Nov-11 10:00:48.834 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/magmap -r dev -profile pdc_kth -params-file params.yml -c nextflow.config Nov-11 10:00:48.992 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.7 Nov-11 10:00:49.032 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/cfs/klemming/home/n/nicoivan/.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 Nov-11 10:00:49.070 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Nov-11 10:00:49.072 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Nov-11 10:00:49.077 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Nov-11 10:00:49.097 [main] INFO org.pf4j.AbstractPluginManager - No plugins Nov-11 10:00:49.117 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /cfs/klemming/home/n/nicoivan/.nextflow/scm Nov-11 10:00:50.501 [main] DEBUG nextflow.scm.AssetManager - Git config: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/magmap.git Nov-11 10:00:50.552 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Nov-11 10:00:50.567 [main] DEBUG nextflow.scm.AssetManager - Git config: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/magmap.git Nov-11 10:00:51.512 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/nextflow.config Nov-11 10:00:51.514 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/nextflow.config Nov-11 10:00:51.517 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/nextflow.config Nov-11 10:00:51.519 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/nextflow.config Nov-11 10:00:51.520 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/nextflow.config Nov-11 10:00:51.520 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/nextflow.config Nov-11 10:00:51.533 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /cfs/klemming/home/n/nicoivan/.nextflow/secrets/store.json Nov-11 10:00:51.537 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2b53840a] - activable => nextflow.secret.LocalSecretsProvider@2b53840a Nov-11 10:00:51.691 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `pdc_kth` Nov-11 10:00:53.813 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `pdc_kth` Nov-11 10:00:53.882 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `pdc_kth` Nov-11 10:00:53.903 [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, test_duplicates, 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, test_metadata, 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, munin, rosalind, hasta, cfc, emulate_amd64, 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, alliance_canada, arm64, test_sourmash, mpcdf, leicester, vsc_ugent, create, sage, cambridge, test_single, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, gpu, 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, phoenix, seawulf, uod_hpc, fub_curta, test_sourmash_mix, lovelace, uct_hpc, aws_tower, binac, fsu_draco] Nov-11 10:00:53.984 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default Nov-11 10:00:53.985 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/magmap` [compassionate_noyce] DSL2 - revision: 6f58b2b3ad [dev] Nov-11 10:00:53.988 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.5.1] Nov-11 10:00:53.989 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Nov-11 10:00:53.990 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.5.1] Nov-11 10:00:53.993 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.5.1 Nov-11 10:00:54.152 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.5.1' resolved Nov-11 10:00:54.153 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.5.1' Nov-11 10:00:54.223 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.5.1 Nov-11 10:00:54.403 [main] DEBUG nextflow.Session - Session UUID: 8ee3a7bd-3427-4823-944f-23ead943a526 Nov-11 10:00:54.404 [main] DEBUG nextflow.Session - Run name: compassionate_noyce Nov-11 10:00:54.456 [main] DEBUG nextflow.Session - Executor pool size: 256 Nov-11 10:00:54.470 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Nov-11 10:00:54.477 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Nov-11 10:00:54.682 [main] DEBUG nextflow.cli.CmdRun - Version: 25.04.7 build 5955 Created: 08-09-2025 13:29 UTC (15:29 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: 2210286@login1 [10.253.0.5] CPUs: 256 - Mem: 502.2 GB (207.9 GB) - Swap: 0 (0) Nov-11 10:00:54.723 [main] DEBUG nextflow.Session - Work-dir: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work [lustre] Nov-11 10:00:54.724 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/bin Nov-11 10:00:54.743 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Nov-11 10:00:54.756 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Nov-11 10:00:54.782 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory Nov-11 10:00:54.786 [main] DEBUG nextflow.Session - Observer factory (v2): ValidationObserverFactory Nov-11 10:00:54.839 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Nov-11 10:00:54.849 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 257; maxThreads: 1000 Nov-11 10:00:55.037 [main] DEBUG nextflow.Session - Session start Nov-11 10:00:55.041 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/results_magmap/pipeline_info/execution_trace_2025-11-11_10-00-51.txt Nov-11 10:00:55.519 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Nov-11 10:00:58.985 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Nov-11 10:00:59.002 [main] DEBUG n.validation.config.ValidationConfig - Set `validation.monochromeLogs` to false Nov-11 10:00:59.006 [main] DEBUG n.validation.config.ValidationConfig - Added the following parameters to the ignored parameters: [cluster-options, clusterOptions, clusterName, genomes, ignore_params_list, input_paths, max_cpus, max_memory, max_time, project, schema_ignore_params, validationSchemaIgnoreParams] Nov-11 10:00:59.006 [main] DEBUG n.validation.config.ValidationConfig - Added the following parameters to the ignored parameters: [genomes] Nov-11 10:00:59.037 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Nov-11 10:00:59.038 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Nov-11 10:00:59.043 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Nov-11 10:00:59.044 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Nov-11 10:00:59.045 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Nov-11 10:00:59.356 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Nov-11 10:01:00.143 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Nov-11 10:01:00.144 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Nov-11 10:01:00.145 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Nov-11 10:01:00.147 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Nov-11 10:01:00.147 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Nov-11 10:01:00.148 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Nov-11 10:01:00.367 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/magmap 1.0.0 ------------------------------------------------------ Nov-11 10:01:00.422 [main] INFO nextflow.Nextflow - Input/output options input : fastq_samplesheet.csv genomeinfo : MAG_samplesheet.csv outdir : results_magmap Quality control options skip_qc : true skip_fastqc : true Trimming options skip_trimming : true Mapping options bbmap_save_bam : true bbmap_save_index : true save_concatenated_genomes : true Sourmash skip_sourmash : false sourmash_save_sourmash : true sourmash_save_prefetch_csv: true 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 : 2025-11-11_10-00-51 Core Nextflow options revision : dev runName : compassionate_noyce containerEngine : singularity launchDir : /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap workDir : /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work projectDir : /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap userName : nicoivan profile : pdc_kth configFiles : /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/nextflow.config, /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/nextflow.config, /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ Nov-11 10:01:00.424 [main] INFO nextflow.Nextflow - * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/magmap/blob/master/CITATIONS.md Nov-11 10:01:00.434 [main] DEBUG n.v.parameters.ParameterValidator - Starting parameters validation Nov-11 10:01:00.608 [main] DEBUG n.v.v.evaluators.SchemaEvaluator - Started validating /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/MAG_samplesheet.csv Nov-11 10:01:01.682 [main] DEBUG n.v.v.evaluators.SchemaEvaluator - Validation of file 'MAG_samplesheet.csv' passed! Nov-11 10:01:01.685 [main] DEBUG n.v.v.evaluators.SchemaEvaluator - Started validating /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/fastq_samplesheet.csv Nov-11 10:01:01.798 [main] DEBUG n.v.v.evaluators.SchemaEvaluator - Validation of file 'fastq_samplesheet.csv' passed! Nov-11 10:01:01.852 [main] DEBUG n.v.parameters.ParameterValidator - Finishing parameters validation Nov-11 10:01:02.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_MAGMAP:MAGMAP:CHECK_DUPLICATES Nov-11 10:01:02.247 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.248 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.263 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Nov-11 10:01:02.270 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Nov-11 10:01:02.272 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Nov-11 10:01:02.275 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Nov-11 10:01:02.307 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CHECK_DUPLICATES': maxForks=0; fair=false; array=0 Nov-11 10:01:02.407 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_MAGMAP:MAGMAP:RENAME_CONTIGS Nov-11 10:01:02.416 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.417 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.419 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:RENAME_CONTIGS': maxForks=0; fair=false; array=0 Nov-11 10:01:02.449 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:FASTQC Nov-11 10:01:02.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_MAGMAP:MAGMAP:FASTQC Nov-11 10:01:02.461 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.461 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.463 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:FASTQC': maxForks=0; fair=false; array=0 Nov-11 10:01:02.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:CAT_FASTQ Nov-11 10:01:02.497 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.497 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.498 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CAT_FASTQ': maxForks=0; fair=false; array=0 Nov-11 10:01:02.569 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:SOURMASH:SAMPLE_SKETCH Nov-11 10:01:02.572 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLE_SKETCH` matches process NFCORE_MAGMAP:MAGMAP:SOURMASH:SAMPLE_SKETCH Nov-11 10:01:02.577 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.577 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.578 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:SOURMASH:SAMPLE_SKETCH': maxForks=0; fair=false; array=0 Nov-11 10:01:02.592 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_SKETCH Nov-11 10:01:02.595 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GENOME_SKETCH` matches process NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_SKETCH Nov-11 10:01:02.599 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.599 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.600 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_SKETCH': maxForks=0; fair=false; array=0 Nov-11 10:01:02.618 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_INDEX Nov-11 10:01:02.620 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SOURMASH_INDEX` matches process NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_INDEX Nov-11 10:01:02.622 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GENOME_INDEX` matches process NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_INDEX Nov-11 10:01:02.628 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.628 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.629 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_INDEX': maxForks=0; fair=false; array=0 Nov-11 10:01:02.659 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:SOURMASH:GATHER_USER_GENOMES Nov-11 10:01:02.663 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SOURMASH_GATHER` matches process NFCORE_MAGMAP:MAGMAP:SOURMASH:GATHER_USER_GENOMES Nov-11 10:01:02.670 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.670 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.672 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:SOURMASH:GATHER_USER_GENOMES': maxForks=0; fair=false; array=0 Nov-11 10:01:02.736 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:TIDYVERSE_JOINMETADATA Nov-11 10:01:02.737 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TIDYVERSE_JOINMETADATA` matches process NFCORE_MAGMAP:MAGMAP:TIDYVERSE_JOINMETADATA Nov-11 10:01:02.741 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.741 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.742 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:TIDYVERSE_JOINMETADATA': maxForks=0; fair=false; array=0 Nov-11 10:01:02.779 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_MAGMAP:MAGMAP:PROKKA Nov-11 10:01:02.780 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PROKKA` matches process NFCORE_MAGMAP:MAGMAP:PROKKA Nov-11 10:01:02.789 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.789 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.790 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:PROKKA': maxForks=0; fair=false; array=0 Nov-11 10:01:02.815 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV Nov-11 10:01:02.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PROKKAGFF2TSV` matches process NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV Nov-11 10:01:02.820 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.820 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.822 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV': maxForks=0; fair=false; array=0 Nov-11 10:01:02.841 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:CATPROKKATSVS Nov-11 10:01:02.842 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CATPROKKATSVS` matches process NFCORE_MAGMAP:MAGMAP:CATPROKKATSVS Nov-11 10:01:02.845 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.846 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.847 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CATPROKKATSVS': maxForks=0; fair=false; array=0 Nov-11 10:01:02.871 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:CAT_FNA Nov-11 10:01:02.872 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_MANY` matches process NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:CAT_FNA Nov-11 10:01:02.876 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.876 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.877 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:CAT_FNA': maxForks=0; fair=false; array=0 Nov-11 10:01:02.890 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:BBMAP_INDEX Nov-11 10:01:02.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_INDEX` matches process NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:BBMAP_INDEX Nov-11 10:01:02.894 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.894 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.895 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:BBMAP_INDEX': maxForks=0; fair=false; array=0 Nov-11 10:01:02.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:CAT_GFF Nov-11 10:01:02.921 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_MANY` matches process NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:CAT_GFF Nov-11 10:01:02.925 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.925 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.926 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:CAT_GFF': maxForks=0; fair=false; array=0 Nov-11 10:01:02.940 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:GENOMES2ORFS Nov-11 10:01:02.941 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GENOMES2ORFS` matches process NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:GENOMES2ORFS Nov-11 10:01:02.945 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.945 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.946 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:GENOMES2ORFS': maxForks=0; fair=false; array=0 Nov-11 10:01:02.962 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_MAGMAP:MAGMAP:BBMAP_ALIGN Nov-11 10:01:02.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_ALIGN` matches process NFCORE_MAGMAP:MAGMAP:BBMAP_ALIGN Nov-11 10:01:02.967 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:02.967 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:02.970 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:BBMAP_ALIGN': maxForks=5; fair=false; array=0 Nov-11 10:01:02.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Nov-11 10:01:02.998 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_SORT` matches process NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Nov-11 10:01:03.003 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.003 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.004 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT': maxForks=0; fair=false; array=0 Nov-11 10:01:03.021 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Nov-11 10:01:03.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_INDEX` matches process NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Nov-11 10:01:03.025 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.025 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.026 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX': maxForks=0; fair=false; array=0 Nov-11 10:01:03.051 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Nov-11 10:01:03.054 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.055 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.056 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS': maxForks=0; fair=false; array=0 Nov-11 10:01:03.068 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Nov-11 10:01:03.072 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.072 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.073 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT': maxForks=0; fair=false; array=0 Nov-11 10:01:03.085 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Nov-11 10:01:03.089 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.089 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.090 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS': maxForks=0; fair=false; array=0 Nov-11 10:01:03.132 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:FEATURECOUNTS Nov-11 10:01:03.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FEATURECOUNTS` matches process NFCORE_MAGMAP:MAGMAP:FEATURECOUNTS Nov-11 10:01:03.137 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.137 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.138 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:FEATURECOUNTS': maxForks=0; fair=false; array=0 Nov-11 10:01:03.165 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_MAGMAP:MAGMAP:COLLECT_FEATURECOUNTS Nov-11 10:01:03.166 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLECT_FEATURECOUNTS` matches process NFCORE_MAGMAP:MAGMAP:COLLECT_FEATURECOUNTS Nov-11 10:01:03.170 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.170 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.171 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:COLLECT_FEATURECOUNTS': maxForks=0; fair=false; array=0 Nov-11 10:01:03.201 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_MAGMAP:MAGMAP:COLLECT_STATS Nov-11 10:01:03.202 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLECT_STATS` matches process NFCORE_MAGMAP:MAGMAP:COLLECT_STATS Nov-11 10:01:03.205 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.205 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.206 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:COLLECT_STATS': maxForks=0; fair=false; array=0 Nov-11 10:01:03.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_MAGMAP:MAGMAP:MULTIQC Nov-11 10:01:03.325 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_MAGMAP:MAGMAP:MULTIQC Nov-11 10:01:03.328 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Nov-11 10:01:03.328 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Nov-11 10:01:03.329 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_MAGMAP:MAGMAP:MULTIQC': maxForks=0; fair=false; array=0 Nov-11 10:01:03.353 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Nov-11 10:01:03.361 [main] DEBUG nextflow.Session - Igniting dataflow network (59) Nov-11 10:01:03.374 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CHECK_DUPLICATES Nov-11 10:01:03.375 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:RENAME_CONTIGS Nov-11 10:01:03.376 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:FASTQC Nov-11 10:01:03.376 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CAT_FASTQ Nov-11 10:01:03.377 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:SOURMASH:SAMPLE_SKETCH Nov-11 10:01:03.379 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_SKETCH Nov-11 10:01:03.380 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_INDEX Nov-11 10:01:03.380 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:SOURMASH:GATHER_USER_GENOMES Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:TIDYVERSE_JOINMETADATA Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:PROKKA Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CATPROKKATSVS Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:CAT_FNA Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:BBMAP_INDEX Nov-11 10:01:03.381 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:CAT_GFF Nov-11 10:01:03.382 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:GENOMES2ORFS Nov-11 10:01:03.382 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:BBMAP_ALIGN Nov-11 10:01:03.382 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Nov-11 10:01:03.382 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Nov-11 10:01:03.382 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Nov-11 10:01:03.383 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Nov-11 10:01:03.383 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Nov-11 10:01:03.383 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:FEATURECOUNTS Nov-11 10:01:03.383 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:COLLECT_FEATURECOUNTS Nov-11 10:01:03.383 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:COLLECT_STATS Nov-11 10:01:03.383 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_MAGMAP:MAGMAP:MULTIQC Nov-11 10:01:03.385 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_8251928f53ed1e0e: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/multiqc/main.nf Script_34b663632f5dcc61: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/main.nf Script_4e610db5143dfa3f: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/samtools/sort/main.nf Script_ae950eeec1345c8e: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/check_duplicates/main.nf Script_a89a8eb0e38bd916: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/local/utils_nfcore_magmap_pipeline/main.nf Script_776359021c0ac0a7: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/bbmap/align/main.nf Script_cdbce3e23a8f89e8: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/nf-core/bam_stats_samtools/main.nf Script_ab9d37b7e19e2782: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/wget/main.nf Script_9e61b79b569950a4: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/fastqc/main.nf Script_8974b9e137818591: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/sourmash/gather/main.nf Script_5c4e8d4051efa81e: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/nf-core/utils_nfcore_pipeline/main.nf Script_103cc12b4357ab09: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/sourmash/sketch/main.nf Script_4e51b53ff7a33a0f: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/bbmap/bbduk/main.nf Script_5c5e6babfb5fb619: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/trimgalore/main.nf Script_064989274e168ddc: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/local/fastqc_trimgalore/main.nf Script_e1be835428ea039c: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/nf-core/bam_sort_stats_samtools/main.nf Script_b4dc0339975d9eb7: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/local/create_bbmap_index/main.nf Script_a0ac0f9abefeffd0: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/samtools/idxstats/main.nf Script_3a292bdd82144bb0: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/subread/featurecounts/main.nf Script_a4c3fa6815f7b5b5: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/prokkagff2tsv/main.nf Script_a64a54a01f8015c7: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/nf-core/utils_nfschema_plugin/main.nf Script_d1559ea7c4f51362: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/tidyverse/joinmetadata/main.nf Script_c3332886c873cfed: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/local/sourmash/main.nf Script_42a4e6f8689cd5f7: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/local/concatenate_gffs/main.nf Script_56ce3a4ba927db10: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/sourmash/index/main.nf Script_91dc0e2bf71ccbd5: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/samtools/index/main.nf Script_4f612cfd8c52e8cd: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/subworkflows/nf-core/utils_nextflow_pipeline/main.nf Script_0adc741e8c6203ff: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/cat/many/main.nf Script_b0b356a5a2de7bc6: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/samtools/flagstat/main.nf Script_97dbaa14cb0e7c10: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/bbmap/index/main.nf Script_dc23542cc2d5cc52: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/prokka/main.nf Script_100de6434084c6fe: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/workflows/magmap.nf Script_4779b6382e5427ab: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/cat/fastq/main.nf Script_2cfdc1c6875129ad: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/nf-core/samtools/stats/main.nf Script_dfc7d9812f22461b: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/genomes_2_orfs/main.nf Script_b4cb463a550a49dc: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/collect/stats/main.nf Script_4b983426db329789: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/collect/featurecounts/main.nf Script_7abf5aaad25d1c3a: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/catprokkatsvs/main.nf Script_24a1c7bf00e5ff99: /cfs/klemming/home/n/nicoivan/.nextflow/assets/nf-core/magmap/modules/local/rename_contigs/main.nf Nov-11 10:01:03.386 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Nov-11 10:01:03.386 [main] DEBUG nextflow.Session - Session await Nov-11 10:01:03.387 [Actor Thread 250] ERROR nextflow.extension.OperatorImpl - @unknown java.lang.NullPointerException: Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null at java.base/java.nio.file.Files.provider(Files.java:105) at java.base/java.nio.file.Files.newInputStream(Files.java:160) at nextflow.file.SlurperEx.load(SlurperEx.groovy:67) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_5c4e8d4051efa81e.processVersionsFromYAML(Script_5c4e8d4051efa81e:82) 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:343) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_5c4e8d4051efa81e$_softwareVersionsToYAML_closure2.doCall(Script_5c4e8d4051efa81e:101) 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 org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56) at jdk.internal.reflect.GeneratedMethodAccessor118.invoke(Unknown Source) 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 groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108) at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43) at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293) at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:833) Nov-11 10:01:03.404 [Actor Thread 250] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke "java.nio.file.Path.getFileSystem()" because "path" is null Nov-11 10:01:03.488 [Actor Thread 250] DEBUG nextflow.Session - The following nodes are still active: [process] NFCORE_MAGMAP:MAGMAP:CHECK_DUPLICATES status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:RENAME_CONTIGS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:FASTQC status=ACTIVE port 0: (queue) closed; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:CAT_FASTQ [process] NFCORE_MAGMAP:MAGMAP:SOURMASH:SAMPLE_SKETCH status=ACTIVE port 0: (queue) closed; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_SKETCH status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:SOURMASH:GENOME_INDEX status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: ksize port 2: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:SOURMASH:GATHER_USER_GENOMES status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) OPEN ; channel: - port 2: (value) bound ; channel: save_unassigned port 3: (value) bound ; channel: save_matches_sig port 4: (value) bound ; channel: save_prefetch port 5: (value) bound ; channel: save_prefetch_csv port 6: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:TIDYVERSE_JOINMETADATA status=ACTIVE port 0: (queue) OPEN ; channel: genomes port 1: (value) bound ; channel: gtdb_metadata port 2: (value) bound ; channel: gtdbtk_metadata port 3: (value) bound ; channel: checkm_metadata port 4: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:PROKKA status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: proteins port 2: (value) bound ; channel: prodigal_tf port 3: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:PROKKAGFF2TSV status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:CATPROKKATSVS status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:CAT_FNA status=ACTIVE port 0: (value) bound ; channel: meta port 1: (value) OPEN ; channel: files2cat port 2: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:CREATE_BBMAP_INDEX:BBMAP_INDEX status=ACTIVE port 0: (value) OPEN ; channel: fasta port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:CAT_GFF status=ACTIVE port 0: (value) bound ; channel: meta port 1: (value) OPEN ; channel: files2cat port 2: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:CONCATENATE_GFFS:GENOMES2ORFS status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:BBMAP_ALIGN status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) OPEN ; channel: ref port 2: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) OPEN ; channel: - port 2: (value) bound ; channel: index_format port 3: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) OPEN ; channel: - port 2: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:FEATURECOUNTS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:COLLECT_FEATURECOUNTS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:COLLECT_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_MAGMAP:MAGMAP:MULTIQC status=ACTIVE port 0: (value) OPEN ; channel: multiqc_files port 1: (value) bound ; channel: multiqc_config port 2: (value) bound ; channel: extra_multiqc_config port 3: (value) bound ; channel: multiqc_logo port 4: (value) bound ; channel: replace_names port 5: (value) bound ; channel: sample_names port 6: (cntrl) - ; channel: $ Nov-11 10:01:03.501 [Actor Thread 250] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting Nov-11 10:01:03.505 [main] DEBUG nextflow.Session - Session await > all processes finished Nov-11 10:01:03.506 [main] DEBUG nextflow.Session - Session await > all barriers passed Nov-11 10:01:03.506 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Nov-11 10:01:03.514 [Actor Thread 144] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Nov-11 10:01:03.514 [Actor Thread 192] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_MAGMAP:MAGMAP:SOURMASH:SAMPLE_SKETCH; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Nov-11 10:01:03.514 [Actor Thread 133] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_MAGMAP:MAGMAP:BBMAP_ALIGN; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Nov-11 10:01:03.515 [Actor Thread 127] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_MAGMAP:MAGMAP:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Nov-11 10:01:03.515 [Actor Thread 215] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_MAGMAP:MAGMAP:FASTQC; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException Nov-11 10:01:03.516 [Actor Thread 120] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Nov-11 10:01:03.537 [main] INFO nextflow.Nextflow - -[nf-core/magmap] Pipeline completed with errors- Nov-11 10:01:03.554 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] Nov-11 10:01:03.554 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Nov-11 10:01:03.556 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Nov-11 10:01:03.574 [Actor Thread 140] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.008 s; external sort time: 0.041 s; total time: 0.049 s Nov-11 10:01:03.574 [Actor Thread 253] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.008 s; external sort time: 0.041 s; total time: 0.049 s Nov-11 10:01:03.574 [Actor Thread 255] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.008 s; external sort time: 0.041 s; total time: 0.049 s Nov-11 10:01:03.583 [Actor Thread 255] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work/collect-file/802e22f57b30bd29f0336cbb6e1f4162 Nov-11 10:01:03.583 [Actor Thread 253] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work/collect-file/a947b341248e794cba70b258d250b25b Nov-11 10:01:03.584 [Actor Thread 140] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work/collect-file/7661a8ca4719d3ded5cbf603ae89e20a Nov-11 10:01:03.619 [Actor Thread 253] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-11601566545154270031 Nov-11 10:01:03.619 [Actor Thread 140] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-3907349689611092145 Nov-11 10:01:03.619 [Actor Thread 255] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-14836014928945865164 Nov-11 10:01:03.673 [Actor Thread 255] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Nov-11 10:01:03.674 [Actor Thread 255] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/sourmash:4.9.4--hdfd78af_0 [cache /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work/singularity/depot.galaxyproject.org-singularity-sourmash-4.9.4--hdfd78af_0.img] Nov-11 10:01:03.674 [Actor Thread 253] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0 [cache /cfs/klemming/scratch/n/nicoivan/Project_1/Mutation_analysis/magmap/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img] Nov-11 10:01:04.345 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Nov-11 10:01:04.570 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Nov-11 10:01:04.610 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.5.1' Nov-11 10:01:04.611 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema Nov-11 10:01:04.616 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye