 [Actor Thread 442] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.006 s; total time: 0.007 s May-03 22:25:48.427 [Actor Thread 443] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/arriyaz/temp/nextflow-practice/work/collect-file/4b5098cbd54257c4cad613fb5fefbbc5 May-03 22:25:48.427 [Actor Thread 442] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/arriyaz/temp/nextflow-practice/work/collect-file/509511daf0e2011d14d49f9213274f30 May-03 22:25:48.430 [Actor Thread 443] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-15721866018121153831 May-03 22:25:48.430 [Actor Thread 442] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8578157801501383297 May-03 22:25:48.784 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/gfp.fa.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/ed/be0154c732ead65f06622d1e89e016/gfp.fa.gz May-03 22:25:48.784 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/5f/ffea4c9e675f833ca6523dcf7663f8/SRR6357072_1.fastq.gz May-03 22:25:48.785 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/a6/4b837d2d6f1aa39b82419b9e32b393/SRR6357072_2.fastq.gz May-03 22:25:48.837 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/genes_with_empty_tid.gtf.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/f9/31d42e50b17716be08c9640e9c3b9e/genes_with_empty_tid.gtf.gz May-03 22:25:48.837 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357073_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/34/7289d6bd54daef156be1b3d3271afa/SRR6357073_1.fastq.gz May-03 22:25:48.837 [FileTransfer-6] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/reference/salmon.tar.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/00/20f1122b7391bd4629e8bfb2977cd3/salmon.tar.gz May-03 22:25:48.838 [FileTransfer-7] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357074_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/df/872371173000c4c3780aa1092c1e37/SRR6357074_1.fastq.gz May-03 22:25:48.838 [FileTransfer-8] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357075_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/a9/270ec458823f414ca381d4322e897b/SRR6357075_1.fastq.gz May-03 22:25:48.839 [FileTransfer-9] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/23/e9225c322addefa904734921ff719e/SRR6357076_1.fastq.gz May-03 22:25:48.839 [FileTransfer-10] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_2.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/d1/8986f9544c632f8116be8b376111e8/SRR6357076_2.fastq.gz May-03 22:25:48.888 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-03 22:25:48.889 [Task submitter] INFO nextflow.Session - [0c/1c54e3] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz) May-03 22:25:48.895 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-03 22:25:48.895 [Task submitter] INFO nextflow.Session - [79/dde02c] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz) May-03 22:25:48.895 [FileTransfer-11] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/9a/56bd5c11d16b19b7c6359f099b5d38/SRR6357070_1.fastq.gz May-03 22:25:48.895 [FileTransfer-12] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/b4/386498e1f64f1eba7229908dfc68f9/SRR6357070_2.fastq.gz May-03 22:25:48.896 [FileTransfer-14] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/de/851ca1cc17883db82e9a3a85be8aaa/SRR6357071_2.fastq.gz May-03 22:25:48.896 [FileTransfer-13] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz to work dir: /home/arriyaz/temp/nextflow-practice/work/stage-b32e4ed8-a816-496c-8c79-d7c3ec5f758c/02/18973ce768bd7dccab47b690638e9c/SRR6357071_1.fastq.gz May-03 22:25:48.948 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-03 22:25:48.948 [Task submitter] INFO nextflow.Session - [50/e78cde] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2) May-03 22:25:48.953 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-03 22:25:48.953 [Task submitter] INFO nextflow.Session - [df/53ae11] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz) May-03 22:25:48.958 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-03 22:25:48.958 [Task submitter] INFO nextflow.Session - [1d/f49845] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2) May-03 22:25:54.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2); status: COMPLETED; exit: 1; error: -; workDir: /home/arriyaz/temp/nextflow-practice/work/1d/f49845a12800d622ab339e74ab7172] May-03 22:25:54.404 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2); work-dir=/home/arriyaz/temp/nextflow-practice/work/1d/f49845a12800d622ab339e74ab7172 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)` terminated with an error exit status (1) May-03 22:25:54.405 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-03 22:25:54.405 [Task submitter] INFO nextflow.Session - [a3/18d389] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1) May-03 22:25:54.411 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)' Caused by: Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)` terminated with an error exit status (1) Command executed: [ ! -f WT_REP2_1.fastq.gz ] && ln -s SRR6357072_1.fastq.gz WT_REP2_1.fastq.gz [ ! -f WT_REP2_2.fastq.gz ] && ln -s SRR6357072_2.fastq.gz WT_REP2_2.fastq.gz trim_galore \ --fastqc_args '-t 2' \ --cores 1 \ --paired \ --gzip \ WT_REP2_1.fastq.gz \ WT_REP2_2.fastq.gz cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE": trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//') cutadapt: $(cutadapt --version) END_VERSIONS Command exit status: 1 Command output: (empty) Command error: touch: .command.trace: Permission denied Work dir: /home/arriyaz/temp/nextflow-practice/work/1d/f49845a12800d622ab339e74ab7172 Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` May-03 22:25:54.417 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit May-03 22:25:54.418 [main] DEBUG nextflow.Session - Session await > all processes finished May-03 22:25:54.422 [Actor Thread 525] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException May-03 22:25:54.423 [Actor Thread 588] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException May-03 22:25:54.424 [Actor Thread 638] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-03 22:25:54.431 [Actor Thread 809] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-03 22:25:54.431 [Actor Thread 812] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-03 22:25:54.431 [Actor Thread 815] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-03 22:25:54.564 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz); status: COMPLETED; exit: 1; error: -; workDir: /home/arriyaz/temp/nextflow-practice/work/0c/1c54e3cfaec9a56d216d68813d80aa] May-03 22:25:54.565 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz); work-dir=/home/arriyaz/temp/nextflow-practice/work/0c/1c54e3cfaec9a56d216d68813d80aa error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (1) May-03 22:25:54.578 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz); status: COMPLETED; exit: 1; error: -; workDir: /home/arriyaz/temp/nextflow-practice/work/79/dde02c182026b1d901351254531c9d] May-03 22:25:54.578 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz); work-dir=/home/arriyaz/temp/nextflow-practice/work/79/dde02c182026b1d901351254531c9d error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)` terminated with an error exit status (1) May-03 22:25:54.590 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz); status: COMPLETED; exit: 1; error: -; workDir: /home/arriyaz/temp/nextflow-practice/work/df/53ae11f7bb26f8fbe13b6eab9fa675] May-03 22:25:54.591 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz); work-dir=/home/arriyaz/temp/nextflow-practice/work/df/53ae11f7bb26f8fbe13b6eab9fa675 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)` terminated with an error exit status (1) May-03 22:25:54.633 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2); status: COMPLETED; exit: 1; error: -; workDir: /home/arriyaz/temp/nextflow-practice/work/50/e78cdedaa888c1b4121beb08a38455] May-03 22:25:54.633 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2); work-dir=/home/arriyaz/temp/nextflow-practice/work/50/e78cdedaa888c1b4121beb08a38455 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)` terminated with an error exit status (1) May-03 22:25:54.859 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1); status: COMPLETED; exit: 1; error: -; workDir: /home/arriyaz/temp/nextflow-practice/work/a3/18d3899cedda579bc88e5139aa5d69] May-03 22:25:54.859 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1); work-dir=/home/arriyaz/temp/nextflow-practice/work/a3/18d3899cedda579bc88e5139aa5d69 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)` terminated with an error exit status (1) May-03 22:25:54.861 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop May-03 22:25:54.861 [main] DEBUG nextflow.Session - Session await > all barriers passed May-03 22:25:54.875 [main] INFO nextflow.Nextflow - -[nf-core/rnaseq] Pipeline completed with errors- May-03 22:25:54.877 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=6; ignoredCount=0; cachedCount=0; pendingCount=5; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=39.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=5; peakCpus=7; peakMemory=30 GB; ] May-03 22:25:54.877 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file May-03 22:25:54.878 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report May-03 22:25:55.221 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline May-03 22:25:55.429 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-03 22:25:55.429 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3' May-03 22:25:55.429 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation May-03 22:25:55.438 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) May-03 22:25:55.438 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye