(base) [beggsa@bear-pg-login06 KNNGS]$ cat .nextflow.log Oct-31 12:00:43.057 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/oncoanalyser -revision 2.0.0 -config nextflow-oncoanalyser-bear-noref.config -config TwistExomeForOncoAnalyzer-withRNA.config -profile singularity --mode targeted --panel TwistExomeV2 --genome GRCh38_hmf --force_panel --input SampleSheet-Oncoanalyser.csv --outdir output/ -resume Oct-31 12:00:43.363 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.7 Oct-31 12:00:43.413 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/rds/homes/b/beggsa/.nextflow/plugins; core-plugins: nf-amazon@2.15.0-patch1,nf-azure@1.16.0-patch1,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.1,nf-k8s@1.0.0,nf-tower@1.11.4-patch1,nf-wave@1.12.1 Oct-31 12:00:43.440 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-31 12:00:43.440 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-31 12:00:43.443 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Oct-31 12:00:43.451 [main] INFO org.pf4j.AbstractPluginManager - No plugins Oct-31 12:00:43.460 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /rds/homes/b/beggsa/.nextflow/scm Oct-31 12:00:44.044 [main] DEBUG nextflow.scm.AssetManager - Git config: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/oncoanalyser.git Oct-31 12:00:44.067 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Oct-31 12:00:44.073 [main] DEBUG nextflow.scm.AssetManager - Git config: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/oncoanalyser.git Oct-31 12:00:44.883 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/nextflow.config Oct-31 12:00:44.886 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /rds/projects/b/beggsa-hpbcancer/KNNGS/nextflow-oncoanalyser-bear-noref.config Oct-31 12:00:44.886 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /rds/projects/b/beggsa-hpbcancer/KNNGS/TwistExomeForOncoAnalyzer-withRNA.config Oct-31 12:00:44.887 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/nextflow.config Oct-31 12:00:44.887 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /rds/projects/b/beggsa-hpbcancer/KNNGS/nextflow-oncoanalyser-bear-noref.config Oct-31 12:00:44.887 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /rds/projects/b/beggsa-hpbcancer/KNNGS/TwistExomeForOncoAnalyzer-withRNA.config Oct-31 12:00:44.893 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /rds/homes/b/beggsa/.nextflow/secrets/store.json Oct-31 12:00:44.895 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2744dcae] - activable => nextflow.secret.LocalSecretsProvider@2744dcae Oct-31 12:00:44.903 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Oct-31 12:00:45.701 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Oct-31 12:00:45.718 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Oct-31 12:00:45.734 [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, apollo, ipop_up, vsc_calcua, pdc_kth, ceci_nic5, ccga_cau, humantechnopole, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, rki, ucl_myriad, utd_ganymede, charliecloud, fred_hutch, 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, eva_grace, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, test_stub, 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, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, seadragon, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, dirac, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, hki_genie, genouest, cbe, unsw_katana, utd_juno, gitpod, phoenix, seawulf, uod_hpc, fub_curta, lovelace, uct_hpc, aws_tower, binac, fsu_draco] Oct-31 12:00:45.761 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Oct-31 12:00:45.762 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/oncoanalyser` [berserk_bardeen] DSL2 - revision: d1218d24a1 [2.0.0] Oct-31 12:00:45.763 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.3.0] Oct-31 12:00:45.763 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Oct-31 12:00:45.764 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.3.0] Oct-31 12:00:45.765 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.3.0 Oct-31 12:00:45.975 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.3.0' resolved Oct-31 12:00:45.975 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.3.0' Oct-31 12:00:46.062 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.3.0 Oct-31 12:00:46.100 [main] DEBUG nextflow.Session - Session UUID: 49539eb0-3870-4f88-b7be-3ce5b6c3f5cd Oct-31 12:00:46.100 [main] DEBUG nextflow.Session - Run name: berserk_bardeen Oct-31 12:00:46.100 [main] DEBUG nextflow.Session - Executor pool size: 32 Oct-31 12:00:46.106 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Oct-31 12:00:46.110 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Oct-31 12:00:46.142 [main] DEBUG nextflow.cli.CmdRun - Version: 25.04.7 build 5955 Created: 08-09-2025 13:29 UTC (14:29 BST) System: Linux 4.18.0-553.78.1.el8_10.x86_64 Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 21.0.7+6-LTS Encoding: UTF-8 (UTF-8) Process: 12799@bear-pg0210u13b [10.20.21.55] CPUs: 32 - Mem: 128 GB (127.6 GB) - Swap: 0 (0) Oct-31 12:00:46.172 [main] DEBUG nextflow.Session - Work-dir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work [gpfs] Oct-31 12:00:46.172 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/bin Oct-31 12:00:46.203 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Oct-31 12:00:46.210 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-31 12:00:46.225 [main] DEBUG nextflow.Session - Observer factory: ValidationObserverFactory Oct-31 12:00:46.272 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory Oct-31 12:00:46.298 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Oct-31 12:00:46.305 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000 Oct-31 12:00:46.509 [main] DEBUG nextflow.Session - Session start Oct-31 12:00:46.532 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /rds/projects/b/beggsa-hpbcancer/KNNGS/output/pipeline_info/execution_trace_2025-10-31_12-00-45.txt Oct-31 12:00:46.598 [main] DEBUG nextflow.Session - Using default localLib path: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/lib Oct-31 12:00:46.603 [main] DEBUG nextflow.Session - Adding to the classpath library: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/lib Oct-31 12:00:47.145 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-31 12:00:47.284 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Oct-31 12:00:47.292 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Oct-31 12:00:47.303 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Oct-31 12:00:47.303 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Oct-31 12:00:47.493 [main] WARN nextflow.Nextflow - provided panel TwistExomeV2 does not have built-in support but forcing to proceed Oct-31 12:00:53.578 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/oncoanalyser 2.0.0 ------------------------------------------------------ Input/output options input : SampleSheet-Oncoanalyser.csv outdir : output/ Other options mode : targeted panel : TwistExomeV2 force_panel : true Reference data options genome : GRCh38_hmf genome_version : 38 genome_type : no_alt ref_data_hmf_data_path : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/hmf_reference_data/hmftools/hmf_pipeline_resources.38_v2.0.0--3.tar.gz ref_data_panel_data_path : /rds/projects/b/beggsa-nostra/Exomes/250910_VH01150_154_222CFY5NX/output-twist-reference/panel_resources/ ref_data_genome_fasta : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/GRCh38_masked_exclusions_alts_hlas.fasta ref_data_genome_fai : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/samtools_index-1.16/GRCh38_masked_exclusions_alts_hlas.fasta.fai ref_data_genome_dict : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/samtools_index-1.16/GRCh38_masked_exclusions_alts_hlas.fasta.dict ref_data_genome_bwamem2_index: https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/bwa-mem2_index-2.2.1.tar.gz ref_data_genome_img : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/bwa_index_image-gatk-4.6.1.0/GRCh38_masked_exclusions_alts_hlas.fasta.img ref_data_genome_gridss_index : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/gridss_index-2.13.2.tar.gz ref_data_genome_star_index : https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/star_index-gencode_38-2.7.3a.tar.gz Institutional config options config_profile_description : The University of Birmingham BEAR profile provided by nf-core/configs. config_profile_contact : Andrew Beggs (@adbeggs) config_profile_url : https://intranet.birmingham.ac.uk/it/teams/infrastructure/research/bear/index.aspx Core Nextflow options revision : 2.0.0 runName : berserk_bardeen containerEngine : singularity launchDir : /rds/projects/b/beggsa-hpbcancer/KNNGS workDir : /rds/projects/b/beggsa-hpbcancer/KNNGS/work projectDir : /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser userName : beggsa profile : singularity configFiles : /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/nextflow.config, /rds/projects/b/beggsa-hpbcancer/KNNGS/nextflow-oncoanalyser-bear-noref.config, /rds/projects/b/beggsa-hpbcancer/KNNGS/TwistExomeForOncoAnalyzer-withRNA.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/oncoanalyser/blob/master/CITATIONS.md Oct-31 12:00:53.580 [main] DEBUG n.validation.ValidationExtension - Starting parameters validation Oct-31 12:00:53.668 [main] WARN n.validation.ValidationExtension - The following invalid input values have been detected: * --max_memory: 128 GB * --max_cpus: 32 * --max_time: 96.h Oct-31 12:00:53.859 [main] DEBUG nextflow.validation.SchemaEvaluator - Started validating /rds/projects/b/beggsa-hpbcancer/KNNGS/SampleSheet-Oncoanalyser.csv Oct-31 12:00:53.889 [main] DEBUG nextflow.validation.SchemaEvaluator - Validation of file 'SampleSheet-Oncoanalyser.csv' passed! Oct-31 12:00:54.327 [main] DEBUG n.file.http.XFileSystemProvider - Got HTTP error=404 waiting for 250ms (attempt=1) Oct-31 12:00:54.948 [main] DEBUG n.file.http.XFileSystemProvider - Got HTTP error=404 waiting for 750ms (attempt=2) Oct-31 12:00:56.023 [main] DEBUG n.file.http.XFileSystemProvider - Got HTTP error=404 waiting for 2250ms (attempt=3) Oct-31 12:00:58.734 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://ngi-igenomes/igenomes/' Oct-31 12:00:58.736 [main] DEBUG n.validation.ValidationExtension - Finishing parameters validation Oct-31 12:00:58.796 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_BWAMEM2_INDEX Oct-31 12:00:58.801 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:58.801 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:58.808 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Oct-31 12:00:58.813 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Oct-31 12:00:58.814 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Oct-31 12:00:58.816 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Oct-31 12:00:58.830 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_BWAMEM2_INDEX': maxForks=0; fair=false; array=0 Oct-31 12:00:58.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_HMF_DATA Oct-31 12:00:58.853 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:58.853 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:58.853 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_HMF_DATA': maxForks=0; fair=false; array=0 Oct-31 12:00:58.993 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:FASTP Oct-31 12:00:58.994 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:FASTP Oct-31 12:00:58.999 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:58.999 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:58.999 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:FASTP': maxForks=0; fair=false; array=0 Oct-31 12:00:59.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN Oct-31 12:00:59.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_ALIGN` matches process NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN Oct-31 12:00:59.010 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.010 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.010 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN': maxForks=0; fair=false; array=0 Oct-31 12:00:59.051 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:STAR_ALIGN Oct-31 12:00:59.053 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.053 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.054 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:STAR_ALIGN': maxForks=0; fair=false; array=0 Oct-31 12:00:59.060 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:SAMTOOLS_SORT Oct-31 12:00:59.062 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.062 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.063 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:SAMTOOLS_SORT': maxForks=0; fair=false; array=0 Oct-31 12:00:59.080 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:SAMBAMBA_MERGE Oct-31 12:00:59.082 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.082 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.082 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:SAMBAMBA_MERGE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.097 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:GATK4_MARKDUPLICATES Oct-31 12:00:59.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:GATK4_MARKDUPLICATES Oct-31 12:00:59.101 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.101 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.101 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:GATK4_MARKDUPLICATES': maxForks=0; fair=false; array=0 Oct-31 12:00:59.154 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX Oct-31 12:00:59.154 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:REDUX` matches process NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX Oct-31 12:00:59.157 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.157 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.158 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX': maxForks=0; fair=false; array=0 Oct-31 12:00:59.231 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:ISOFOX_QUANTIFICATION:ISOFOX Oct-31 12:00:59.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ISOFOX` matches process NFCORE_ONCOANALYSER:TARGETED:ISOFOX_QUANTIFICATION:ISOFOX Oct-31 12:00:59.244 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.245 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:ISOFOX_QUANTIFICATION:ISOFOX': maxForks=0; fair=false; array=0 Oct-31 12:00:59.281 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:AMBER_PROFILING:AMBER Oct-31 12:00:59.282 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:AMBER` matches process NFCORE_ONCOANALYSER:TARGETED:AMBER_PROFILING:AMBER Oct-31 12:00:59.284 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.284 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.284 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:AMBER_PROFILING:AMBER': maxForks=0; fair=false; array=0 Oct-31 12:00:59.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:COBALT_PROFILING:COBALT Oct-31 12:00:59.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COBALT` matches process NFCORE_ONCOANALYSER:TARGETED:COBALT_PROFILING:COBALT Oct-31 12:00:59.325 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:^.*COBALT_PROFILING:COBALT` matches process NFCORE_ONCOANALYSER:TARGETED:COBALT_PROFILING:COBALT Oct-31 12:00:59.326 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.326 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.327 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:COBALT_PROFILING:COBALT': maxForks=0; fair=false; array=0 Oct-31 12:00:59.365 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_PREP Oct-31 12:00:59.366 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ESVEE_CALLING:ESVEE_(PREP|ASSEMBLE|DEPTH_ANNOTATOR|CALL)` matches process NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_PREP Oct-31 12:00:59.367 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.367 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.367 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_PREP': maxForks=0; fair=false; array=0 Oct-31 12:00:59.390 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_ASSEMBLE Oct-31 12:00:59.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ESVEE_CALLING:ESVEE_(PREP|ASSEMBLE|DEPTH_ANNOTATOR|CALL)` matches process NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_ASSEMBLE Oct-31 12:00:59.392 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.392 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.392 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_ASSEMBLE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.410 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_DEPTH_ANNOTATOR Oct-31 12:00:59.410 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ESVEE_CALLING:ESVEE_(PREP|ASSEMBLE|DEPTH_ANNOTATOR|CALL)` matches process NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_DEPTH_ANNOTATOR Oct-31 12:00:59.411 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.412 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.412 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_DEPTH_ANNOTATOR': maxForks=0; fair=false; array=0 Oct-31 12:00:59.429 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_CALL Oct-31 12:00:59.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:ESVEE_CALLING:ESVEE_(PREP|ASSEMBLE|DEPTH_ANNOTATOR|CALL)` matches process NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_CALL Oct-31 12:00:59.431 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.431 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.432 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_CALL': maxForks=0; fair=false; array=0 Oct-31 12:00:59.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_GERMLINE Oct-31 12:00:59.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:SAGE_CALLING:SAGE_GERMLINE` matches process NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_GERMLINE Oct-31 12:00:59.503 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.503 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.503 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_GERMLINE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.517 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_SOMATIC Oct-31 12:00:59.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:SAGE_CALLING:SAGE_SOMATIC` matches process NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_SOMATIC Oct-31 12:00:59.519 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.519 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.520 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_SOMATIC': maxForks=0; fair=false; array=0 Oct-31 12:00:59.591 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_GERMLINE Oct-31 12:00:59.592 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:PAVE_ANNOTATION:PAVE_(?:GERMLINE|SOMATIC)` matches process NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_GERMLINE Oct-31 12:00:59.594 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.594 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.594 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_GERMLINE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_SOMATIC Oct-31 12:00:59.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:PAVE_ANNOTATION:PAVE_(?:GERMLINE|SOMATIC)` matches process NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_SOMATIC Oct-31 12:00:59.612 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.612 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.613 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_SOMATIC': maxForks=0; fair=false; array=0 Oct-31 12:00:59.675 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE Oct-31 12:00:59.675 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PURPLE` matches process NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE Oct-31 12:00:59.677 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.677 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.677 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.723 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_GERMLINE Oct-31 12:00:59.724 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:SAGE_APPEND:SAGE_APPEND_(?:GERMLINE|SOMATIC)` matches process NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_GERMLINE Oct-31 12:00:59.726 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.726 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.726 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_GERMLINE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.737 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_SOMATIC Oct-31 12:00:59.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:SAGE_APPEND:SAGE_APPEND_(?:GERMLINE|SOMATIC)` matches process NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_SOMATIC Oct-31 12:00:59.739 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.739 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.739 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_SOMATIC': maxForks=0; fair=false; array=0 Oct-31 12:00:59.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_GERMLINE Oct-31 12:00:59.790 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:LINX_ANNOTATION:LINX_GERMLINE` matches process NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_GERMLINE Oct-31 12:00:59.791 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.791 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.792 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_GERMLINE': maxForks=0; fair=false; array=0 Oct-31 12:00:59.805 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_SOMATIC Oct-31 12:00:59.806 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:LINX_ANNOTATION:LINX_SOMATIC` matches process NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_SOMATIC Oct-31 12:00:59.807 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.807 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.808 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_SOMATIC': maxForks=0; fair=false; array=0 Oct-31 12:00:59.857 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINX_VISUALISER Oct-31 12:00:59.858 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:LINX_PLOTTING:LINX_VISUALISER` matches process NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINX_VISUALISER Oct-31 12:00:59.859 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.859 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.859 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINX_VISUALISER': maxForks=0; fair=false; array=0 Oct-31 12:00:59.887 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINXREPORT Oct-31 12:00:59.888 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:LINX_PLOTTING:LINXREPORT` matches process NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINXREPORT Oct-31 12:00:59.889 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.889 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.889 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINXREPORT': maxForks=0; fair=false; array=0 Oct-31 12:00:59.931 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:BAMTOOLS_METRICS:BAMTOOLS Oct-31 12:00:59.932 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAMTOOLS` matches process NFCORE_ONCOANALYSER:TARGETED:BAMTOOLS_METRICS:BAMTOOLS Oct-31 12:00:59.933 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:00:59.933 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:00:59.934 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:BAMTOOLS_METRICS:BAMTOOLS': maxForks=0; fair=false; array=0 Oct-31 12:01:00.006 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_ONCOANALYSER:TARGETED:LILAC_CALLING:LILAC Oct-31 12:01:00.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:LILAC` matches process NFCORE_ONCOANALYSER:TARGETED:LILAC_CALLING:LILAC Oct-31 12:01:00.008 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:01:00.008 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:01:00.009 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:LILAC_CALLING:LILAC': maxForks=0; fair=false; array=0 Oct-31 12:01:00.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE Oct-31 12:01:00.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ORANGE` matches process NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE Oct-31 12:01:00.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-31 12:01:00.100 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-31 12:01:00.100 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE': maxForks=0; fair=false; array=0 Oct-31 12:01:00.141 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Oct-31 12:01:00.144 [main] DEBUG nextflow.Session - Igniting dataflow network (146) Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_BWAMEM2_INDEX Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_HMF_DATA Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:FASTP Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:STAR_ALIGN Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:SAMTOOLS_SORT Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:SAMBAMBA_MERGE Oct-31 12:01:00.156 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_RNA:GATK4_MARKDUPLICATES Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:ISOFOX_QUANTIFICATION:ISOFOX Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:AMBER_PROFILING:AMBER Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:COBALT_PROFILING:COBALT Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_PREP Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_ASSEMBLE Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_DEPTH_ANNOTATOR Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:ESVEE_CALLING:ESVEE_CALL Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_GERMLINE Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:SAGE_CALLING:SAGE_SOMATIC Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_GERMLINE Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:PAVE_ANNOTATION:PAVE_SOMATIC Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_GERMLINE Oct-31 12:01:00.157 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:SAGE_APPEND:SAGE_APPEND_SOMATIC Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_GERMLINE Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:LINX_ANNOTATION:LINX_SOMATIC Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINX_VISUALISER Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:LINX_PLOTTING:LINXREPORT Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:BAMTOOLS_METRICS:BAMTOOLS Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:LILAC_CALLING:LILAC Oct-31 12:01:00.158 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE Oct-31 12:01:00.159 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_9cee0a7d835f4d0f: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/chord/main.nf Script_778a7c45b23e83e9: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/utils_nfcore_oncoanalyser_pipeline/main.nf Script_6fbcf8477f9d7d4c: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/nf-core/utils_nfcore_pipeline/main.nf Script_261fdaae3bf5d3ba: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/cobalt_profiling/main.nf Script_b964a1498e764655: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/esvee/prep/main.nf Script_c354d6bc16508bc9: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/cobalt/main.nf Script_9ba045ee13cef287: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/pave/germline/main.nf Script_c05eeaddcbeea95c: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/main.nf Script_19abf10e4896d7f7: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/esvee/depth_annotator/main.nf Script_9abcab3d0bdee3be: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/samtools/faidx/main.nf Script_434cc8cf500ac080: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/samtools/dict/main.nf Script_699c29a0df101b7f: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/sage/somatic/main.nf Script_eaea21ee0d8e2d4d: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/bwamem2/index/main.nf Script_48b741f4bbb16dbe: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/read_alignment_rna/main.nf Script_da85ce313a730e78: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/virusbreakend_calling/main.nf Script_9c257fb18fb56fca: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/bamtools/main.nf Script_ea1a8b792f276e4b: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/star/genomegenerate/main.nf Script_065c967274ac986e: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/sage/germline/main.nf Script_6f8f6fd655808700: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/star/align/main.nf Script_3bef418f1ff4bef7: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/gatk4/bwaindeximage/main.nf Script_b7ebd695bb00b3d5: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/sage/append/main.nf Script_f5cb13b5fe7ff0e2: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/prepare_reference/main.nf Script_f7e2e7c4db60ec97: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/gatk4/markduplicates/main.nf Script_0ce72e734ad77725: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/nf-core/utils_nextflow_pipeline/main.nf Script_2f8b269a69a5bca9: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/bwa/index/main.nf Script_d8b34b28c3042470: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/linx/germline/main.nf Script_fa0c398072f025b3: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/redux_processing/main.nf Script_4813ec5f4817f92f: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/sambamba/merge/main.nf Script_6a29cbcffdc53114: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/amber_profiling/main.nf Script_9789786853b398e3: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/sigs/main.nf Script_4b43cc259fe04212: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/linx_annotation/main.nf Script_9370d8a23054809a: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/fastp/main.nf Script_bebfb99f9eb931f6: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/purple_calling/main.nf Script_39f83d8979161e0a: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/custom/lilac_extract_and_index_contig/main.nf Script_ec6841c85f918c37: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/sage_calling/main.nf Script_8462266fec51fb58: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/virusinterpreter/main.nf Script_0a01436ea969f0dc: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/nf-core/samtools/sort/main.nf Script_c84696fa33d39a1e: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/linx/visualiser/main.nf Script_c8556a17d86276e7: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/custom/write_reference_data/main.nf Script_79a2a914f979653e: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/linxreport/main.nf Script_dabea116585c7965: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/custom/lilac_realign_reads_lilac/main.nf Script_95d756606ec07c28: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/workflows/wgts.nf Script_9019371f629336c6: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/purple/main.nf Script_bbf7cbbf056ac7ae: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/custom/extract_tarball/main.nf Script_7b555575044c30c2: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/esvee/assemble/main.nf Script_9b83485e7e97681f: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/linx_plotting/main.nf Script_66f227e949009287: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/neo_prediction/main.nf Script_2b074a84c3269973: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/isofox/main.nf Script_31053e1ff8ec0cda: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/virusbreakend/main.nf Script_99d6e9dfd4cd2f2d: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/orange/main.nf Script_6328d4cded3d38a4: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/cuppa/main.nf Script_a09cae02d9cea602: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/neo/finder/main.nf Script_4eb50016b469849d: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/workflows/targeted.nf Script_94253b1e3a4d9333: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/cuppa_prediction/main.nf Script_ed8dc4c407252d5b: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/linx/somatic/main.nf Script_b32a50e044416db0: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/esvee/call/main.nf Script_99f0e8de7a769c67: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/gridss/index/main.nf Script_1352d856742e1eb0: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/esvee_calling/main.nf Script_ea82b3516c9b2e70: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/chord_prediction/main.nf Script_739552aa56240093: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/orange_reporting/main.nf Script_9e248563f6679fca: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/lilac_calling/main.nf Script_480e15e618cb5eb2: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/read_alignment_dna/main.nf Script_571bea88e5350867: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/lilac/main.nf Script_215a636da7ab24a2: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/nf-core/utils_nfschema_plugin/main.nf Script_41e4af544572002b: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/isofox_quantification/main.nf Script_aa0d8cde8f027a71: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/custom/lilac_slice/main.nf Script_5c92460b9d9c4d04: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/neo/annotate_fusions/main.nf Script_45f2cca6f29341f5: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/amber/main.nf Script_a8d26716978b5628: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/pave/somatic/main.nf Script_7b4c1f51febb1bb7: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/sigs_fitting/main.nf Script_30b9efe616edea40: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/redux/main.nf Script_f6a3d85e61b3a704: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/bwa-mem2/mem/main.nf Script_e34e1b0d5bcc2c73: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/sage_append/main.nf Script_372159104c2a0c5f: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/bamtools_metrics/main.nf Script_fea454200f34d681: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/modules/local/neo/scorer/main.nf Script_0ee7ff4b7b6e44bf: /rds/homes/b/beggsa/.nextflow/assets/nf-core/oncoanalyser/subworkflows/local/pave_annotation/main.nf Oct-31 12:01:00.159 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Oct-31 12:01:00.159 [main] DEBUG nextflow.Session - Session await Oct-31 12:01:00.259 [Actor Thread 37] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastp:0.23.4--hadf994f_2; path=/rds/projects/b/beggsa-hpbcancer/KNNGS/work/singularity/depot.galaxyproject.org-singularity-fastp-0.23.4--hadf994f_2.img Oct-31 12:01:00.365 [Actor Thread 4] INFO nextflow.processor.TaskProcessor - [8e/73f416] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:FASTP (KN-01_KN-01_NORMAL) Oct-31 12:01:00.365 [Actor Thread 74] INFO nextflow.processor.TaskProcessor - [d3/54cfed] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:FASTP (KN-01_KN-01_TUMOUR) Oct-31 12:01:09.005 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/hmf_reference_data/hmftools/hmf_pipeline_resources.38_v2.0.0--3.tar.gz at /rds/projects/b/beggsa-hpbcancer/KNNGS/work/stage-49539eb0-3870-4f88-b7be-3ce5b6c3f5cd/fc/337f130998408e6448aee61b60d36b/hmf_pipeline_resources.38_v2.0.0--3.tar.gz Oct-31 12:01:09.005 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/bwa-mem2_index-2.2.1.tar.gz at /rds/projects/b/beggsa-hpbcancer/KNNGS/work/stage-49539eb0-3870-4f88-b7be-3ce5b6c3f5cd/dd/f14598ed9a2c75c26c6bfd0849301a/bwa-mem2_index-2.2.1.tar.gz Oct-31 12:01:09.007 [Actor Thread 4] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ubuntu:20.04; path=/rds/projects/b/beggsa-hpbcancer/KNNGS/work/singularity/depot.galaxyproject.org-singularity-ubuntu-20.04.img Oct-31 12:01:09.013 [Actor Thread 69] INFO nextflow.processor.TaskProcessor - [68/c9d210] Cached process > NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_HMF_DATA (1) Oct-31 12:01:09.013 [Actor Thread 14] INFO nextflow.processor.TaskProcessor - [55/0d5109] Cached process > NFCORE_ONCOANALYSER:TARGETED:PREPARE_REFERENCE:DECOMP_BWAMEM2_INDEX (1) Oct-31 12:01:34.626 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/GRCh38_masked_exclusions_alts_hlas.fasta at /rds/projects/b/beggsa-hpbcancer/KNNGS/work/stage-49539eb0-3870-4f88-b7be-3ce5b6c3f5cd/58/ec6fff908b0770538303d08298de1b/GRCh38_masked_exclusions_alts_hlas.fasta Oct-31 12:01:34.629 [Actor Thread 57] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:b39930b2feee9b7a3e5cbef88b34f0d5c5f64897-0; path=/rds/projects/b/beggsa-hpbcancer/KNNGS/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084-b39930b2feee9b7a3e5cbef88b34f0d5c5f64897-0.img Oct-31 12:01:34.655 [Actor Thread 69] INFO nextflow.processor.TaskProcessor - [ce/bd4266] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0005) Oct-31 12:01:34.658 [Actor Thread 14] INFO nextflow.processor.TaskProcessor - [f5/cc483f] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0004) Oct-31 12:01:34.660 [Actor Thread 4] INFO nextflow.processor.TaskProcessor - [9b/b7af20] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0004) Oct-31 12:01:34.754 [Actor Thread 74] INFO nextflow.processor.TaskProcessor - [dc/e5d21c] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0009) Oct-31 12:01:34.761 [Actor Thread 4] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.761 [Actor Thread 4] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.762 [Actor Thread 4] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.762 [Actor Thread 4] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.781 [Actor Thread 37] INFO nextflow.processor.TaskProcessor - [95/e8b219] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0007) Oct-31 12:01:34.783 [Actor Thread 4] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.788 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [70/895cdd] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0011) Oct-31 12:01:34.791 [Actor Thread 26] INFO nextflow.processor.TaskProcessor - [73/90c27d] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0012) Oct-31 12:01:34.791 [Actor Thread 63] INFO nextflow.processor.TaskProcessor - [71/a90006] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0002) Oct-31 12:01:34.793 [Actor Thread 62] INFO nextflow.processor.TaskProcessor - [0c/2d3b16] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0012) Oct-31 12:01:34.793 [Actor Thread 74] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.794 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.794 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [81/4f39fd] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0006) Oct-31 12:01:34.794 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.794 [Actor Thread 64] INFO nextflow.processor.TaskProcessor - [30/3bbac6] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0007) Oct-31 12:01:34.794 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [82/c6e7a7] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0008) Oct-31 12:01:34.795 [Actor Thread 60] INFO nextflow.processor.TaskProcessor - [fc/b1556e] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0005) Oct-31 12:01:34.795 [Actor Thread 50] INFO nextflow.processor.TaskProcessor - [b9/6a65b5] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0017) Oct-31 12:01:34.795 [Actor Thread 11] INFO nextflow.processor.TaskProcessor - [3a/ff129c] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0015) Oct-31 12:01:34.795 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.795 [Actor Thread 73] INFO nextflow.processor.TaskProcessor - [ea/5e3321] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0016) Oct-31 12:01:34.795 [Actor Thread 55] INFO nextflow.processor.TaskProcessor - [39/4d88cc] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0001) Oct-31 12:01:34.795 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.795 [Actor Thread 39] INFO nextflow.processor.TaskProcessor - [b5/cced78] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0009) Oct-31 12:01:34.796 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [1a/48ff4b] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0002) Oct-31 12:01:34.796 [Actor Thread 58] INFO nextflow.processor.TaskProcessor - [fd/0908b7] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0010) Oct-31 12:01:34.796 [Actor Thread 64] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.796 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.797 [Actor Thread 59] INFO nextflow.processor.TaskProcessor - [00/3b8b0d] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0003) Oct-31 12:01:34.797 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [3a/134f92] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0010) Oct-31 12:01:34.797 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [57/1aad9e] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0011) Oct-31 12:01:34.797 [Actor Thread 2] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.797 [Actor Thread 72] INFO nextflow.processor.TaskProcessor - [91/a65d1f] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0003) Oct-31 12:01:34.797 [Actor Thread 66] INFO nextflow.processor.TaskProcessor - [58/cbb906] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0018) Oct-31 12:01:34.797 [Actor Thread 73] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.798 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [43/c151b3] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0006) Oct-31 12:01:34.798 [Actor Thread 73] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.798 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [17/040242] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0014) Oct-31 12:01:34.798 [Actor Thread 52] INFO nextflow.processor.TaskProcessor - [83/9664c1] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0008) Oct-31 12:01:34.798 [Actor Thread 50] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.799 [Actor Thread 50] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.799 [Actor Thread 50] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.799 [Actor Thread 50] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.799 [Actor Thread 50] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.799 [Actor Thread 73] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.800 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.800 [Actor Thread 54] INFO nextflow.processor.TaskProcessor - [db/8a61e8] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_TUMOUR_0001) Oct-31 12:01:34.800 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.800 [Actor Thread 55] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.800 [Actor Thread 72] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.801 [Actor Thread 72] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.801 [Actor Thread 14] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:34.801 [Actor Thread 59] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.802 [Actor Thread 38] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:tumor] size=12 Oct-31 12:01:34.809 [Actor Thread 71] INFO nextflow.processor.TaskProcessor - [7b/77544f] Cached process > NFCORE_ONCOANALYSER:TARGETED:READ_ALIGNMENT_DNA:BWAMEM2_ALIGN (KN-01_KN-01_NORMAL_0013) Oct-31 12:01:34.810 [Actor Thread 77] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[key:KN-01, sample_type:normal] size=18 Oct-31 12:01:38.965 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/samtools_index-1.16/GRCh38_masked_exclusions_alts_hlas.fasta.fai at /rds/projects/b/beggsa-hpbcancer/KNNGS/work/stage-49539eb0-3870-4f88-b7be-3ce5b6c3f5cd/03/7208bcd7c8edd2480a9eb177f3c05c/GRCh38_masked_exclusions_alts_hlas.fasta.fai Oct-31 12:01:38.965 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes/GRCh38_hmf/25.1/samtools_index-1.16/GRCh38_masked_exclusions_alts_hlas.fasta.dict at /rds/projects/b/beggsa-hpbcancer/KNNGS/work/stage-49539eb0-3870-4f88-b7be-3ce5b6c3f5cd/fc/2d3fb946d7c0429d301e71ae6af8c2/GRCh38_masked_exclusions_alts_hlas.fasta.dict Oct-31 12:01:38.967 [Actor Thread 38] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/hmftools-redux:1.1.2--hdfd78af_0; path=/rds/projects/b/beggsa-hpbcancer/KNNGS/work/singularity/depot.galaxyproject.org-singularity-hmftools-redux-1.1.2--hdfd78af_0.img Oct-31 12:01:39.094 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR) > jobId: 30986889; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 Oct-31 12:01:39.095 [Task submitter] INFO nextflow.Session - [58/54a1dd] Submitted process > NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR) Oct-31 12:01:39.167 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL) > jobId: 30986890; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e Oct-31 12:01:39.167 [Task submitter] INFO nextflow.Session - [12/f1b8dd] Submitted process > NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL) Oct-31 12:06:03.832 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[jobId: 30986889; id: 35; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 started: 1761912123823; exited: -; ] ~> TaskHandler[jobId: 30986890; id: 36; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e started: 1761912128828; exited: -; ] Oct-31 12:10:58.846 [Task monitor] DEBUG nextflow.file.FileHelper - FS path type (false): /rds/projects/b/beggsa-hpbcancer/KNNGS/work Oct-31 12:11:03.846 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[jobId: 30986889; id: 35; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 started: 1761912123823; exited: -; ] ~> TaskHandler[jobId: 30986890; id: 36; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e started: 1761912128828; exited: -; ] Oct-31 12:15:28.856 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 30986889; id: 35; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 started: 1761912123823; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 274858 Current queue status: > job: 30982716: RUNNING > job: 30982378: RUNNING > job: 30986890: DONE > job: 30986889: DONE > job: 30986824: RUNNING Content of workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 null Oct-31 12:15:28.856 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30986889; id: 35; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR); status: COMPLETED; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 started: 1761912123823; exited: -; ] Oct-31 12:15:28.857 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Oct-31 12:15:28.879 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR); work-dir=/rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR)` terminated for an unknown reason -- Likely it has been terminated by the external system Oct-31 12:15:28.924 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR)' Caused by: Process `NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_TUMOUR)` terminated for an unknown reason -- Likely it has been terminated by the external system Command executed: redux \ -Xmx73443940762 \ \ -sample KN-01_TUMOUR \ -input_bam 0005.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0004.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0009.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0007.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0011.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0012.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0002.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0003.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0008.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0006.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0010.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam,0001.KN-01_TUMOUR.KN-01_TUMOUR.S1.001.bam \ -output_dir ./ \ -output_bam ./KN-01_TUMOUR.redux.bam \ -ref_genome GRCh38_masked_exclusions_alts_hlas.fasta \ -ref_genome_version 38 \ -unmap_regions unmap_regions.38.tsv \ -ref_genome_msi_file msi_jitter_sites.38.tsv.gz \ -bamtool $(which samtools) \ -form_consensus \ \ -write_stats \ -threads 12 \ -log_level DEBUG cat <<-END_VERSIONS > versions.yml "NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX": redux: $(redux -version | sed -n '/^Redux version/ { s/^.* //p }') samtools: $(samtools --version | sed -n '/^samtools / { s/^.* //p }') END_VERSIONS Command exit status: - Command output: (empty) Command error: 12:08:08.188 [Thread-22] [DEBUG] sorted-writer records written(11663874 writes=44557 avg=261 max=8776) maxCache(8777) to BAM(KN-01_TUMOUR.redux.21.sorted.bam) 12:08:12.341 [Thread-14] [DEBUG] region(chr17:1-83257441) position(41873801) processed 19M reads, cache(coords=268 reads=398) 12:08:14.341 [Thread-13] [DEBUG] region(chrX:1-102791667) position(85046367) processed 19M reads, cache(coords=34 reads=45) 12:08:14.416 [Thread-15] [DEBUG] region(chr16:1-62636568) position(28648265) processed 19M reads, cache(coords=446 reads=596) 12:08:19.120 [Thread-20] [DEBUG] region(chr19:1-58617616) position(45830015) processed 19M reads, cache(coords=99 reads=149) 12:08:25.228 [Thread-13] [DEBUG] region(chrX:1-102791667) complete, processed 19719797 reads 12:08:25.229 [Thread-13] [DEBUG] partition(22: 2 regions: chr22:24931535-50818468;chrX:1-102791667) reader complete, total reads(8893293) 12:08:25.229 [Thread-13] [DEBUG] completed 21 partition readers 12:08:25.229 [Thread-13] [DEBUG] sorted-writer records written(11021303 writes=46600 avg=236 max=11045) maxCache(14334) to BAM(KN-01_TUMOUR.redux.22.sorted.bam) 12:08:27.417 [Thread-14] [DEBUG] region(chr17:1-83257441) position(45081633) processed 20M reads, cache(coords=241 reads=385) 12:08:29.387 [Thread-15] [DEBUG] region(chr16:1-62636568) position(31330071) processed 20M reads, cache(coords=174 reads=257) 12:08:34.321 [Thread-20] [DEBUG] region(chr19:1-58617616) position(49960237) processed 20M reads, cache(coords=623 reads=882) 12:08:42.392 [Thread-14] [DEBUG] region(chr17:1-83257441) position(50195260) processed 21M reads, cache(coords=254 reads=388) 12:08:43.700 [Thread-15] [DEBUG] region(chr16:1-62636568) position(56568911) processed 21M reads, cache(coords=338 reads=567) 12:08:49.207 [Thread-20] [DEBUG] region(chr19:1-58617616) position(54634978) processed 21M reads, cache(coords=8 reads=13) 12:08:51.178 [Thread-15] [DEBUG] region(chr16:1-62636568) complete, processed 21510744 reads 12:08:51.178 [Thread-15] [DEBUG] partition(18: 2 regions: chr15:35949157-101991189;chr16:1-62636568) reader complete, total reads(12525224) 12:08:51.178 [Thread-15] [DEBUG] completed 22 partition readers 12:08:51.178 [Thread-15] [DEBUG] sorted-writer records written(15390910 writes=63034 avg=244 max=4820) maxCache(6999) to BAM(KN-01_TUMOUR.redux.18.sorted.bam) 12:08:57.040 [Thread-14] [DEBUG] region(chr17:1-83257441) position(61368457) processed 22M reads, cache(coords=631 reads=1110) 12:09:03.644 [Thread-20] [DEBUG] region(chr19:1-58617616) position(58480565) processed 22M reads, cache(coords=224 reads=388) 12:09:04.250 [Thread-20] [DEBUG] region(chr19:1-58617616) complete, processed 22042924 reads 12:09:11.664 [Thread-14] [DEBUG] region(chr17:1-83257441) position(68524898) processed 23M reads, cache(coords=492 reads=882) 12:09:13.430 [Thread-20] [DEBUG] region(chr20:1-7407083) complete, processed 22681868 reads 12:09:13.430 [Thread-20] [DEBUG] partition(20: 3 regions: chr18:17719384-80373285;chr19:1-58617616;chr20:1-7407083) reader complete, total reads(13286060) 12:09:13.430 [Thread-20] [DEBUG] completed 23 partition readers 12:09:13.430 [Thread-20] [DEBUG] sorted-writer records written(16461688 writes=70476 avg=233 max=6531) maxCache(6532) to BAM(KN-01_TUMOUR.redux.20.sorted.bam) 12:09:26.028 [Thread-14] [DEBUG] region(chr17:1-83257441) position(76155674) processed 24M reads, cache(coords=511 reads=794) 12:09:40.317 [Thread-14] [DEBUG] region(chr17:1-83257441) position(81833670) processed 25M reads, cache(coords=61 reads=90) 12:09:45.047 [Thread-14] [DEBUG] region(chr17:1-83257441) complete, processed 25330794 reads 12:09:54.779 [Thread-14] [DEBUG] region(chr18:1-17719383) position(14538169) processed 26M reads, cache(coords=603 reads=897) 12:09:55.405 [Thread-14] [DEBUG] region(chr18:1-17719383) complete, processed 26041962 reads 12:09:55.405 [Thread-14] [DEBUG] partition(19: 3 regions: chr16:62636569-90338345;chr17:1-83257441;chr18:1-17719383) reader complete, total reads(16484177) 12:09:55.405 [Thread-14] [DEBUG] completed 24 partition readers 12:09:55.405 [Thread-14] [DEBUG] sorted-writer records written(20441950 writes=74163 avg=275 max=6484) maxCache(6806) to BAM(KN-01_TUMOUR.redux.19.sorted.bam) 12:09:55.408 [main] [INFO ] all partition tasks complete 12:09:55.408 [main] [INFO ] analysing microsatellite jitter 12:10:02.289 [main] [DEBUG] unsorted-writer records written(603032) to BAM(KN-01_TUMOUR.redux.full_unmapped.bam) 12:10:02.293 [main] [DEBUG] concatenating 25 BAMs 12:10:09.813 [main] [DEBUG] final concatenate complete: ./KN-01_TUMOUR.redux.bam 12:10:09.813 [main] [DEBUG] indexing BAM: ./KN-01_TUMOUR.redux.bam 12:10:27.988 [main] [DEBUG] final BAM complete: ./KN-01_TUMOUR.redux.bam 12:10:27.998 [main] [INFO ] stats: totalReads(217990136) duplicates(80722205) dupGroups(51704141) umiGroups(0) 12:10:27.998 [main] [INFO ] consensus stats: dualStrandMismatches(groups=2761802 reads=7663428) outcomes(ALIGNMENT_ONLY=50895123, INDEL_MATCH=315254, INDEL_MISMATCH=429486) 12:10:27.999 [main] [DEBUG] duplicate frequency: 1=84781666, 2=33099715, 3=11982976, 4=4240344, 5=1511025, 6=543456, 7=201275, 8=75810, 9=29378, 10=20080, 20=56, 30=6, 50=2, 60=4, 70=2, 80=4, 90=2, 100=4, 300=2 12:10:27.999 [main] [DEBUG] re-unmapped stats: reads(203966) mates(206189) both(429116 existing=0) supps(read=149042 align=82787) seconds(0) reasons(depth=643178 softClip=78412 chimeric=8126) 12:10:28.000 [main] [INFO ] PerfStat(Total) intervals(44) total(3365.263 avg=76.483 max=192.572) 12:10:28.000 [main] [INFO ] PerfStat(ProcessDuplicates) intervals(44) total(2545.846 avg=57.860 max=146.593) 12:10:28.000 [main] [INFO ] Redux complete, mins(8.380) /usr/local/bin/redux: line 6: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory Work dir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/58/54a1ddabf59b1bc07224e116ce2616 Container: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/singularity/depot.galaxyproject.org-singularity-hmftools-redux-1.1.2--hdfd78af_0.img Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` Oct-31 12:15:28.931 [TaskFinalizer-1] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Oct-31 12:15:28.936 [TaskFinalizer-1] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting Oct-31 12:15:28.937 [main] DEBUG nextflow.Session - Session await > all processes finished Oct-31 12:15:28.948 [Actor Thread 64] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 3; slices: 1; internal sort time: 0.002 s; external sort time: 0.001 s; total time: 0.003 s Oct-31 12:15:28.950 [Actor Thread 64] DEBUG nextflow.file.FileCollector - >> temp file exists? true Oct-31 12:15:28.978 [Actor Thread 64] DEBUG nextflow.file.FileCollector - Retrieved cached collect-files from: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/collect-file/bbeae3eed6f3a80c8902eaff4d147127 Oct-31 12:15:28.983 [Actor Thread 64] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-5746126379053732103 Oct-31 12:16:03.938 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 30986890; id: 36; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e started: 1761912128828; exited: -; ] Oct-31 12:18:28.939 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 30986890; id: 36; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL); status: RUNNING; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e started: 1761912128828; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270070 Current queue status: > job: 30982716: RUNNING > job: 30982378: RUNNING > job: 30986890: DONE > job: 30986824: RUNNING Content of workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e null Oct-31 12:18:28.940 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 30986890; id: 36; name: NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL); status: COMPLETED; exit: -; error: -; workDir: /rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e started: 1761912128828; exited: -; ] Oct-31 12:18:28.940 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Oct-31 12:18:28.940 [main] DEBUG nextflow.Session - Session await > all barriers passed Oct-31 12:18:28.956 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL); work-dir=/rds/projects/b/beggsa-hpbcancer/KNNGS/work/12/f1b8ddf53dc8390ab6a9ae618f8b7e error [nextflow.exception.ProcessFailedException]: Process `NFCORE_ONCOANALYSER:TARGETED:REDUX_PROCESSING:REDUX (KN-01_KN-01_NORMAL)` terminated for an unknown reason -- Likely it has been terminated by the external system Oct-31 12:18:28.958 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) Oct-31 12:18:28.962 [main] INFO nextflow.Nextflow - -[nf-core/oncoanalyser] Pipeline completed with errors- Oct-31 12:18:28.965 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=2; ignoredCount=0; cachedCount=34; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=3h 57m 12s; cachedDuration=14h 15m 19s;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=24; peakMemory=144 GB; ] Oct-31 12:18:28.965 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Oct-31 12:18:28.968 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Oct-31 12:18:29.609 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Oct-31 12:18:30.028 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Oct-31 12:18:30.065 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.3.0' Oct-31 12:18:30.065 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema Oct-31 12:18:30.066 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Oct-31 12:18:30.067 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye