Jun-11 11:28:20.728 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/nascent -profile pdc_kth --project=naiss2025-22-154 --input /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/combine/Proseq1.csv --outdir /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/result1/ --email tarazhang@foxmail.com --assay_type PROseq --genome GRCm38 -r 2.3.0 -work-dir /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ --save_reference FALSE --scratch=TRUE Jun-11 11:28:21.081 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.3 Jun-11 11:28:21.165 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/cfs/klemming/home/d/dhrubatm/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.0,nf-k8s@1.0.0,nf-tower@1.11.3,nf-wave@1.12.1 Jun-11 11:28:21.220 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jun-11 11:28:21.226 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jun-11 11:28:21.229 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Jun-11 11:28:21.350 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jun-11 11:28:21.379 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /cfs/klemming/home/d/dhrubatm/.nextflow/scm Jun-11 11:28:23.044 [main] DEBUG nextflow.scm.AssetManager - Git config: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/nascent.git Jun-11 11:28:23.097 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Jun-11 11:28:23.118 [main] DEBUG nextflow.scm.AssetManager - Git config: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/nascent.git Jun-11 11:28:24.917 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/nextflow.config Jun-11 11:28:24.921 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/nextflow.config Jun-11 11:28:24.936 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /cfs/klemming/home/d/dhrubatm/.nextflow/secrets/store.json Jun-11 11:28:24.940 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@55c57422] - activable => nextflow.secret.LocalSecretsProvider@55c57422 Jun-11 11:28:24.959 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `pdc_kth` Jun-11 11:28:27.834 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, giga, incliva, ilifu, ki_luria, uge, icr_alma, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, ceci_nic5, ccga_cau, humantechnopole, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, test_copro, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, seattlechildrens, icr_davros, ceres, arm, munin, rosalind, hasta, cfc, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, alliance_canada, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, mssm, sanger, dkfz, test_grocap, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, seadragon, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, genouest, cbe, unsw_katana, gitpod, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac, fsu_draco] Jun-11 11:28:27.914 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default Jun-11 11:28:27.915 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/nascent` [friendly_joliot] DSL2 - revision: 7d4fe61975 [2.3.0] Jun-11 11:28:27.917 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.2.0] Jun-11 11:28:27.917 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jun-11 11:28:27.918 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.2.0] Jun-11 11:28:27.919 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.2.0 Jun-11 11:28:27.967 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.2.0' resolved Jun-11 11:28:27.967 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.2.0' Jun-11 11:28:28.032 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.2.0 Jun-11 11:28:28.117 [main] DEBUG nextflow.Session - Session UUID: ca021dfe-f379-4f47-8986-358559ace3e2 Jun-11 11:28:28.118 [main] DEBUG nextflow.Session - Run name: friendly_joliot Jun-11 11:28:28.118 [main] DEBUG nextflow.Session - Executor pool size: 256 Jun-11 11:28:28.129 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Jun-11 11:28:28.136 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Jun-11 11:28:28.645 [main] DEBUG nextflow.cli.CmdRun - Version: 25.04.3 build 5949 Created: 02-06-2025 20:56 UTC (22:56 CEST) System: Linux 5.14.21-150500.55.65_13.0.73-cray_shasta_c Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 17.0.4+8 Encoding: UTF-8 (UTF-8) Process: 3872579@login1 [10.253.0.5] CPUs: 256 - Mem: 502.2 GB (98.3 GB) - Swap: 0 (0) Jun-11 11:28:28.780 [main] DEBUG nextflow.Session - Work-dir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore [lustre] Jun-11 11:28:28.837 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jun-11 11:28:28.850 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jun-11 11:28:28.876 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory Jun-11 11:28:28.939 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jun-11 11:28:28.949 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 257; maxThreads: 1000 Jun-11 11:28:29.033 [main] DEBUG nextflow.Session - Session start Jun-11 11:28:29.039 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/result1/pipeline_info/execution_trace_2025-06-11_11-28-25.txt Jun-11 11:28:29.218 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-11 11:28:39.340 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jun-11 11:28:40.469 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Jun-11 11:28:40.475 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Jun-11 11:28:40.478 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jun-11 11:28:40.479 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jun-11 11:28:47.791 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Jun-11 11:28:47.799 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Jun-11 11:28:47.802 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jun-11 11:28:47.803 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jun-11 11:28:48.792 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/nascent 2.3.0 ------------------------------------------------------ Input/output options input : /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/combine/Proseq1.csv outdir : /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/result1/ email : tarazhang@foxmail.com Transcript Identification Options assay_type : PROseq Reference genome options genome : GRCm38 fasta : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa gtf : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf gene_bed : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed bwa_index : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/ bowtie2_index : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/ Institutional config options config_profile_description: PDC profile. config_profile_contact : Pontus Freyhult (@pontus) config_profile_url : https://www.pdc.kth.se/ Generic options trace_report_suffix : 2025-06-11_11-28-25 Core Nextflow options revision : 2.3.0 runName : friendly_joliot containerEngine : singularity launchDir : /cfs/klemming/home/d/dhrubatm workDir : /cfs/klemming/projects/supr/naiss2025-22-154/nfcore projectDir : /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent userName : dhrubatm profile : pdc_kth configFiles :  !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * The pipeline https://doi.org/10.5281/zenodo.7245273 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/nascent/blob/master/CITATIONS.md Jun-11 11:28:48.795 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation Jun-11 11:28:48.862 [main] WARN nextflow.validation.SchemaValidator - The following invalid input values have been detected: * --project: naiss2025-22-154 * --scratch: true * --max_memory: 1.7 TB * --max_cpus: 256 * --max_time: 7d * --schema_ignore_params: genomes,input_paths,cluster-options,clusterOptions,project,validationSchemaIgnoreParams * --validationSchemaIgnoreParams: genomes,input_paths,cluster-options,clusterOptions,project,schema_ignore_params Jun-11 11:28:49.058 [main] DEBUG nextflow.validation.SchemaEvaluator - Started validating /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/combine/Proseq1.csv Jun-11 11:28:49.228 [main] DEBUG nextflow.validation.SchemaEvaluator - Validation of file '/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/combine/Proseq1.csv' passed! Jun-11 11:28:49.229 [main] DEBUG n.validation.FormatFilePathEvaluator - S3 paths are not supported by 'FormatFilePathEvaluator': 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed' Jun-11 11:28:49.230 [main] DEBUG n.validation.FormatFilePathEvaluator - S3 paths are not supported by 'FormatFilePathEvaluator': 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa' Jun-11 11:28:49.230 [main] DEBUG nextflow.validation.ExistsEvaluator - S3 paths are not supported by 'ExistsEvaluator': 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa' Jun-11 11:28:49.230 [main] DEBUG n.validation.FormatFilePathEvaluator - S3 paths are not supported by 'FormatFilePathEvaluator': 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf' Jun-11 11:28:49.230 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://ngi-igenomes/igenomes/' Jun-11 11:28:49.231 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation Jun-11 11:28:49.544 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 2.15.0 Jun-11 11:28:49.632 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@2.15.0' resolved Jun-11 11:28:49.632 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@2.15.0' Jun-11 11:28:51.008 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@2.15.0 Jun-11 11:28:51.059 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3] Jun-11 11:28:51.059 [main] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa Jun-11 11:28:51.093 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider Jun-11 11:28:51.127 [main] DEBUG nextflow.cloud.aws.config.AwsConfig - AWS S3 config properties: {max_error_retry=5} Jun-11 11:28:52.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jun-11 11:28:52.700 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:PREPARE_GENOME:.*` matches process NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jun-11 11:28:52.723 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:52.723 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:52.819 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Jun-11 11:28:52.881 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Jun-11 11:28:52.885 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Jun-11 11:28:52.893 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jun-11 11:28:53.083 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES': maxForks=0; fair=false; array=0 Jun-11 11:28:53.255 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:FASTQC Jun-11 11:28:53.257 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_NASCENT:NASCENT:FASTQC Jun-11 11:28:53.267 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.268 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.269 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQC': maxForks=0; fair=false; array=0 Jun-11 11:28:53.326 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:FASTP Jun-11 11:28:53.327 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_NASCENT:NASCENT:FASTP Jun-11 11:28:53.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.338 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.339 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTP': maxForks=0; fair=false; array=0 Jun-11 11:28:53.374 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM Jun-11 11:28:53.375 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWA_MEM` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM Jun-11 11:28:53.382 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.382 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.383 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM': maxForks=0; fair=false; array=0 Jun-11 11:28:53.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Jun-11 11:28:53.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Jun-11 11:28:53.410 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Jun-11 11:28:53.415 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.416 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.417 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT': maxForks=0; fair=false; array=0 Jun-11 11:28:53.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Jun-11 11:28:53.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Jun-11 11:28:53.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Jun-11 11:28:53.443 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.443 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.444 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX': maxForks=0; fair=false; array=0 Jun-11 11:28:53.496 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-11 11:28:53.498 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-11 11:28:53.503 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.503 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.504 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS': maxForks=0; fair=false; array=0 Jun-11 11:28:53.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-11 11:28:53.520 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-11 11:28:53.524 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.524 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.526 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT': maxForks=0; fair=false; array=0 Jun-11 11:28:53.539 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-11 11:28:53.542 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_SORT_STATS_SAMTOOLS:.*` matches process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-11 11:28:53.546 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.546 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.547 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS': maxForks=0; fair=false; array=0 Jun-11 11:28:53.581 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single,error_ignore` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE Jun-11 11:28:53.582 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches labels `process_single,error_ignore` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE Jun-11 11:28:53.583 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PRESEQ_.*` matches process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE Jun-11 11:28:53.589 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.590 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.591 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE': maxForks=0; fair=false; array=0 Jun-11 11:28:53.606 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single,error_retry` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP Jun-11 11:28:53.607 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_retry` matches labels `process_single,error_retry` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP Jun-11 11:28:53.609 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PRESEQ_.*` matches process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP Jun-11 11:28:53.613 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.613 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.614 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP': maxForks=0; fair=false; array=0 Jun-11 11:28:53.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT Jun-11 11:28:53.717 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT` matches process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT Jun-11 11:28:53.729 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.729 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.731 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT': maxForks=0; fair=false; array=0 Jun-11 11:28:53.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION Jun-11 11:28:53.777 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_READDISTRIBUTION` matches process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION Jun-11 11:28:53.781 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.781 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.782 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION': maxForks=0; fair=false; array=0 Jun-11 11:28:53.810 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION Jun-11 11:28:53.813 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:BAM_RSEQC:RSEQC_READDUPLICATION` matches process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION Jun-11 11:28:53.819 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.820 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.822 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION': maxForks=0; fair=false; array=0 Jun-11 11:28:53.856 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP Jun-11 11:28:53.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_PILEUP` matches process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP Jun-11 11:28:53.864 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.865 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.866 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP': maxForks=0; fair=false; array=0 Jun-11 11:28:53.943 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS Jun-11 11:28:53.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV_PLUS` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS Jun-11 11:28:53.949 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:COVERAGE_GRAPHS:.*` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS Jun-11 11:28:53.955 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.955 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.957 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS': maxForks=0; fair=false; array=0 Jun-11 11:28:53.971 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS Jun-11 11:28:53.974 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV_MINUS` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS Jun-11 11:28:53.976 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:COVERAGE_GRAPHS:.*` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS Jun-11 11:28:53.980 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:53.980 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:53.986 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS': maxForks=0; fair=false; array=0 Jun-11 11:28:54.005 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS Jun-11 11:28:54.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DEEPTOOLS_BAMCOVERAGE_PLUS` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS Jun-11 11:28:54.010 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:COVERAGE_GRAPHS:.*` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS Jun-11 11:28:54.013 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.014 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.015 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS': maxForks=0; fair=false; array=0 Jun-11 11:28:54.033 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS Jun-11 11:28:54.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DEEPTOOLS_BAMCOVERAGE_MINUS` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS Jun-11 11:28:54.037 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:COVERAGE_GRAPHS:.*` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS Jun-11 11:28:54.041 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.041 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.042 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS': maxForks=0; fair=false; array=0 Jun-11 11:28:54.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP Jun-11 11:28:54.071 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DREG_PREP` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP Jun-11 11:28:54.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:COVERAGE_GRAPHS:.*` matches process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP Jun-11 11:28:54.078 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.078 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.079 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP': maxForks=0; fair=false; array=0 Jun-11 11:28:54.210 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:SAMTOOLS_MERGE Jun-11 11:28:54.217 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.218 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:SAMTOOLS_MERGE': maxForks=0; fair=false; array=0 Jun-11 11:28:54.254 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:PINTS_CALLER Jun-11 11:28:54.256 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PINTS_CALLER` matches process NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:PINTS_CALLER Jun-11 11:28:54.262 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.262 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.263 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:PINTS_CALLER': maxForks=0; fair=false; array=0 Jun-11 11:28:54.309 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:CAT_CAT Jun-11 11:28:54.317 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.317 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.319 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:CAT_CAT': maxForks=0; fair=false; array=0 Jun-11 11:28:54.341 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_SORT Jun-11 11:28:54.344 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_SORT` matches process NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_SORT Jun-11 11:28:54.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.350 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.351 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_SORT': maxForks=0; fair=false; array=0 Jun-11 11:28:54.374 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_MERGE Jun-11 11:28:54.376 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_MERGE` matches process NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_MERGE Jun-11 11:28:54.381 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.381 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.383 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_MERGE': maxForks=0; fair=false; array=0 Jun-11 11:28:54.429 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:BED2SAF Jun-11 11:28:54.431 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BED2SAF` matches process NFCORE_NASCENT:NASCENT:BED2SAF Jun-11 11:28:54.436 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.436 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.438 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:BED2SAF': maxForks=0; fair=false; array=0 Jun-11 11:28:54.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_PREDICTED Jun-11 11:28:54.468 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SUBREAD_FEATURECOUNTS_PREDICTED` matches process NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_PREDICTED Jun-11 11:28:54.474 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.474 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.475 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_PREDICTED': maxForks=0; fair=false; array=0 Jun-11 11:28:54.502 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE Jun-11 11:28:54.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SUBREAD_FEATURECOUNTS_GENE` matches process NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE Jun-11 11:28:54.511 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:54.512 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:54.513 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE': maxForks=0; fair=false; array=0 Jun-11 11:28:55.034 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NASCENT:NASCENT:MULTIQC Jun-11 11:28:55.036 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_NASCENT:NASCENT:MULTIQC Jun-11 11:28:55.046 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-11 11:28:55.047 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-11 11:28:55.048 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_NASCENT:NASCENT:MULTIQC': maxForks=0; fair=false; array=0 Jun-11 11:28:55.120 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Jun-11 11:28:55.269 [main] DEBUG nextflow.Session - Igniting dataflow network (93) Jun-11 11:28:55.275 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jun-11 11:28:55.276 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQC Jun-11 11:28:55.276 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTP Jun-11 11:28:55.278 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM Jun-11 11:28:55.279 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Jun-11 11:28:55.280 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Jun-11 11:28:55.283 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-11 11:28:55.287 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-11 11:28:55.288 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-11 11:28:55.290 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE Jun-11 11:28:55.290 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP Jun-11 11:28:55.291 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT Jun-11 11:28:55.291 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION Jun-11 11:28:55.291 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION Jun-11 11:28:55.291 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP Jun-11 11:28:55.296 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS Jun-11 11:28:55.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS Jun-11 11:28:55.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS Jun-11 11:28:55.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS Jun-11 11:28:55.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP Jun-11 11:28:55.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:SAMTOOLS_MERGE Jun-11 11:28:55.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:PINTS_CALLER Jun-11 11:28:55.300 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:CAT_CAT Jun-11 11:28:55.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_SORT Jun-11 11:28:55.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_MERGE Jun-11 11:28:55.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:BED2SAF Jun-11 11:28:55.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_PREDICTED Jun-11 11:28:55.301 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE Jun-11 11:28:55.402 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NASCENT:NASCENT:MULTIQC Jun-11 11:28:55.406 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_d3865926248d0c08: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/samtools/stats/main.nf Script_81f84e28bf2da9e9: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/homer/makeucscfile/main.nf Script_67fbb224ec5793f0: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/align_bwamem2/main.nf Script_e927852b807f691d: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/inferexperiment/main.nf Script_ab04ad1e9696cdc9: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/dragmap/align/main.nf Script_4fb9e5798185138e: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/fastq_align_hisat2/main.nf Script_cdbce3e23a8f89e8: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/bam_stats_samtools/main.nf Script_2fa3c1f588d620ba: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/subread/featurecounts/main.nf Script_18089a64b4672be8: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/bam_rseqc/main.nf Script_a6d079f06ea2b7df: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/preseq/ccurve/main.nf Script_49a410273a0d4342: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bwamem2/mem/main.nf Script_a780234b47eb3af3: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/gunzip/main.nf Script_4133e0a81c0b1738: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/fastq_align_star/main.nf Script_632c7b6a2079825a: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bbmap/pileup/main.nf Script_76de3f747352eea2: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/local/grohmm/transcriptcalling/main.nf Script_0fdb2e5f8575be0c: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/multiqc/main.nf Script_3ff1656b1d66c1f2: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/samtools/index/main.nf Script_2bd699064a751e9f: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/prepare_genome.nf Script_72cdcd84c09c8f34: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bedtools/sort/main.nf Script_106c67721b5d7179: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bowtie2/align/main.nf Script_223ca400878df5b0: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/untar/main.nf Script_1d0f07faf68f43a0: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/local/grohmm/parametertuning/main.nf Script_02a0b17a6c4c63ba: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/grohmm/main.nf Script_df270ba5596724f2: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/main.nf Script_6ccd45d793c901af: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/pints/caller/main.nf Script_59101990e865c327: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/umitools/dedup/main.nf Script_a2aa0d1ede76c3e4: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/cat/cat/main.nf Script_2cd3960e599fb6c8: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/samtools/idxstats/main.nf Script_1adca4cb4e6fb5ea: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf Script_65193b46ad5c0993: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/homer_groseq/main.nf Script_cf1e17a1e4a14232: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/bamstat/main.nf Script_b666edf0129ec7fc: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/gffread/main.nf Script_e0e7b45107ecefae: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bedtools/merge/main.nf Script_21c16f921f153f23: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/local/bed2saf.nf Script_17deba9b7d790b7e: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/local/gtf2bed.nf Script_215a636da7ab24a2: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/utils_nfschema_plugin/main.nf Script_25b02493e5c1a6a6: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bwamem2/index/main.nf Script_0127e7d26108d0ac: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/hisat2/align/main.nf Script_c60352b720010bb2: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/coverage_graphs.nf Script_d622935abeccdbf0: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/fastq_align_bwa/main.nf Script_5c4e8d4051efa81e: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/utils_nfcore_pipeline/main.nf Script_cc2a9c8ba5b8cc15: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/tin/main.nf Script_de1c7c124fa4c7b4: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/samtools/sort/main.nf Script_14eb30e706d67c91: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/transcript_identification/main.nf Script_1a6fe1de0094c202: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bedtools/genomecov/main.nf Script_9f6ce129b29ed4a5: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/fastp/main.nf Script_bc0d9cd83e954a94: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/utils_nfcore_nascent_pipeline/main.nf Script_ad3cd4f4d98d2267: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bedtools/intersect/main.nf Script_9a4cdfd93ff6efe3: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/align_dragmap/main.nf Script_dbe8fbfa975cebf1: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/junctionsaturation/main.nf Script_498db87a6d4f03d8: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/samtools/flagstat/main.nf Script_00f15dacb1370c16: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/junctionannotation/main.nf Script_01fe4de28a5ea5f6: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/workflows/nascent.nf Script_7acb62b9e60b283e: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/readduplication/main.nf Script_4f612cfd8c52e8cd: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/utils_nextflow_pipeline/main.nf Script_e5fccee2ba9a7b56: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/samtools/merge/main.nf Script_8b4cd5023b0747bc: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/star/genomegenerate/main.nf Script_6b9506f083c48b86: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bowtie2/build/main.nf Script_5d261b30ca6cdcdb: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/custom/getchromsizes/main.nf Script_997cce4b25cc363d: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/preseq/lcextrap/main.nf Script_6832762354939fbb: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/star/align/main.nf Script_6bd473c81c8aa0e5: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bwa/index/main.nf Script_0efe1bd11f3c1ecf: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/bwa/mem/main.nf Script_2b62527c40aaa906: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/fastq_align_bowtie2/main.nf Script_dc41886bdbd95b0b: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/fastqc/main.nf Script_4eef83468da8cd6e: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/deeptools/bamcoverage/main.nf Script_d72aad1dae59332d: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/dragmap/hashtable/main.nf Script_d70973a14508bfea: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/homer/maketagdirectory/main.nf Script_30b62d329939bde2: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/local/dreg_prep/main.nf Script_e8dad3041e2131a9: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/homer/pos2bed/main.nf Script_256717b794dd0d4c: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/homer/findpeaks/main.nf Script_22b56b1276140bf5: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/local/quality_control.nf Script_fe6f9a2d2d32c34f: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/innerdistance/main.nf Script_bd8537eec78d4f82: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/rseqc/readdistribution/main.nf Script_2ebe1d1a775a7432: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/subworkflows/nf-core/bam_sort_stats_samtools/main.nf Script_8b560cf26a0f6f39: /cfs/klemming/home/d/dhrubatm/.nextflow/assets/nf-core/nascent/modules/nf-core/unzip/main.nf Jun-11 11:28:55.407 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Jun-11 11:28:55.407 [main] DEBUG nextflow.Session - Session await Jun-11 11:28:55.794 [Actor Thread 224] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img] Jun-11 11:28:55.795 [Actor Thread 233] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-fastp-0.23.4--h5f740d0_0.img] Jun-11 11:28:55.893 [Actor Thread 256] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.009 s; external sort time: 0.042 s; total time: 0.051 s Jun-11 11:28:55.893 [Actor Thread 241] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.009 s; external sort time: 0.042 s; total time: 0.051 s Jun-11 11:28:55.903 [Actor Thread 241] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/collect-file/095e3a749dd3457805f9cbfff7315d6f Jun-11 11:28:55.903 [Actor Thread 256] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/collect-file/90aae70ae090616647330a6c06c2162c Jun-11 11:28:55.936 [Actor Thread 256] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-1787987703862574282 Jun-11 11:28:55.936 [Actor Thread 241] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7274407585413943361 Jun-11 11:28:56.744 [Actor Thread 233] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-fastp-0.23.4--h5f740d0_0.img Jun-11 11:28:57.094 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP2) > jobId: 10537251; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/83/61a919fb17574243d13ba99d1aa29d Jun-11 11:28:57.094 [Task submitter] INFO nextflow.Session - [83/61a919] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP2) Jun-11 11:28:57.143 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP3) > jobId: 10537252; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/19/b56bbf86184c60d9c66532de6d9542 Jun-11 11:28:57.144 [Task submitter] INFO nextflow.Session - [19/b56bbf] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP3) Jun-11 11:28:57.180 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP3) > jobId: 10537253; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c1/3d230a458cf5429487aa4ec5056175 Jun-11 11:28:57.180 [Task submitter] INFO nextflow.Session - [c1/3d230a] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP3) Jun-11 11:28:57.215 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP2) > jobId: 10537254; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6f/706c148b3166ddd1373179fcebe580 Jun-11 11:28:57.215 [Task submitter] INFO nextflow.Session - [6f/706c14] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP2) Jun-11 11:28:57.248 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP1) > jobId: 10537255; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/21/45fad648073be72c3754d09dedb7e9 Jun-11 11:28:57.248 [Task submitter] INFO nextflow.Session - [21/45fad6] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP1) Jun-11 11:28:57.281 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP1) > jobId: 10537256; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c5/01098ea51d064e8fe907b60316c199 Jun-11 11:28:57.283 [Task submitter] INFO nextflow.Session - [c5/01098e] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP1) Jun-11 11:28:57.346 [Actor Thread 230] DEBUG n.c.aws.util.S3CredentialsProvider - No AWS credentials available - falling back to anonymous access Jun-11 11:28:57.375 [Actor Thread 224] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img Jun-11 11:28:57.424 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP3) > jobId: 10537257; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c6/e3782f14d58c630829ab28bd8b97b1 Jun-11 11:28:57.424 [Task submitter] INFO nextflow.Session - [c6/e3782f] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP3) Jun-11 11:28:57.460 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP1) > jobId: 10537258; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ef/e690bca56c9e4bcb20481667aa9d40 Jun-11 11:28:57.461 [Task submitter] INFO nextflow.Session - [ef/e690bc] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP1) Jun-11 11:28:57.581 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP2) > jobId: 10537259; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6c/116f473cc64b8d4bcfe5d9fe49369a Jun-11 11:28:57.581 [Task submitter] INFO nextflow.Session - [6c/116f47] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP2) Jun-11 11:28:57.669 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP3) > jobId: 10537260; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/d5bfd5e30e04b351b7282638bf10fa Jun-11 11:28:57.670 [Task submitter] INFO nextflow.Session - [0e/d5bfd5] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP3) Jun-11 11:28:57.713 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP1) > jobId: 10537261; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/98/e74f93d33b7e43feae7174ac596738 Jun-11 11:28:57.714 [Task submitter] INFO nextflow.Session - [98/e74f93] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP1) Jun-11 11:28:57.759 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP2) > jobId: 10537262; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8d/ab94e5fe34318e6ff35eb95937857f Jun-11 11:28:57.759 [Task submitter] INFO nextflow.Session - [8d/ab94e5] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP2) Jun-11 11:28:59.347 [Actor Thread 255] DEBUG n.c.aws.util.S3CredentialsProvider - No AWS credentials available - falling back to anonymous access Jun-11 11:28:59.985 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa to work dir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/stage-ca021dfe-f379-4f47-8986-358559ace3e2/a3/6a5b25b961e1ec592068420d44a444/genome.fa Jun-11 11:29:00.058 [FileTransfer-1] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa to=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/stage-ca021dfe-f379-4f47-8986-358559ace3e2/a3/6a5b25b961e1ec592068420d44a444/genome.fa Jun-11 11:29:00.059 [FileTransfer-1] DEBUG nextflow.cloud.aws.nio.S3Client - Creating S3 transfer manager pool - chunk-size=104857600; max-treads=10; Jun-11 11:29:00.059 [FileTransfer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'S3TransferManager' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Jun-11 11:29:01.985 [Actor Thread 255] INFO nextflow.file.FilePorter - Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa Jun-11 11:29:15.712 [Actor Thread 254] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-samtools-1.20--h50ea8bc_0.img] Jun-11 11:29:16.980 [Actor Thread 254] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-samtools-1.20--h50ea8bc_0.img Jun-11 11:29:17.026 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) > jobId: 10537283; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08 Jun-11 11:29:17.027 [Task submitter] INFO nextflow.Session - [b8/be51b0] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) Jun-11 11:30:12.945 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537283; id: 1; name: NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08 started: 1749634204330; exited: 2025-06-11T09:30:09Z; ] Jun-11 11:30:12.976 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Jun-11 11:30:13.901 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:31:22.944 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537252; id: 13; name: NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/19/b56bbf86184c60d9c66532de6d9542 started: 1749634152915; exited: 2025-06-11T09:31:19Z; ] Jun-11 11:31:22.989 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-11 11:31:22.989 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-11 11:31:22.999 [TaskFinalizer-2] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Jun-11 11:31:23.328 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0 to work dir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/stage-ca021dfe-f379-4f47-8986-358559ace3e2/5c/f6e89dec969d97e191f3c88c5098fa/version0.6.0 Jun-11 11:31:23.384 [FileTransfer-2] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download directory from=s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0 to=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/stage-ca021dfe-f379-4f47-8986-358559ace3e2/5c/f6e89dec969d97e191f3c88c5098fa/version0.6.0 Jun-11 11:31:25.318 [Actor Thread 230] INFO nextflow.file.FilePorter - Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0 Jun-11 11:31:52.950 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537251; id: 12; name: NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/83/61a919fb17574243d13ba99d1aa29d started: 1749634142914; exited: 2025-06-11T09:31:48Z; ] Jun-11 11:31:53.005 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-11 11:31:53.006 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-11 11:31:53.938 [Actor Thread 255] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40-1bd8542a8a0b42e0981337910954371d0230828e-0.img] Jun-11 11:31:55.721 [Actor Thread 255] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40-1bd8542a8a0b42e0981337910954371d0230828e-0.img Jun-11 11:31:55.789 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP3) > jobId: 10537371; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/c4056911863a2f26845ac35046d310 Jun-11 11:31:55.790 [Task submitter] INFO nextflow.Session - [66/c40569] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP3) Jun-11 11:31:55.825 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2) > jobId: 10537372; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 Jun-11 11:31:55.825 [Task submitter] INFO nextflow.Session - [b1/897d9c] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2) Jun-11 11:32:12.941 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537253; id: 9; name: NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c1/3d230a458cf5429487aa4ec5056175 started: 1749634157916; exited: 2025-06-11T09:32:12Z; ] Jun-11 11:32:12.945 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537255; id: 11; name: NFCORE_NASCENT:NASCENT:FASTP (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/21/45fad648073be72c3754d09dedb7e9 started: 1749634167925; exited: 2025-06-11T09:32:12Z; ] Jun-11 11:32:12.996 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-11 11:32:12.997 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-11 11:32:13.001 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-11 11:32:13.001 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-11 11:32:13.495 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3) > jobId: 10537385; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/54/1fcd208e20d9db941cee64a42b384f Jun-11 11:32:13.496 [Task submitter] INFO nextflow.Session - [54/1fcd20] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3) Jun-11 11:32:13.599 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1) > jobId: 10537386; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/f5/49af4c0817f6e7e1752d2c8942be8c Jun-11 11:32:13.600 [Task submitter] INFO nextflow.Session - [f5/49af4c] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1) Jun-11 11:32:53.020 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537254; id: 5; name: NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6f/706c148b3166ddd1373179fcebe580 started: 1749634157920; exited: 2025-06-11T09:32:52Z; ] Jun-11 11:32:53.147 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-11 11:32:53.148 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-11 11:32:53.682 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2) > jobId: 10537413; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 Jun-11 11:32:53.683 [Task submitter] INFO nextflow.Session - [6b/e6598e] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2) Jun-11 11:33:57.973 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 12 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537256; id: 2; name: NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c5/01098ea51d064e8fe907b60316c199 started: 1749634197925; exited: -; ] ~> TaskHandler[jobId: 10537257; id: 6; name: NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c6/e3782f14d58c630829ab28bd8b97b1 started: 1749634197927; exited: -; ] ~> TaskHandler[jobId: 10537258; id: 7; name: NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ef/e690bca56c9e4bcb20481667aa9d40 started: 1749634204326; exited: -; ] ~> TaskHandler[jobId: 10537259; id: 4; name: NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6c/116f473cc64b8d4bcfe5d9fe49369a started: 1749634207932; exited: -; ] ~> TaskHandler[jobId: 10537260; id: 10; name: NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/d5bfd5e30e04b351b7282638bf10fa started: 1749634232952; exited: -; ] ~> TaskHandler[jobId: 10537261; id: 3; name: NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/98/e74f93d33b7e43feae7174ac596738 started: 1749634247936; exited: -; ] ~> TaskHandler[jobId: 10537262; id: 8; name: NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8d/ab94e5fe34318e6ff35eb95937857f started: 1749634247939; exited: -; ] ~> TaskHandler[jobId: 10537371; id: 14; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/c4056911863a2f26845ac35046d310 started: 1749634377973; exited: -; ] ~> TaskHandler[jobId: 10537372; id: 15; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2); status: SUBMITTED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 started: -; exited: -; ] ~> TaskHandler[jobId: 10537385; id: 16; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3); status: SUBMITTED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/54/1fcd208e20d9db941cee64a42b384f started: -; exited: -; ] .. remaining tasks omitted. Jun-11 11:34:12.983 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537256; id: 2; name: NFCORE_NASCENT:NASCENT:FASTP (SA_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c5/01098ea51d064e8fe907b60316c199 started: 1749634197925; exited: 2025-06-11T09:34:08Z; ] Jun-11 11:34:13.066 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-11 11:34:13.066 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-11 11:34:13.952 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1) > jobId: 10537440; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 Jun-11 11:34:13.953 [Task submitter] INFO nextflow.Session - [04/75a92e] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1) Jun-11 11:34:38.171 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537260; id: 10; name: NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/d5bfd5e30e04b351b7282638bf10fa started: 1749634232952; exited: 2025-06-11T09:34:36Z; ] Jun-11 11:35:03.178 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537258; id: 7; name: NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ef/e690bca56c9e4bcb20481667aa9d40 started: 1749634204326; exited: 2025-06-11T09:35:02Z; ] Jun-11 11:35:13.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537257; id: 6; name: NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/c6/e3782f14d58c630829ab28bd8b97b1 started: 1749634197927; exited: 2025-06-11T09:35:12Z; ] Jun-11 11:36:13.149 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537262; id: 8; name: NFCORE_NASCENT:NASCENT:FASTQC (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8d/ab94e5fe34318e6ff35eb95937857f started: 1749634247939; exited: 2025-06-11T09:36:10Z; ] Jun-11 11:37:08.151 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537259; id: 4; name: NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6c/116f473cc64b8d4bcfe5d9fe49369a started: 1749634207932; exited: 2025-06-11T09:37:07Z; ] Jun-11 11:38:48.195 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537261; id: 3; name: NFCORE_NASCENT:NASCENT:FASTQC (SA_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/98/e74f93d33b7e43feae7174ac596738 started: 1749634247936; exited: 2025-06-11T09:38:46Z; ] Jun-11 11:38:58.190 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 6 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537371; id: 14; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/c4056911863a2f26845ac35046d310 started: 1749634377973; exited: -; ] ~> TaskHandler[jobId: 10537372; id: 15; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 started: 1749634518049; exited: -; ] ~> TaskHandler[jobId: 10537385; id: 16; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/54/1fcd208e20d9db941cee64a42b384f started: 1749634523053; exited: -; ] ~> TaskHandler[jobId: 10537386; id: 17; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/f5/49af4c0817f6e7e1752d2c8942be8c started: 1749634698216; exited: -; ] ~> TaskHandler[jobId: 10537413; id: 18; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2); status: SUBMITTED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 started: -; exited: -; ] ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: SUBMITTED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: -; exited: -; ] Jun-11 11:43:58.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 6 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537371; id: 14; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/c4056911863a2f26845ac35046d310 started: 1749634377973; exited: -; ] ~> TaskHandler[jobId: 10537372; id: 15; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 started: 1749634518049; exited: -; ] ~> TaskHandler[jobId: 10537385; id: 16; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/54/1fcd208e20d9db941cee64a42b384f started: 1749634523053; exited: -; ] ~> TaskHandler[jobId: 10537386; id: 17; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/f5/49af4c0817f6e7e1752d2c8942be8c started: 1749634698216; exited: -; ] ~> TaskHandler[jobId: 10537413; id: 18; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 started: 1749634773197; exited: -; ] ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: SUBMITTED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: -; exited: -; ] Jun-11 11:44:23.927 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537371; id: 14; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/c4056911863a2f26845ac35046d310 started: 1749634377973; exited: 2025-06-11T09:44:20Z; ] Jun-11 11:44:23.987 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:44:24.011 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:44:24.012 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:44:24.348 [Actor Thread 247] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-samtools-1.21--h50ea8bc_0.img] Jun-11 11:44:25.723 [Actor Thread 247] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-samtools-1.21--h50ea8bc_0.img Jun-11 11:44:27.062 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP3) > jobId: 10537742; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/83382a17f534c9946a7f54461e07ea Jun-11 11:44:27.062 [Task submitter] INFO nextflow.Session - [b8/83382a] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP3) Jun-11 11:46:14.067 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537742; id: 20; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/83382a17f534c9946a7f54461e07ea started: 1749635073886; exited: 2025-06-11T09:46:12Z; ] Jun-11 11:46:14.140 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:46:14.140 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:46:14.140 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:46:15.267 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP3) > jobId: 10537806; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/9a/3d537b6278e07b3c29b055f25e24db Jun-11 11:46:15.268 [Task submitter] INFO nextflow.Session - [9a/3d537b] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP3) Jun-11 11:46:34.026 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537806; id: 21; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/9a/3d537b6278e07b3c29b055f25e24db started: 1749635179022; exited: 2025-06-11T09:46:29Z; ] Jun-11 11:46:34.047 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:46:34.047 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:46:34.062 [Actor Thread 257] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb:4238fb992d2a93e648108c86e3a9f51348e834a9-0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb-4238fb992d2a93e648108c86e3a9f51348e834a9-0.img] Jun-11 11:46:34.062 [Actor Thread 250] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-preseq-3.1.2--h445547b_2.img] Jun-11 11:46:34.063 [Actor Thread 224] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-bedtools-2.31.1--hf5e1c6e_0.img] Jun-11 11:46:34.063 [Actor Thread 246] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-rseqc-5.0.3--py39hf95cd2a_0.img] Jun-11 11:46:34.071 [Actor Thread 236] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690-e8a286b2e789c091bac0a57302cdc78aa0112353-0.img] Jun-11 11:46:34.576 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed to work dir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/stage-ca021dfe-f379-4f47-8986-358559ace3e2/91/bcf36025705a495615359d3ee386f8/genes.bed Jun-11 11:46:34.591 [Actor Thread 252] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:41defd13a6f2ce014549fcc05d0b051f655777f9-0 [cache /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a-41defd13a6f2ce014549fcc05d0b051f655777f9-0.img] Jun-11 11:46:34.627 [FileTransfer-3] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed to=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/stage-ca021dfe-f379-4f47-8986-358559ace3e2/91/bcf36025705a495615359d3ee386f8/genes.bed Jun-11 11:46:34.835 [Actor Thread 224] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-bedtools-2.31.1--hf5e1c6e_0.img Jun-11 11:46:35.087 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP3) > jobId: 10537814; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/e6/76c540943231367fa529aa89f9b209 Jun-11 11:46:35.087 [Task submitter] INFO nextflow.Session - [e6/76c540] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP3) Jun-11 11:46:35.122 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP3) > jobId: 10537815; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/97/2a2c445e9331196502b66eec7164a8 Jun-11 11:46:35.123 [Task submitter] INFO nextflow.Session - [97/2a2c44] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP3) Jun-11 11:46:35.330 [Actor Thread 257] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb:4238fb992d2a93e648108c86e3a9f51348e834a9-0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-f01e242bdea19948f0576fdca94777242fe4c2cb-4238fb992d2a93e648108c86e3a9f51348e834a9-0.img Jun-11 11:46:35.375 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP3) > jobId: 10537816; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/44f98f57f5e7072c79e7b30e54f7f1 Jun-11 11:46:35.376 [Task submitter] INFO nextflow.Session - [66/44f98f] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP3) Jun-11 11:46:35.654 [Actor Thread 246] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/rseqc:5.0.3--py39hf95cd2a_0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-rseqc-5.0.3--py39hf95cd2a_0.img Jun-11 11:46:35.662 [Actor Thread 252] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:41defd13a6f2ce014549fcc05d0b051f655777f9-0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a-41defd13a6f2ce014549fcc05d0b051f655777f9-0.img Jun-11 11:46:35.745 [Actor Thread 236] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690-e8a286b2e789c091bac0a57302cdc78aa0112353-0.img Jun-11 11:46:36.853 [Actor Thread 250] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2 path=/cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-preseq-3.1.2--h445547b_2.img Jun-11 11:46:37.694 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP3) > jobId: 10537817; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7c/e949a233c38c7ac906161a83fd2c9a Jun-11 11:46:37.694 [Task submitter] INFO nextflow.Session - [7c/e949a2] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP3) Jun-11 11:46:37.933 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP3) > jobId: 10537818; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/de/67d96fed98bb7e8b6155c91dd1deb4 Jun-11 11:46:37.934 [Task submitter] INFO nextflow.Session - [de/67d96f] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP3) Jun-11 11:46:37.979 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP3) > jobId: 10537819; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/4760e4a6cf361698c8e5aae12ccb84 Jun-11 11:46:37.980 [Task submitter] INFO nextflow.Session - [56/4760e4] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP3) Jun-11 11:46:38.014 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP3) > jobId: 10537820; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/ecdecececbfbe165922847dfea50da Jun-11 11:46:38.015 [Task submitter] INFO nextflow.Session - [0e/ecdece] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP3) Jun-11 11:46:38.058 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP3) > jobId: 10537821; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0d/ac9181b7eee9e82037b31a2fc2c555 Jun-11 11:46:38.059 [Task submitter] INFO nextflow.Session - [0d/ac9181] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP3) Jun-11 11:46:40.095 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP3) > jobId: 10537822; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5e/971c70edf58877475ba7ca80b0501d Jun-11 11:46:40.095 [Task submitter] INFO nextflow.Session - [5e/971c70] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP3) Jun-11 11:46:40.171 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP3) > jobId: 10537823; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/cd/bc75d669b7736aaabe655a1f4ebbc6 Jun-11 11:46:40.171 [Task submitter] INFO nextflow.Session - [cd/bc75d6] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP3) Jun-11 11:46:40.325 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP3) > jobId: 10537824; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/93/6a55c5aeb77a1fd9516c693da08319 Jun-11 11:46:40.325 [Task submitter] INFO nextflow.Session - [93/6a55c5] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP3) Jun-11 11:46:44.029 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537817; id: 28; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7c/e949a233c38c7ac906161a83fd2c9a started: 1749635199027; exited: 2025-06-11T09:46:43Z; ] Jun-11 11:47:39.033 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537822; id: 26; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5e/971c70edf58877475ba7ca80b0501d started: 1749635204050; exited: 2025-06-11T09:47:36Z; ] Jun-11 11:48:09.709 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537814; id: 31; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/e6/76c540943231367fa529aa89f9b209 started: 1749635199023; exited: 2025-06-11T09:48:07Z; ] Jun-11 11:48:09.713 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537815; id: 32; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/97/2a2c445e9331196502b66eec7164a8 started: 1749635199024; exited: 2025-06-11T09:48:06Z; ] Jun-11 11:48:59.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 12 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537372; id: 15; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 started: 1749634518049; exited: -; ] ~> TaskHandler[jobId: 10537385; id: 16; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/54/1fcd208e20d9db941cee64a42b384f started: 1749634523053; exited: -; ] ~> TaskHandler[jobId: 10537386; id: 17; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/f5/49af4c0817f6e7e1752d2c8942be8c started: 1749634698216; exited: -; ] ~> TaskHandler[jobId: 10537413; id: 18; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 started: 1749634773197; exited: -; ] ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: 1749635068885; exited: -; ] ~> TaskHandler[jobId: 10537816; id: 23; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/44f98f57f5e7072c79e7b30e54f7f1 started: 1749635199026; exited: -; ] ~> TaskHandler[jobId: 10537818; id: 25; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/de/67d96fed98bb7e8b6155c91dd1deb4 started: 1749635204030; exited: -; ] ~> TaskHandler[jobId: 10537819; id: 30; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/4760e4a6cf361698c8e5aae12ccb84 started: 1749635204034; exited: 2025-06-11T09:48:55Z; ] ~> TaskHandler[jobId: 10537820; id: 24; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/ecdecececbfbe165922847dfea50da started: 1749635204040; exited: -; ] ~> TaskHandler[jobId: 10537821; id: 22; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0d/ac9181b7eee9e82037b31a2fc2c555 started: 1749635204045; exited: -; ] .. remaining tasks omitted. Jun-11 11:48:59.388 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537819; id: 30; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/4760e4a6cf361698c8e5aae12ccb84 started: 1749635204034; exited: 2025-06-11T09:48:55Z; ] Jun-11 11:49:54.437 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537385; id: 16; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/54/1fcd208e20d9db941cee64a42b384f started: 1749634523053; exited: 2025-06-11T09:49:50Z; ] Jun-11 11:49:54.505 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:49:54.505 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:49:54.505 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:49:54.910 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SA_5m_REP3) > jobId: 10537917; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b4/2e08471187f1bb9ca5286ffa3bf8b1 Jun-11 11:49:54.910 [Task submitter] INFO nextflow.Session - [b4/2e0847] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SA_5m_REP3) Jun-11 11:50:04.411 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537818; id: 25; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/de/67d96fed98bb7e8b6155c91dd1deb4 started: 1749635204030; exited: 2025-06-11T09:50:03Z; ] Jun-11 11:50:10.316 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537824; id: 27; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/93/6a55c5aeb77a1fd9516c693da08319 started: 1749635209060; exited: 2025-06-11T09:50:05Z; ] Jun-11 11:50:19.412 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537823; id: 29; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/cd/bc75d669b7736aaabe655a1f4ebbc6 started: 1749635204054; exited: 2025-06-11T09:50:15Z; ] Jun-11 11:52:09.539 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537917; id: 33; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b4/2e08471187f1bb9ca5286ffa3bf8b1 started: 1749635399408; exited: 2025-06-11T09:52:04Z; ] Jun-11 11:52:09.726 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:52:09.727 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:52:09.727 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:52:10.063 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (SA_5m_REP3) > jobId: 10538034; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0f/da2d81a7765541e4fae8a4dcb007bd Jun-11 11:52:10.063 [Task submitter] INFO nextflow.Session - [0f/da2d81] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (SA_5m_REP3) Jun-11 11:52:34.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538034; id: 34; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0f/da2d81a7765541e4fae8a4dcb007bd started: 1749635534480; exited: 2025-06-11T09:52:30Z; ] Jun-11 11:52:34.821 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:52:34.821 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:52:36.742 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3) > jobId: 10538043; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 Jun-11 11:52:36.751 [Task submitter] INFO nextflow.Session - [56/e86e77] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3) Jun-11 11:52:37.218 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (SA_5m_REP3) > jobId: 10538048; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/2d4fdc368472f045ca3c845b948672 Jun-11 11:52:37.229 [Task submitter] INFO nextflow.Session - [0e/2d4fdc] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (SA_5m_REP3) Jun-11 11:52:39.475 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (SA_5m_REP3) > jobId: 10538049; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/98/2102f76f38b5f701d1195b7e5e7c77 Jun-11 11:52:39.505 [Task submitter] INFO nextflow.Session - [98/2102f7] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (SA_5m_REP3) Jun-11 11:52:39.693 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537821; id: 22; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0d/ac9181b7eee9e82037b31a2fc2c555 started: 1749635204045; exited: 2025-06-11T09:52:38Z; ] Jun-11 11:52:39.733 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:52:41.786 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3) > jobId: 10538050; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8b/3f0f48299e50ef1ce39cb0b0ecd5b7 Jun-11 11:52:41.800 [Task submitter] INFO nextflow.Session - [8b/3f0f48] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3) Jun-11 11:52:42.219 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3) > jobId: 10538052; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 Jun-11 11:52:42.224 [Task submitter] INFO nextflow.Session - [4e/e26811] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3) Jun-11 11:52:44.495 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (SA_5m_REP3) > jobId: 10538054; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/58/b735039ce0d72d75979f842ff430c6 Jun-11 11:52:44.507 [Task submitter] INFO nextflow.Session - [58/b73503] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (SA_5m_REP3) Jun-11 11:52:44.674 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (SA_5m_REP3) > jobId: 10538058; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/48/6b03355e28270c578498294e98782b Jun-11 11:52:44.674 [Task submitter] INFO nextflow.Session - [48/6b0335] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (SA_5m_REP3) Jun-11 11:52:46.788 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (SA_5m_REP3) > jobId: 10538059; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7e/bda843b400894e5eab9c225b75608b Jun-11 11:52:46.831 [Task submitter] INFO nextflow.Session - [7e/bda843] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (SA_5m_REP3) Jun-11 11:52:47.127 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (SA_5m_REP3) > jobId: 10538062; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b0/25ec568e6952c434339ccf97a926b3 Jun-11 11:52:47.134 [Task submitter] INFO nextflow.Session - [b0/25ec56] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (SA_5m_REP3) Jun-11 11:52:47.169 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (SA_5m_REP3) > jobId: 10538063; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/61/654f58534bc78c2bf8d903867ab3f1 Jun-11 11:52:47.170 [Task submitter] INFO nextflow.Session - [61/654f58] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (SA_5m_REP3) Jun-11 11:52:47.224 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (SA_5m_REP3) > jobId: 10538065; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/37/304ab8537a160c4e259bda41cbf5a7 Jun-11 11:52:47.224 [Task submitter] INFO nextflow.Session - [37/304ab8] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (SA_5m_REP3) Jun-11 11:53:29.669 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538063; id: 40; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/61/654f58534bc78c2bf8d903867ab3f1 started: 1749635604662; exited: 2025-06-11T09:53:29Z; ] Jun-11 11:53:54.663 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538048; id: 45; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/2d4fdc368472f045ca3c845b948672 started: 1749635564616; exited: 2025-06-11T09:53:51Z; ] Jun-11 11:53:59.659 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 15 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537372; id: 15; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 started: 1749634518049; exited: -; ] ~> TaskHandler[jobId: 10537386; id: 17; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/f5/49af4c0817f6e7e1752d2c8942be8c started: 1749634698216; exited: -; ] ~> TaskHandler[jobId: 10537413; id: 18; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 started: 1749634773197; exited: -; ] ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: 1749635068885; exited: -; ] ~> TaskHandler[jobId: 10537816; id: 23; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/44f98f57f5e7072c79e7b30e54f7f1 started: 1749635199026; exited: -; ] ~> TaskHandler[jobId: 10537820; id: 24; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/ecdecececbfbe165922847dfea50da started: 1749635204040; exited: -; ] ~> TaskHandler[jobId: 10538043; id: 44; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 started: 1749635559700; exited: -; ] ~> TaskHandler[jobId: 10538049; id: 42; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/98/2102f76f38b5f701d1195b7e5e7c77 started: 1749635564618; exited: -; ] ~> TaskHandler[jobId: 10538050; id: 36; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8b/3f0f48299e50ef1ce39cb0b0ecd5b7 started: 1749635564620; exited: -; ] ~> TaskHandler[jobId: 10538052; id: 39; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 started: 1749635569759; exited: -; ] .. remaining tasks omitted. Jun-11 11:54:19.906 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537816; id: 23; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/66/44f98f57f5e7072c79e7b30e54f7f1 started: 1749635199026; exited: 2025-06-11T09:54:17Z; ] Jun-11 11:54:40.016 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537372; id: 15; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/897d9c3fd42be2a286608105bf2ad7 started: 1749634518049; exited: 2025-06-11T09:54:39Z; ] Jun-11 11:54:40.119 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:54:40.119 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:54:40.120 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:54:41.337 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP2) > jobId: 10538136; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/91/a9b90b3cb2d728fab700dabace24c4 Jun-11 11:54:41.362 [Task submitter] INFO nextflow.Session - [91/a9b90b] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP2) Jun-11 11:55:14.860 [Task monitor] DEBUG nextflow.file.FileHelper - FS path type (true): /cfs/klemming/projects/supr/naiss2025-22-154/nfcore Jun-11 11:55:54.918 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537386; id: 17; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/f5/49af4c0817f6e7e1752d2c8942be8c started: 1749634698216; exited: 2025-06-11T09:55:51Z; ] Jun-11 11:55:55.177 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:55:55.179 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:55:55.179 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:55:55.621 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP1) > jobId: 10538181; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0b/30dee62d2ce375f8891104b8680631 Jun-11 11:55:55.623 [Task submitter] INFO nextflow.Session - [0b/30dee6] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP1) Jun-11 11:56:49.935 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537820; id: 24; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0e/ecdecececbfbe165922847dfea50da started: 1749635204040; exited: 2025-06-11T09:56:49Z; ] Jun-11 11:56:49.968 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:57:20.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538054; id: 41; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/58/b735039ce0d72d75979f842ff430c6 started: 1749635569768; exited: 2025-06-11T09:57:18Z; ] Jun-11 11:57:30.012 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538049; id: 42; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/98/2102f76f38b5f701d1195b7e5e7c77 started: 1749635564618; exited: 2025-06-11T09:57:26Z; ] Jun-11 11:57:35.005 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538136; id: 46; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/91/a9b90b3cb2d728fab700dabace24c4 started: 1749635719944; exited: 2025-06-11T09:57:31Z; ] Jun-11 11:57:35.030 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:57:35.030 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:57:35.030 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:57:35.135 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP2) > jobId: 10538259; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/bc/6cc616be7f2727242d473876be3987 Jun-11 11:57:35.136 [Task submitter] INFO nextflow.Session - [bc/6cc616] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP2) Jun-11 11:58:25.532 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538181; id: 47; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0b/30dee62d2ce375f8891104b8680631 started: 1749635780396; exited: 2025-06-11T09:58:24Z; ] Jun-11 11:58:25.682 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:58:25.682 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:58:25.682 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 11:58:27.745 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP1) > jobId: 10538278; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/63/11052482532367d74ce794d6d8349b Jun-11 11:58:27.745 [Task submitter] INFO nextflow.Session - [63/110524] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP1) Jun-11 11:58:30.024 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538259; id: 48; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/bc/6cc616be7f2727242d473876be3987 started: 1749635884965; exited: 2025-06-11T09:58:29Z; ] Jun-11 11:58:30.085 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:58:30.085 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:58:30.192 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP2) > jobId: 10538293; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b0/e558609290941688bc5362febd0b7f Jun-11 11:58:30.192 [Task submitter] INFO nextflow.Session - [b0/e55860] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP2) Jun-11 11:58:30.235 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP2) > jobId: 10538294; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/505d2846d13e8835d436864e795b0d Jun-11 11:58:30.236 [Task submitter] INFO nextflow.Session - [b1/505d28] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP2) Jun-11 11:58:30.269 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2) > jobId: 10538295; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5c/f87a72fc7577224cf20f4889edba9f Jun-11 11:58:30.269 [Task submitter] INFO nextflow.Session - [5c/f87a72] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2) Jun-11 11:58:30.305 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP2) > jobId: 10538296; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2f/ba4bdbe0f33df71fab7cff311c3fdb Jun-11 11:58:30.306 [Task submitter] INFO nextflow.Session - [2f/ba4bdb] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP2) Jun-11 11:58:30.344 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP2) > jobId: 10538297; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/94/4843f85db3b273207c2e09a1d82767 Jun-11 11:58:30.344 [Task submitter] INFO nextflow.Session - [94/4843f8] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP2) Jun-11 11:58:30.376 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2) > jobId: 10538298; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2e/171a77c01230a0f0ef9b54fc1118ba Jun-11 11:58:30.377 [Task submitter] INFO nextflow.Session - [2e/171a77] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2) Jun-11 11:58:30.412 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2) > jobId: 10538299; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ed/0210f55bd8e697884a6af4b5b43778 Jun-11 11:58:30.413 [Task submitter] INFO nextflow.Session - [ed/0210f5] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2) Jun-11 11:58:30.616 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP2) > jobId: 10538300; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7c/9acc21c41374f308f25152ff03b52e Jun-11 11:58:30.616 [Task submitter] INFO nextflow.Session - [7c/9acc21] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP2) Jun-11 11:58:30.653 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP2) > jobId: 10538301; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/30c2362398507f1b1d90232425c9e0 Jun-11 11:58:30.654 [Task submitter] INFO nextflow.Session - [7b/30c236] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP2) Jun-11 11:58:30.687 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP2) > jobId: 10538302; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/a2/55361457c650f5a30ccbfb69c16c2b Jun-11 11:58:30.687 [Task submitter] INFO nextflow.Session - [a2/553614] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP2) Jun-11 11:58:30.723 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP2) > jobId: 10538303; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/1b/a82ce4d7ad2deb16c84c08e2aaa2e4 Jun-11 11:58:30.723 [Task submitter] INFO nextflow.Session - [1b/a82ce4] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP2) Jun-11 11:58:59.954 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 21 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537413; id: 18; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 started: 1749634773197; exited: -; ] ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: 1749635068885; exited: -; ] ~> TaskHandler[jobId: 10538043; id: 44; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 started: 1749635559700; exited: -; ] ~> TaskHandler[jobId: 10538050; id: 36; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8b/3f0f48299e50ef1ce39cb0b0ecd5b7 started: 1749635564620; exited: -; ] ~> TaskHandler[jobId: 10538052; id: 39; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 started: 1749635569759; exited: -; ] ~> TaskHandler[jobId: 10538058; id: 38; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/48/6b03355e28270c578498294e98782b started: 1749635569769; exited: -; ] ~> TaskHandler[jobId: 10538059; id: 35; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7e/bda843b400894e5eab9c225b75608b started: 1749635574660; exited: -; ] ~> TaskHandler[jobId: 10538062; id: 43; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b0/25ec568e6952c434339ccf97a926b3 started: 1749635604660; exited: -; ] ~> TaskHandler[jobId: 10538065; id: 37; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/37/304ab8537a160c4e259bda41cbf5a7 started: 1749635604670; exited: -; ] ~> TaskHandler[jobId: 10538278; id: 49; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP1); status: SUBMITTED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/63/11052482532367d74ce794d6d8349b started: -; exited: -; ] .. remaining tasks omitted. Jun-11 11:59:10.009 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538302; id: 57; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/a2/55361457c650f5a30ccbfb69c16c2b started: 1749635945017; exited: 2025-06-11T09:59:06Z; ] Jun-11 11:59:25.007 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538062; id: 43; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b0/25ec568e6952c434339ccf97a926b3 started: 1749635604660; exited: 2025-06-11T09:59:24Z; ] Jun-11 11:59:25.011 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538278; id: 49; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/63/11052482532367d74ce794d6d8349b started: 1749635940004; exited: 2025-06-11T09:59:20Z; ] Jun-11 11:59:25.029 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 11:59:25.029 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 11:59:25.960 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP1) > jobId: 10538315; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/27/f33f9f6c92a606ce1f9ed967bd7c5a Jun-11 11:59:25.960 [Task submitter] INFO nextflow.Session - [27/f33f9f] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP1) Jun-11 11:59:26.061 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP1) > jobId: 10538316; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/07e7770d7aaf63ac6353c234f1058c Jun-11 11:59:26.062 [Task submitter] INFO nextflow.Session - [7b/07e777] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP1) Jun-11 11:59:26.108 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP1) > jobId: 10538317; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/61/7f4b6bca4298ffc7bbcac109448c3a Jun-11 11:59:26.109 [Task submitter] INFO nextflow.Session - [61/7f4b6b] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP1) Jun-11 11:59:26.164 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP1) > jobId: 10538318; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/a9db143f7f39d8d51a1ccedd05d96d Jun-11 11:59:26.165 [Task submitter] INFO nextflow.Session - [b8/a9db14] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP1) Jun-11 11:59:26.201 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP1) > jobId: 10538319; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/29/25d9af106fdfb53dcca2948481ec4e Jun-11 11:59:26.201 [Task submitter] INFO nextflow.Session - [29/25d9af] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP1) Jun-11 11:59:26.228 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP1) > jobId: 10538320; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/81/1c2c11976e578de8d35b91066cd961 Jun-11 11:59:26.228 [Task submitter] INFO nextflow.Session - [81/1c2c11] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP1) Jun-11 11:59:26.262 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP1) > jobId: 10538321; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/d9/158776eaad31ca5df570d296be5d2e Jun-11 11:59:26.263 [Task submitter] INFO nextflow.Session - [d9/158776] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP1) Jun-11 11:59:28.061 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP1) > jobId: 10538322; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/9b/97a29253f2d388bd301652d45a02bf Jun-11 11:59:28.061 [Task submitter] INFO nextflow.Session - [9b/97a292] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP1) Jun-11 11:59:28.118 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP1) > jobId: 10538324; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/9e/c05aee6ee3c017f766543740c06b9f Jun-11 11:59:28.118 [Task submitter] INFO nextflow.Session - [9e/c05aee] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP1) Jun-11 11:59:28.159 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP1) > jobId: 10538325; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/93/88d52edc155db7acf6b315e341a3ef Jun-11 11:59:28.160 [Task submitter] INFO nextflow.Session - [93/88d52e] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP1) Jun-11 11:59:28.250 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP1) > jobId: 10538327; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2b/28c3d239de4ee6f18e8e2d30c71782 Jun-11 11:59:28.251 [Task submitter] INFO nextflow.Session - [2b/28c3d2] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP1) Jun-11 11:59:30.006 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538058; id: 38; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/48/6b03355e28270c578498294e98782b started: 1749635569769; exited: 2025-06-11T09:59:29Z; ] Jun-11 11:59:39.979 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 10538043; id: 44; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 started: 1749635559700; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270016 Current queue status: > job: 10537386: DONE > job: 10537372: DONE > job: 10538302: DONE > job: 10538259: DONE > job: 10538181: DONE > job: 10538136: DONE > job: 10538054: DONE > job: 10538049: DONE > job: 10537820: DONE > job: 10537816: DONE > job: 10538052: null > job: 10538043: null > job: 10537413: RUNNING > job: 10538296: RUNNING > job: 10538297: RUNNING > job: 10538298: RUNNING > job: 10538299: RUNNING > job: 10538300: RUNNING > job: 10538301: RUNNING > job: 10538303: RUNNING > job: 10538278: RUNNING > job: 10538293: RUNNING > job: 10538294: RUNNING > job: 10538295: RUNNING > job: 10538062: RUNNING > job: 10538065: RUNNING > job: 10538059: RUNNING > job: 10538058: RUNNING > job: 10538050: RUNNING > job: 10537440: RUNNING Content of workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 > total 44 > drwxr-sr-x 2 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:52 . > drwxr-sr-x 4 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:52 .. > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 .command.begin > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 452 Jun 11 11:52 .command.err > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 919 Jun 11 11:53 .command.log > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 .command.out > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 12430 Jun 11 11:52 .command.run > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 355 Jun 11 11:52 .command.sh > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 .command.trace > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 101 Jun 11 11:52 genome.fa.sizes -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08/genome.fa.sizes > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 SA_5m_REP3.minus.bedGraph > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 107 Jun 11 11:52 SA_5m_REP3.sorted.bam -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b4/2e08471187f1bb9ca5286ffa3bf8b1/SA_5m_REP3.sorted.bam Jun-11 11:59:39.979 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538043; id: 44; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3); status: COMPLETED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 started: 1749635559700; exited: -; ] Jun-11 11:59:40.107 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3); work-dir=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3)` terminated for an unknown reason -- Likely it has been terminated by the external system Jun-11 11:59:40.271 [TaskFinalizer-4] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3)' Caused by: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (SA_5m_REP3)` terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: bedtools \ genomecov \ -ibam SA_5m_REP3.sorted.bam \ -bg -strand - \ | bedtools sort \ > SA_5m_REP3.minus.bedGraph cat <<-END_VERSIONS > versions.yml "NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS": bedtools: $(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS Command exit status: - Command output: (empty) Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: fuse2fs not found, will not be able to mount EXT3 filesystems INFO: gocryptfs not found, will not be able to use gocryptfs Work dir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/56/e86e77f3009640f45b17b64a3f87f1 Container: /cfs/klemming/projects/supr/naiss2025-22-154/Proseqfastq/cache/depot.galaxyproject.org-singularity-bedtools-2.31.1--hf5e1c6e_0.img Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Jun-11 11:59:40.275 [TaskFinalizer-4] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Jun-11 11:59:40.350 [TaskFinalizer-4] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting Jun-11 11:59:40.351 [main] DEBUG nextflow.Session - Session await > all processes finished Jun-11 11:59:40.366 [Actor Thread 253] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 15; slices: 1; internal sort time: 0.011 s; external sort time: 0.002 s; total time: 0.013 s Jun-11 11:59:40.372 [Actor Thread 253] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/collect-file/94de88f5cb708a098fa9d1cfdbedc90c Jun-11 11:59:40.373 [Actor Thread 253] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-2173825061973262804 Jun-11 11:59:50.376 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 10538052; id: 39; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 started: 1749635569759; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270435 Current queue status: > job: 10537386: DONE > job: 10537372: DONE > job: 10538302: DONE > job: 10538259: DONE > job: 10538181: DONE > job: 10538136: DONE > job: 10538054: DONE > job: 10538049: DONE > job: 10537820: DONE > job: 10537816: DONE > job: 10538052: null > job: 10538043: null > job: 10537413: RUNNING > job: 10538296: RUNNING > job: 10538297: RUNNING > job: 10538298: RUNNING > job: 10538299: RUNNING > job: 10538300: RUNNING > job: 10538301: RUNNING > job: 10538303: RUNNING > job: 10538278: RUNNING > job: 10538293: RUNNING > job: 10538294: RUNNING > job: 10538295: RUNNING > job: 10538062: RUNNING > job: 10538065: RUNNING > job: 10538059: RUNNING > job: 10538058: RUNNING > job: 10538050: RUNNING > job: 10537440: RUNNING Content of workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 > total 44 > drwxr-sr-x 2 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:52 . > drwxr-sr-x 3 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:52 .. > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 .command.begin > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 452 Jun 11 11:52 .command.err > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 919 Jun 11 11:53 .command.log > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 .command.out > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 12428 Jun 11 11:52 .command.run > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 353 Jun 11 11:52 .command.sh > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 .command.trace > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 101 Jun 11 11:52 genome.fa.sizes -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08/genome.fa.sizes > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:52 SA_5m_REP3.plus.bedGraph > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 107 Jun 11 11:52 SA_5m_REP3.sorted.bam -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b4/2e08471187f1bb9ca5286ffa3bf8b1/SA_5m_REP3.sorted.bam Jun-11 11:59:50.377 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538052; id: 39; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3); status: COMPLETED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 started: 1749635569759; exited: -; ] Jun-11 11:59:50.380 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3); work-dir=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/4e/e26811aa72ea46d732022946732b29 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (SA_5m_REP3)` terminated for an unknown reason -- Likely it has been terminated by the external system Jun-11 12:00:10.356 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538297; id: 55; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/94/4843f85db3b273207c2e09a1d82767 started: 1749635945008; exited: 2025-06-11T10:00:06Z; ] Jun-11 12:00:10.367 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538324; id: 67; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/9e/c05aee6ee3c017f766543740c06b9f started: 1749636005374; exited: 2025-06-11T10:00:06Z; ] Jun-11 12:01:15.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538315; id: 64; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/27/f33f9f6c92a606ce1f9ed967bd7c5a started: 1749636005356; exited: 2025-06-11T10:01:12Z; ] Jun-11 12:01:40.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537413; id: 18; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/6b/e6598e470dc798d823fb93d223d6c6 started: 1749634773197; exited: 2025-06-11T10:01:38Z; ] Jun-11 12:01:40.501 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:01:40.501 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 12:01:40.501 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 12:04:00.405 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 22 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: 1749635068885; exited: -; ] ~> TaskHandler[jobId: 10538050; id: 36; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8b/3f0f48299e50ef1ce39cb0b0ecd5b7 started: 1749635564620; exited: -; ] ~> TaskHandler[jobId: 10538059; id: 35; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7e/bda843b400894e5eab9c225b75608b started: 1749635574660; exited: -; ] ~> TaskHandler[jobId: 10538065; id: 37; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/37/304ab8537a160c4e259bda41cbf5a7 started: 1749635604670; exited: -; ] ~> TaskHandler[jobId: 10538293; id: 58; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b0/e558609290941688bc5362febd0b7f started: 1749635940006; exited: -; ] ~> TaskHandler[jobId: 10538294; id: 53; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/505d2846d13e8835d436864e795b0d started: 1749635940008; exited: -; ] ~> TaskHandler[jobId: 10538295; id: 59; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5c/f87a72fc7577224cf20f4889edba9f started: 1749635945003; exited: -; ] ~> TaskHandler[jobId: 10538296; id: 56; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2f/ba4bdbe0f33df71fab7cff311c3fdb started: 1749635945006; exited: -; ] ~> TaskHandler[jobId: 10538298; id: 51; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2e/171a77c01230a0f0ef9b54fc1118ba started: 1749635945010; exited: -; ] ~> TaskHandler[jobId: 10538299; id: 60; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ed/0210f55bd8e697884a6af4b5b43778 started: 1749635945012; exited: -; ] .. remaining tasks omitted. Jun-11 12:04:10.496 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538293; id: 58; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b0/e558609290941688bc5362febd0b7f started: 1749635940006; exited: 2025-06-11T10:04:09Z; ] Jun-11 12:04:10.505 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538294; id: 53; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b1/505d2846d13e8835d436864e795b0d started: 1749635940008; exited: 2025-06-11T10:04:10Z; ] Jun-11 12:04:51.536 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538318; id: 66; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/a9db143f7f39d8d51a1ccedd05d96d started: 1749636005363; exited: 2025-06-11T10:04:49Z; ] Jun-11 12:05:05.659 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538321; id: 71; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/d9/158776eaad31ca5df570d296be5d2e started: 1749636005369; exited: 2025-06-11T10:05:01Z; ] Jun-11 12:05:20.639 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538296; id: 56; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2f/ba4bdbe0f33df71fab7cff311c3fdb started: 1749635945006; exited: 2025-06-11T10:05:17Z; ] Jun-11 12:05:55.575 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538300; id: 52; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7c/9acc21c41374f308f25152ff03b52e started: 1749635945014; exited: 2025-06-11T10:05:52Z; ] Jun-11 12:06:05.557 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 10538295; id: 59; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5c/f87a72fc7577224cf20f4889edba9f started: 1749635945003; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270182 Current queue status: > job: 10537413: DONE > job: 10538315: DONE > job: 10538318: DONE > job: 10538321: DONE > job: 10538324: DONE > job: 10538297: DONE > job: 10538293: DONE > job: 10538294: DONE > job: 10538316: null > job: 10538319: null > job: 10538299: null > job: 10538295: null > job: 10538317: RUNNING > job: 10538320: RUNNING > job: 10538322: RUNNING > job: 10538325: RUNNING > job: 10538327: RUNNING > job: 10538296: RUNNING > job: 10538298: RUNNING > job: 10538300: RUNNING > job: 10538301: RUNNING > job: 10538303: RUNNING > job: 10538065: RUNNING > job: 10538059: RUNNING > job: 10538050: RUNNING > job: 10537440: RUNNING Content of workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5c/f87a72fc7577224cf20f4889edba9f > total 44 > drwxr-sr-x 2 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:59 . > drwxr-sr-x 3 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:58 .. > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 .command.begin > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 452 Jun 11 11:59 .command.err > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 919 Jun 11 12:00 .command.log > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 .command.out > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 12430 Jun 11 11:58 .command.run > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 355 Jun 11 11:58 .command.sh > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 .command.trace > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 101 Jun 11 11:59 genome.fa.sizes -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08/genome.fa.sizes > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 WT_5m_REP2.minus.bedGraph > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 107 Jun 11 11:59 WT_5m_REP2.sorted.bam -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/91/a9b90b3cb2d728fab700dabace24c4/WT_5m_REP2.sorted.bam Jun-11 12:06:05.558 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538295; id: 59; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2); status: COMPLETED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5c/f87a72fc7577224cf20f4889edba9f started: 1749635945003; exited: -; ] Jun-11 12:06:05.565 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2); work-dir=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/5c/f87a72fc7577224cf20f4889edba9f error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP2)` terminated for an unknown reason -- Likely it has been terminated by the external system Jun-11 12:06:05.581 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 10538299; id: 60; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ed/0210f55bd8e697884a6af4b5b43778 started: 1749635945012; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270204 Current queue status: > job: 10537413: DONE > job: 10538315: DONE > job: 10538318: DONE > job: 10538321: DONE > job: 10538324: DONE > job: 10538297: DONE > job: 10538293: DONE > job: 10538294: DONE > job: 10538316: null > job: 10538319: null > job: 10538299: null > job: 10538295: null > job: 10538317: RUNNING > job: 10538320: RUNNING > job: 10538322: RUNNING > job: 10538325: RUNNING > job: 10538327: RUNNING > job: 10538296: RUNNING > job: 10538298: RUNNING > job: 10538300: RUNNING > job: 10538301: RUNNING > job: 10538303: RUNNING > job: 10538065: RUNNING > job: 10538059: RUNNING > job: 10538050: RUNNING > job: 10537440: RUNNING Content of workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ed/0210f55bd8e697884a6af4b5b43778 > total 44 > drwxr-sr-x 2 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:59 . > drwxr-sr-x 3 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:58 .. > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 .command.begin > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 452 Jun 11 11:59 .command.err > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 919 Jun 11 12:00 .command.log > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 .command.out > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 12428 Jun 11 11:58 .command.run > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 353 Jun 11 11:58 .command.sh > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 .command.trace > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 101 Jun 11 11:59 genome.fa.sizes -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08/genome.fa.sizes > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 11:59 WT_5m_REP2.plus.bedGraph > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 107 Jun 11 11:59 WT_5m_REP2.sorted.bam -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/91/a9b90b3cb2d728fab700dabace24c4/WT_5m_REP2.sorted.bam Jun-11 12:06:05.581 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538299; id: 60; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2); status: COMPLETED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ed/0210f55bd8e697884a6af4b5b43778 started: 1749635945012; exited: -; ] Jun-11 12:06:05.585 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2); work-dir=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/ed/0210f55bd8e697884a6af4b5b43778 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP2)` terminated for an unknown reason -- Likely it has been terminated by the external system Jun-11 12:06:10.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538059; id: 35; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7e/bda843b400894e5eab9c225b75608b started: 1749635574660; exited: 2025-06-11T10:06:06Z; ] Jun-11 12:06:10.542 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538065; id: 37; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/37/304ab8537a160c4e259bda41cbf5a7 started: 1749635604670; exited: 2025-06-11T10:06:07Z; ] Jun-11 12:06:10.556 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:06:10.560 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:06:35.678 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538322; id: 68; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/9b/97a29253f2d388bd301652d45a02bf started: 1749636005372; exited: 2025-06-11T10:06:34Z; ] Jun-11 12:06:55.662 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538317; id: 65; name: NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/61/7f4b6bca4298ffc7bbcac109448c3a started: 1749636005361; exited: 2025-06-11T10:06:54Z; ] Jun-11 12:07:05.762 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 10538316; id: 70; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/07e7770d7aaf63ac6353c234f1058c started: 1749636005359; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270288 Current queue status: > job: 10537413: DONE > job: 10538315: DONE > job: 10538318: DONE > job: 10538321: DONE > job: 10538324: DONE > job: 10538296: DONE > job: 10538297: DONE > job: 10538300: DONE > job: 10538293: DONE > job: 10538294: DONE > job: 10538065: DONE > job: 10538059: DONE > job: 10538316: null > job: 10538319: null > job: 10538299: null > job: 10538295: null > job: 10538317: RUNNING > job: 10538320: RUNNING > job: 10538322: RUNNING > job: 10538325: RUNNING > job: 10538327: RUNNING > job: 10538298: RUNNING > job: 10538301: RUNNING > job: 10538303: RUNNING > job: 10538050: RUNNING > job: 10537440: RUNNING Content of workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/07e7770d7aaf63ac6353c234f1058c > total 44 > drwxr-sr-x 2 dhrubatm pg_naiss2025-22-154 4096 Jun 11 12:00 . > drwxr-sr-x 4 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:59 .. > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 .command.begin > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 452 Jun 11 12:00 .command.err > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 919 Jun 11 12:01 .command.log > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 .command.out > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 12428 Jun 11 11:59 .command.run > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 353 Jun 11 11:59 .command.sh > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 .command.trace > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 101 Jun 11 12:00 genome.fa.sizes -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08/genome.fa.sizes > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 WT_5m_REP1.plus.bedGraph > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 107 Jun 11 12:00 WT_5m_REP1.sorted.bam -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0b/30dee62d2ce375f8891104b8680631/WT_5m_REP1.sorted.bam Jun-11 12:07:05.764 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538316; id: 70; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP1); status: COMPLETED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/07e7770d7aaf63ac6353c234f1058c started: 1749636005359; exited: -; ] Jun-11 12:07:05.774 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP1); work-dir=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/07e7770d7aaf63ac6353c234f1058c error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (WT_5m_REP1)` terminated for an unknown reason -- Likely it has been terminated by the external system Jun-11 12:07:05.785 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 10538319; id: 69; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/29/25d9af106fdfb53dcca2948481ec4e started: 1749636005365; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270347 Current queue status: > job: 10537413: DONE > job: 10538315: DONE > job: 10538318: DONE > job: 10538321: DONE > job: 10538324: DONE > job: 10538296: DONE > job: 10538297: DONE > job: 10538300: DONE > job: 10538293: DONE > job: 10538294: DONE > job: 10538065: DONE > job: 10538059: DONE > job: 10538316: null > job: 10538319: null > job: 10538299: null > job: 10538295: null > job: 10538317: RUNNING > job: 10538320: RUNNING > job: 10538322: RUNNING > job: 10538325: RUNNING > job: 10538327: RUNNING > job: 10538298: RUNNING > job: 10538301: RUNNING > job: 10538303: RUNNING > job: 10538050: RUNNING > job: 10537440: RUNNING Content of workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/29/25d9af106fdfb53dcca2948481ec4e > total 44 > drwxr-sr-x 2 dhrubatm pg_naiss2025-22-154 4096 Jun 11 12:00 . > drwxr-sr-x 3 dhrubatm pg_naiss2025-22-154 4096 Jun 11 11:59 .. > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 .command.begin > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 452 Jun 11 12:00 .command.err > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 919 Jun 11 12:01 .command.log > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 .command.out > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 12430 Jun 11 11:59 .command.run > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 355 Jun 11 11:59 .command.sh > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 .command.trace > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 101 Jun 11 12:00 genome.fa.sizes -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/b8/be51b067e3bc815122051cecc96a08/genome.fa.sizes > -rw-r--r-- 1 dhrubatm pg_naiss2025-22-154 0 Jun 11 12:00 WT_5m_REP1.minus.bedGraph > lrwxrwxrwx 1 dhrubatm pg_naiss2025-22-154 107 Jun 11 12:00 WT_5m_REP1.sorted.bam -> /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/0b/30dee62d2ce375f8891104b8680631/WT_5m_REP1.sorted.bam Jun-11 12:07:05.786 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538319; id: 69; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP1); status: COMPLETED; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/29/25d9af106fdfb53dcca2948481ec4e started: 1749636005365; exited: -; ] Jun-11 12:07:05.790 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP1); work-dir=/cfs/klemming/projects/supr/naiss2025-22-154/nfcore/29/25d9af106fdfb53dcca2948481ec4e error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (WT_5m_REP1)` terminated for an unknown reason -- Likely it has been terminated by the external system Jun-11 12:09:00.648 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 8 -- submitted tasks are shown below ~> TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: 1749635068885; exited: -; ] ~> TaskHandler[jobId: 10538050; id: 36; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8b/3f0f48299e50ef1ce39cb0b0ecd5b7 started: 1749635564620; exited: -; ] ~> TaskHandler[jobId: 10538298; id: 51; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2e/171a77c01230a0f0ef9b54fc1118ba started: 1749635945010; exited: -; ] ~> TaskHandler[jobId: 10538301; id: 50; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/30c2362398507f1b1d90232425c9e0 started: 1749635945015; exited: -; ] ~> TaskHandler[jobId: 10538303; id: 54; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/1b/a82ce4d7ad2deb16c84c08e2aaa2e4 started: 1749635945019; exited: -; ] ~> TaskHandler[jobId: 10538320; id: 61; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/81/1c2c11976e578de8d35b91066cd961 started: 1749636005367; exited: -; ] ~> TaskHandler[jobId: 10538325; id: 62; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/93/88d52edc155db7acf6b315e341a3ef started: 1749636005375; exited: -; ] ~> TaskHandler[jobId: 10538327; id: 63; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2b/28c3d239de4ee6f18e8e2d30c71782 started: 1749636005377; exited: -; ] Jun-11 12:10:05.795 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538050; id: 36; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (SA_5m_REP3); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/8b/3f0f48299e50ef1ce39cb0b0ecd5b7 started: 1749635564620; exited: 2025-06-11T10:10:04Z; ] Jun-11 12:12:20.750 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10537440; id: 19; name: NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM (SA_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/04/75a92e362bfc51d235c512dbda1a27 started: 1749635068885; exited: 2025-06-11T10:12:18Z; ] Jun-11 12:12:20.801 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:12:20.801 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-11 12:12:20.801 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BWA:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-11 12:13:30.779 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538301; id: 50; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/7b/30c2362398507f1b1d90232425c9e0 started: 1749635945015; exited: 2025-06-11T10:13:30Z; ] Jun-11 12:13:30.828 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:13:35.758 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538303; id: 54; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/1b/a82ce4d7ad2deb16c84c08e2aaa2e4 started: 1749635945019; exited: 2025-06-11T10:13:33Z; ] Jun-11 12:13:35.774 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:14:00.752 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 4 -- submitted tasks are shown below ~> TaskHandler[jobId: 10538298; id: 51; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2e/171a77c01230a0f0ef9b54fc1118ba started: 1749635945010; exited: -; ] ~> TaskHandler[jobId: 10538320; id: 61; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/81/1c2c11976e578de8d35b91066cd961 started: 1749636005367; exited: -; ] ~> TaskHandler[jobId: 10538325; id: 62; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/93/88d52edc155db7acf6b315e341a3ef started: 1749636005375; exited: -; ] ~> TaskHandler[jobId: 10538327; id: 63; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2b/28c3d239de4ee6f18e8e2d30c71782 started: 1749636005377; exited: -; ] Jun-11 12:14:15.848 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538325; id: 62; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/93/88d52edc155db7acf6b315e341a3ef started: 1749636005375; exited: 2025-06-11T10:14:11Z; ] Jun-11 12:14:16.066 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:14:25.992 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538327; id: 63; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2b/28c3d239de4ee6f18e8e2d30c71782 started: 1749636005377; exited: 2025-06-11T10:14:22Z; ] Jun-11 12:14:26.136 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-11 12:19:00.926 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[jobId: 10538298; id: 51; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2e/171a77c01230a0f0ef9b54fc1118ba started: 1749635945010; exited: -; ] ~> TaskHandler[jobId: 10538320; id: 61; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP1); status: RUNNING; exit: -; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/81/1c2c11976e578de8d35b91066cd961 started: 1749636005367; exited: -; ] Jun-11 12:19:45.979 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538298; id: 51; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP2); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/2e/171a77c01230a0f0ef9b54fc1118ba started: 1749635945010; exited: 2025-06-11T10:19:41Z; ] Jun-11 12:20:40.996 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 10538320; id: 61; name: NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (WT_5m_REP1); status: COMPLETED; exit: 0; error: -; workDir: /cfs/klemming/projects/supr/naiss2025-22-154/nfcore/81/1c2c11976e578de8d35b91066cd961 started: 1749636005367; exited: 2025-06-11T10:20:39Z; ] Jun-11 12:20:41.033 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Jun-11 12:20:41.033 [main] DEBUG nextflow.Session - Session await > all barriers passed Jun-11 12:20:41.204 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) Jun-11 12:20:43.890 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Jun-11 12:20:43.939 [main] WARN nextflow.Nextflow - [nf-core/nascent] No reports found from process 'MULTIQC' Jun-11 12:20:44.288 [main] DEBUG nextflow.Nextflow - java.io.IOException: Cannot run program "sendmail": error=2, No such file or directory Jun-11 12:20:44.289 [main] DEBUG nextflow.Nextflow - Trying with mail instead of sendmail Jun-11 12:20:44.314 [main] ERROR nextflow.script.WorkflowMetadata - Failed to invoke `workflow.onComplete` event handler java.lang.reflect.InvocationTargetException: null at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at nextflow.script.FunctionDef.invoke_a(FunctionDef.groovy:64) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:105) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:392) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:331) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:406) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:331) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_bc0d9cd83e954a94$_runScript_closure4$_closure10$_closure11.doCall(Script_bc0d9cd83e954a94:130) at Script_bc0d9cd83e954a94$_runScript_closure4$_closure10$_closure11.doCall(Script_bc0d9cd83e954a94) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:412) at nextflow.script.WorkflowMetadata$_invokeOnComplete_closure3.doCall(WorkflowMetadata.groovy:426) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:422) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2394) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2379) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2420) at nextflow.script.WorkflowMetadata.invokeOnComplete(WorkflowMetadata.groovy:424) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82) at nextflow.script.WorkflowMetadata$_closure2.doCall(WorkflowMetadata.groovy:287) at nextflow.script.WorkflowMetadata$_closure2.call(WorkflowMetadata.groovy) at groovy.lang.Closure.run(Closure.java:505) at nextflow.Session.shutdown0(Session.groovy:760) at nextflow.Session.destroy(Session.groovy:713) at nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:263) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:147) at nextflow.cli.CmdRun.run(CmdRun.groovy:379) at nextflow.cli.Launcher.run(Launcher.groovy:513) at nextflow.cli.Launcher.main(Launcher.groovy:673) Caused by: java.io.IOException: Stream closed at java.base/java.lang.ProcessBuilder$NullOutputStream.write(ProcessBuilder.java:445) at java.base/java.io.OutputStream.write(OutputStream.java:162) at java.base/java.io.BufferedOutputStream.write(BufferedOutputStream.java:123) at java.base/sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:234) at java.base/sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:304) at java.base/sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:282) at java.base/sun.nio.cs.StreamEncoder.write(StreamEncoder.java:132) at java.base/sun.nio.cs.StreamEncoder.write(StreamEncoder.java:142) at java.base/java.io.OutputStreamWriter.write(OutputStreamWriter.java:223) at org.codehaus.groovy.runtime.FlushingStreamWriter.write(FlushingStreamWriter.java:48) at java.base/java.io.Writer.write(Writer.java:249) at org.codehaus.groovy.runtime.FormatHelper.write(FormatHelper.java:485) at org.codehaus.groovy.runtime.IOGroovyMethods.leftShift(IOGroovyMethods.java:92) at org.codehaus.groovy.runtime.IOGroovyMethods.leftShift(IOGroovyMethods.java:181) at org.codehaus.groovy.runtime.ProcessGroovyMethods.leftShift(ProcessGroovyMethods.java:115) at org.codehaus.groovy.runtime.dgm$1040.doMethodInvoke(Unknown Source) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_5c4e8d4051efa81e.completionEmail(Script_5c4e8d4051efa81e:321) ... 67 common frames omitted Jun-11 12:20:44.379 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=65; failedCount=6; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1d 15h 26m 18s; failedDuration=42m 3s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=26; peakCpus=92; peakMemory=552 GB; ] Jun-11 12:20:44.380 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jun-11 12:20:44.383 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jun-11 12:20:45.674 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Jun-11 12:20:46.183 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jun-11 12:20:46.249 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@2.15.0' Jun-11 12:20:46.249 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon Jun-11 12:20:46.249 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.2.0' Jun-11 12:20:46.249 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema Jun-11 12:20:46.251 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Jun-11 12:20:46.254 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'S3TransferManager' shutdown completed (hard=false) Jun-11 12:20:46.254 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye