Mar-17 19:22:16.241 [main] DEBUG nextflow.cli.Launcher - Setting HTTP proxy: ProxyConfig[protocol=http; host=10.129.62.115; port=3128] Mar-17 19:22:16.292 [main] DEBUG nextflow.cli.Launcher - Setting HTTPS proxy: ProxyConfig[protocol=https; host=10.129.62.115; port=3128] Mar-17 19:22:16.293 [main] DEBUG nextflow.cli.Launcher - Setting FTP proxy: ProxyConfig[protocol=ftp; host=10.129.62.115; port=3128] Mar-17 19:22:16.293 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: ProxyConfig[protocol=http; host=10.129.62.115; port=3128] Mar-17 19:22:16.293 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: ProxyConfig[protocol=https; host=10.129.62.115; port=3128] Mar-17 19:22:16.294 [main] DEBUG nextflow.cli.Launcher - Setting ftp proxy: ProxyConfig[protocol=ftp; host=10.129.62.115; port=3128] Mar-17 19:22:16.294 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -r 3.8.1 -offline -c nextflow.config --input samplesheet_C90159.csv --outdir results_C90159/ --genome GATK.GRCh38 --step variant_calling --tools mutect2 -profile singularity Mar-17 19:22:16.429 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.4 Mar-17 19:22:16.460 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/vkanch/.nextflow/plugins; core-plugins: nf-amazon@3.4.4,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.5,nf-k8s@1.2.2,nf-tower@1.17.5,nf-wave@1.16.1 Mar-17 19:22:16.483 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Mar-17 19:22:16.484 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Mar-17 19:22:16.487 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Mar-17 19:22:16.501 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config Mar-17 19:22:16.617 [main] INFO org.pf4j.AbstractPluginManager - No plugins Mar-17 19:22:16.629 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/vkanch/.nextflow/scm Mar-17 19:22:17.468 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/vkanch/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git Mar-17 19:22:17.495 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Mar-17 19:22:17.504 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/vkanch/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git Mar-17 19:22:17.679 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/vkanch/.nextflow/assets/nf-core/sarek/nextflow.config Mar-17 19:22:17.681 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/nextflow.config Mar-17 19:22:17.683 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/nextflow.config Mar-17 19:22:17.684 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/vkanch/.nextflow/assets/nf-core/sarek/nextflow.config Mar-17 19:22:17.684 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/nextflow.config Mar-17 19:22:17.684 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/nextflow.config Mar-17 19:22:17.696 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Mar-17 19:22:20.539 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Mar-17 19:22:20.604 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Mar-17 19:22:20.614 [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_full_germline, unibe_ibu, vai, czbiohub_aws, jax, roslin, iris, 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, spark, utd_ganymede, charliecloud, fred_hutch, seattlechildrens, icr_davros, ceres, munin, rosalind, hasta, cfc, emulate_amd64, test_full_aws, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, lrz_cm4, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, test_aws, awsbatch, wustl_htcf, test_full_germline_ncbench_agilent, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, eva_grace, test_full_germline_aws, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, alliance_canada, arm64, mpcdf, leicester, vsc_ugent, create, sage, cambridge, 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, test_azure, test_full_azure, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, dirac, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, hki_genie, genouest, cbe, unsw_katana, utd_juno, mutect, phoenix, seawulf, uod_hpc, fub_curta, lovelace, uct_hpc, aws_tower, test_full_germline_azure, fsu_draco] Mar-17 19:22:20.662 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-core-utils@0.4.0, nf-fgbio@1.0.0, nf-prov@1.2.2, nf-schema@2.6.1] Mar-17 19:22:20.662 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Mar-17 19:22:20.663 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-core-utils@0.4.0, nf-fgbio@1.0.0, nf-prov@1.2.2, nf-schema@2.6.1] Mar-17 19:22:20.892 [main] DEBUG n.plugin.HttpPluginRepository - Registry request: https://registry.nextflow.io/api/v1/plugins/dependencies?plugins=nf-core-utils%400.4.0%2Cnf-fgbio%401.0.0%2Cnf-prov%401.2.2%2Cnf-schema%402.6.1&nextflowVersion=25.10.4 - code: 200 - body: {"plugins":[{"id":"nf-core-utils","releases":[{"version":"0.4.0","url":"https://registry.nextflow.io/api/v1/plugins/nf-core-utils/0.4.0/download/nf-core-utils-0.4.0.zip","date":"2025-10-31T10:26:21.611196Z","sha512sum":"9b3318b298b972120979bd49dffa83861f207285d3c9b248e25823cc1b5713caae4d7ec3e07fa1cefa389c8b717211df50697b2bca2f52fee24ebb168b216c1f","requires":">=25.10.0","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/nf-core/nf-core-utils","provider":"nf-core"},{"id":"nf-fgbio","releases":[{"version":"1.0.0","url":"https://registry.nextflow.io/api/v1/plugins/nf-fgbio/1.0.0/download/nf-fgbio-1.0.0.zip","date":"2025-05-17T09:00:00.130986Z","sha512sum":"a5987c72f52831e0fb0b4cf5ba8d7a3376ce983111be55b393e6e49aa5c65fa000186ffbfe35fd48393eb47a55bd57b5f0a7fdb1e0b7403fcb86be1f99aa6f7c","requires":">=22.10.2","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/fulcrumgenomics/nf-fgbio","provider":"Fulcrum Genomics"},{"id":"nf-prov","releases":[{"version":"1.2.2","url":"https://registry.nextflow.io/api/v1/plugins/nf-prov/1.2.2/download/nf-prov-1.2.2.zip","date":"2024-03-27T01:22:33.589795Z","sha512sum":"f50f2e6a362bf6930d79689342e95ce8f992aea8c5b6345eae85d81ced4a63c958bdf9bb4a6eb9c9eb96d24d282c30db80b3154d8d0f7eee7213762af58ec571","requires":">=23.04.0","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/nextflow-io/nf-prov","provider":"nextflow"},{"id":"nf-schema","releases":[{"version":"2.6.1","url":"https://registry.nextflow.io/api/v1/plugins/nf-schema/2.6.1/download/nf-schema-2.6.1.zip","date":"2025-10-27T10:50:21.364829Z","sha512sum":"467832f2987f90e2d2aa8e6d8387e45d4a0406ce8b5579a71fcd506155b85491bc6e978a536d767508a8ed1a4610a60c1f0cd3d9dc226f4fea1ce2973a23d043","requires":">=25.10.0","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/nextflow-io/nf-schema","provider":"nextflow-io"}]} Mar-17 19:22:20.925 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-core-utils version: 0.4.0 Mar-17 19:22:20.934 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-core-utils@0.4.0' resolved Mar-17 19:22:20.934 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-core-utils@0.4.0' Mar-17 19:22:20.938 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-core-utils@0.4.0 Mar-17 19:22:20.938 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-fgbio version: 1.0.0 Mar-17 19:22:20.943 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-fgbio@1.0.0' resolved Mar-17 19:22:20.943 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-fgbio@1.0.0' Mar-17 19:22:20.953 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-fgbio@1.0.0 Mar-17 19:22:20.954 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-prov version: 1.2.2 Mar-17 19:22:20.956 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-prov@1.2.2' resolved Mar-17 19:22:20.956 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-prov@1.2.2' Mar-17 19:22:20.957 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-prov@1.2.2 Mar-17 19:22:20.957 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.6.1 Mar-17 19:22:20.960 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.6.1' resolved Mar-17 19:22:20.960 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.6.1' Mar-17 19:22:20.962 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.6.1 Mar-17 19:22:20.967 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/vkanch/.nextflow/secrets/store.json Mar-17 19:22:20.969 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@49994a4] - activable => nextflow.secret.LocalSecretsProvider@49994a4 Mar-17 19:22:20.972 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default Mar-17 19:22:20.972 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [wise_austin] DSL2 - revision: 4bd2948f98 [3.8.1] Mar-17 19:22:21.011 [main] DEBUG nextflow.Session - Session UUID: 860707c1-a589-4f14-b77b-b9d0c051aa9f Mar-17 19:22:21.011 [main] DEBUG nextflow.Session - Run name: wise_austin Mar-17 19:22:21.012 [main] DEBUG nextflow.Session - Executor pool size: 8 Mar-17 19:22:21.018 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Mar-17 19:22:21.021 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Mar-17 19:22:21.036 [main] DEBUG nextflow.cli.CmdRun - Version: 25.10.4 build 11173 Created: 10-02-2026 15:17 UTC (16:17 CEST) System: Linux 6.8.0-100-generic Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 21.0.10-internal-adhoc.conda.src Encoding: UTF-8 (UTF-8) Process: 3839956@u24-cva0000-113 [10.129.63.163] CPUs: 8 - Mem: 117.9 GB (13.5 GB) - Swap: 0 (0) Mar-17 19:22:21.058 [main] DEBUG nextflow.Session - Work-dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work [ceph] Mar-17 19:22:21.072 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Mar-17 19:22:21.080 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory Mar-17 19:22:21.082 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory Mar-17 19:22:21.095 [main] DEBUG nextflow.Session - Observer factory (v2): ValidationObserverFactory Mar-17 19:22:21.099 [main] DEBUG nextflow.Session - Observer factory: ProvObserverFactory Mar-17 19:22:21.105 [main] DEBUG nextflow.Session - Observer factory: NfcorePipelineObserverFactory Mar-17 19:22:21.156 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Mar-17 19:22:21.164 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 Mar-17 19:22:21.410 [main] DEBUG nextflow.Session - Session start Mar-17 19:22:21.419 [main] WARN n.p.nfcore.NfcoreConfigValidator - [nf-core/sarek] You are attempting to run the pipeline without any custom configuration! This will be dependent on your local compute environment but can be achieved via one or more of the following: (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity` (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax` (3) Using your own local custom config e.g. `-c /path/to/your/custom.config` Please refer to the quick start section and usage docs for the pipeline. Mar-17 19:22:21.426 [main] WARN n.p.nfcore.NfcoreConfigValidator - nf-core pipelines do not accept positional arguments. The positional argument `nextflow` has been detected. HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. Mar-17 19:22:21.432 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results_C90159/pipeline_info/execution_trace_2026-03-17_19-22-17.txt Mar-17 19:22:21.922 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Mar-17 19:22:22.365 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Mar-17 19:22:22.371 [main] DEBUG n.validation.config.ValidationConfig - Set `validation.monochromeLogs` to false Mar-17 19:22:22.373 [main] DEBUG n.validation.config.ValidationConfig - Added the following parameters to the ignored parameters: [genomes, freebayes_filter, vep_cache_version] Mar-17 19:22:22.490 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [softwareVersionsToYAML:softwareVersionsToYAML]; plugin Id: nf-core-utils Mar-17 19:22:22.697 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Mar-17 19:22:22.698 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Mar-17 19:22:22.698 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Mar-17 19:22:22.701 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Mar-17 19:22:22.701 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Mar-17 19:22:22.701 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Mar-17 19:22:23.224 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [readStructure:readStructure]; plugin Id: nf-fgbio Mar-17 19:22:53.401 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Mar-17 19:22:53.403 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Mar-17 19:22:53.404 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Mar-17 19:22:53.406 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Mar-17 19:22:53.407 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Mar-17 19:22:53.408 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-schema Mar-17 19:22:54.192 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [readStructure:readStructure]; plugin Id: nf-fgbio Mar-17 19:22:55.666 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Mar-17 19:22:55.749 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  ____  .´ _ `.  / |\`-_ \  __ __ ___   | | \ `-| |__` /\ |__) |__ |__/  \ | \ / .__| /¯¯\ | \ |___ | \  `|____\´  nf-core/sarek 3.8.1 ------------------------------------------------------ Mar-17 19:22:55.928 [main] INFO nextflow.Nextflow - Input/output options input : samplesheet_C90159.csv step : variant_calling outdir : results_C90159/ Main options intervals : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed tools : mutect2 Variant Calling cf_chrom_len : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len pon : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz pon_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi Reference genome options ascat_genome : hg38 ascat_alleles : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip ascat_loci : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip ascat_loci_gc : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip ascat_loci_rt : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip bwa : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/ bwamem2 : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/ chr_dir : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes dbsnp : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz dbsnp_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi dbsnp_vqsr : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz dict : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict dragmap : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/ fasta : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta fasta_fai : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai germline_resource : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz germline_resource_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi known_indels : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz known_indels_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi known_indels_vqsr : --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz known_snps : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz known_snps_tbi : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi known_snps_vqsr : --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz mappability : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem msisensor2_models : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/MSIsensor2/models_hg38// msisensorpro_scan : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/MSIsensorPro/Homo_sapiens_assembly38.msisensor_scan.list ngscheckmate_bed : s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed sentieon_dnascope_model: s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model snpeff_db : GRCh38.99 vep_cache_version : 115 vep_genome : GRCh38 vep_species : homo_sapiens Institutional config options custom_config_base : /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek Generic options trace_report_suffix : 2026-03-17_19-22-17 Core Nextflow options revision : 3.8.1 runName : wise_austin containerEngine : singularity launchDir : /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek workDir : /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work projectDir : /home/vkanch/.nextflow/assets/nf-core/sarek userName : vkanch profile : singularity configFiles : /home/vkanch/.nextflow/assets/nf-core/sarek/nextflow.config, /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/nextflow.config, /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ Mar-17 19:22:56.851 [main] INFO nextflow.Nextflow - * The pipeline https://doi.org/10.12688/f1000research.16665.2 https://doi.org/10.1093/nargab/lqae031 https://doi.org/10.5281/zenodo.3476425 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/sarek/blob/master/CITATIONS.md Mar-17 19:22:56.991 [main] DEBUG n.v.parameters.ParameterValidator - Starting parameters validation Mar-17 19:22:57.228 [main] DEBUG n.v.v.evaluators.SchemaEvaluator - Started validating /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/samplesheet_C90159.csv Mar-17 19:22:57.329 [main] DEBUG n.v.v.evaluators.SchemaEvaluator - Validation of file 'samplesheet_C90159.csv' passed! Mar-17 19:22:57.442 [main] DEBUG n.plugin.HttpPluginRepository - Registry request: https://registry.nextflow.io/api/v1/plugins/dependencies?plugins=nf-amazon%403.4.4&nextflowVersion=25.10.4 - code: 200 - body: {"plugins":[{"id":"nf-amazon","releases":[{"version":"3.4.4","url":"https://registry.nextflow.io/api/v1/plugins/nf-amazon/3.4.4/download/nf-amazon-3.4.4.zip","date":"2026-02-10T15:21:20.535204Z","sha512sum":"76c37dc3b526e6d06b7fb5c171cd0679da4a5f7c6545eb16fba4ca5e7d812c60f555fb7a71718955a93aa02a22fec73b0e220ca0998725a0dbda0333b0f106ac","requires":">=25.09.2-edge","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/nextflow-io/nf-amazon","provider":"nextflow-io"}]} Mar-17 19:22:57.444 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 3.4.4 Mar-17 19:22:57.461 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@3.4.4' resolved Mar-17 19:22:57.462 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@3.4.4' Mar-17 19:22:57.476 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@3.4.4 Mar-17 19:22:57.486 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3] Mar-17 19:22:57.486 [main] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed Mar-17 19:22:57.492 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider; config=[:] Mar-17 19:22:57.500 [main] DEBUG nextflow.cloud.aws.config.AwsConfig - AWS S3 config properties: {max_error_retry=5} Mar-17 19:22:58.294 [main] DEBUG nextflow.cloud.aws.AwsClientFactory - No AWS credentials available - falling back to anonymous access Mar-17 19:22:59.053 [main] DEBUG nextflow.cloud.aws.nio.S3Client - Unable to fetch caller account - (Service: S3, Status Code: 307, Request ID: H0M6XQVS3JHYQDP1, Extended Request ID: o9K4P3Y/HKgwxCD0NFE2G4NzkBaAN/hNxDmC+Qq2kQys7NZCRLjS9P9uwHawcFDDI1coCX4ba4/FDB4jFGWIxPpiQbsFgGT1nPRk/0VPRXI=) (SDK Attempt Count: 1) Mar-17 19:23:03.887 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider; config=[:] Mar-17 19:23:03.888 [main] DEBUG nextflow.cloud.aws.config.AwsConfig - AWS S3 config properties: {max_error_retry=5} Mar-17 19:23:04.074 [main] DEBUG nextflow.cloud.aws.AwsClientFactory - No AWS credentials available - falling back to anonymous access Mar-17 19:23:04.421 [main] DEBUG nextflow.cloud.aws.nio.S3Client - Unable to fetch caller account - (Service: S3, Status Code: 307, Request ID: 4E687X4KXF4HJPCE, Extended Request ID: 0ZHQFKLEzrERhc/DzWf9CGcrlMrKGF9JZiVU7xcb/4/jo28KQJJLQia1zPTFUNqzXnTRsbFqPSuhBEDfv/gWJi7/lWKbBa9ReZc9VXqKi9Y=) (SDK Attempt Count: 1) Mar-17 19:23:08.679 [main] DEBUG n.v.parameters.ParameterValidator - Finishing parameters validation Mar-17 19:23:08.815 [main] WARN nextflow.Nextflow - The default Panel-of-Normals provided by GATK is used for Mutect2. It is highly recommended to generate one from normal samples that are technical similar to the tumor ones. For more information: https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- Mar-17 19:23:08.929 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Mar-17 19:23:08.930 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Mar-17 19:23:08.931 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Mar-17 19:23:08.940 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:08.940 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:08.950 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Mar-17 19:23:08.955 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 50; pollInterval: 30s; dumpInterval: 5m Mar-17 19:23:08.956 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Mar-17 19:23:08.956 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 20 submissions per 60 seconds Mar-17 19:23:08.959 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Mar-17 19:23:08.973 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED': maxForks=0; fair=false; array=0 Mar-17 19:23:09.015 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Mar-17 19:23:09.016 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Mar-17 19:23:09.019 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Mar-17 19:23:09.020 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT|TABIX_BGZIPTABIX_INTERVAL_COMBINED` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Mar-17 19:23:09.027 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.027 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.028 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT': maxForks=0; fair=false; array=0 Mar-17 19:23:09.039 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Mar-17 19:23:09.040 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Mar-17 19:23:09.042 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Mar-17 19:23:09.043 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT|TABIX_BGZIPTABIX_INTERVAL_COMBINED` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Mar-17 19:23:09.049 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.049 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.050 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED': maxForks=0; fair=false; array=0 Mar-17 19:23:09.091 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS Mar-17 19:23:09.093 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS Mar-17 19:23:09.097 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.098 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.098 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS': maxForks=0; fair=false; array=0 Mar-17 19:23:09.104 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH Mar-17 19:23:09.105 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH Mar-17 19:23:09.106 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH Mar-17 19:23:09.110 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.110 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.111 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH': maxForks=0; fair=false; array=0 Mar-17 19:23:09.130 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP Mar-17 19:23:09.131 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP Mar-17 19:23:09.132 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:BCFTOOLS_MPILEUP` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP Mar-17 19:23:09.133 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP Mar-17 19:23:09.137 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.137 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.138 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP': maxForks=0; fair=false; array=0 Mar-17 19:23:09.150 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM Mar-17 19:23:09.153 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*BAM_NGSCHECKMATE:NGSCHECKMATE_NCM` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM Mar-17 19:23:09.156 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.156 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.157 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM': maxForks=0; fair=false; array=0 Mar-17 19:23:09.231 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2 Mar-17 19:23:09.232 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATK4_MUTECT2` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2 Mar-17 19:23:09.234 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MUTECT2.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2 Mar-17 19:23:09.238 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.238 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.239 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2': maxForks=0; fair=false; array=0 Mar-17 19:23:09.254 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:09.255 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:09.257 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MERGE_MUTECT2.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:09.261 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.261 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.261 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2': maxForks=0; fair=false; array=0 Mar-17 19:23:09.265 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS Mar-17 19:23:09.268 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MERGEMUTECTSTATS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS Mar-17 19:23:09.272 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.272 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.272 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS': maxForks=0; fair=false; array=0 Mar-17 19:23:09.288 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL Mar-17 19:23:09.291 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:LEARNREADORIENTATIONMODEL` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL Mar-17 19:23:09.294 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.295 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.295 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL': maxForks=0; fair=false; array=0 Mar-17 19:23:09.300 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES Mar-17 19:23:09.301 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES Mar-17 19:23:09.302 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES Mar-17 19:23:09.303 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES Mar-17 19:23:09.304 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES Mar-17 19:23:09.307 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.307 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.307 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES': maxForks=0; fair=false; array=0 Mar-17 19:23:09.316 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES Mar-17 19:23:09.319 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATHERPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES Mar-17 19:23:09.323 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.323 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.323 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES': maxForks=0; fair=false; array=0 Mar-17 19:23:09.333 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION Mar-17 19:23:09.336 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:CALCULATECONTAMINATION` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION Mar-17 19:23:09.340 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.341 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.342 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION': maxForks=0; fair=false; array=0 Mar-17 19:23:09.357 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS Mar-17 19:23:09.360 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:FILTERMUTECTCALLS.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS Mar-17 19:23:09.364 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.365 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.365 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS': maxForks=0; fair=false; array=0 Mar-17 19:23:09.412 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED Mar-17 19:23:09.413 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATK4_MUTECT2` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED Mar-17 19:23:09.414 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MUTECT2_PAIRED` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED Mar-17 19:23:09.415 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MUTECT2.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED Mar-17 19:23:09.419 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.419 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.420 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED': maxForks=0; fair=false; array=0 Mar-17 19:23:09.437 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:09.437 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:09.439 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MERGE_MUTECT2.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:09.443 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.443 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.443 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2': maxForks=0; fair=false; array=0 Mar-17 19:23:09.448 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS Mar-17 19:23:09.450 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MERGEMUTECTSTATS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS Mar-17 19:23:09.453 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.453 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.454 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS': maxForks=0; fair=false; array=0 Mar-17 19:23:09.472 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL Mar-17 19:23:09.474 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:LEARNREADORIENTATIONMODEL` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL Mar-17 19:23:09.480 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.480 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.480 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL': maxForks=0; fair=false; array=0 Mar-17 19:23:09.489 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.491 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.492 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.492 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.493 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.495 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.495 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.496 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL': maxForks=0; fair=false; array=0 Mar-17 19:23:09.500 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.501 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.502 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.502 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.503 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:.*GETPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.505 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.505 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.506 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR': maxForks=0; fair=false; array=0 Mar-17 19:23:09.518 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.520 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATHERPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL Mar-17 19:23:09.523 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.523 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.523 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL': maxForks=0; fair=false; array=0 Mar-17 19:23:09.528 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.529 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:GATHERPILEUPSUMMARIES.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR Mar-17 19:23:09.532 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.532 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.533 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR': maxForks=0; fair=false; array=0 Mar-17 19:23:09.546 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION Mar-17 19:23:09.548 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:CALCULATECONTAMINATION` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION Mar-17 19:23:09.551 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.551 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.551 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION': maxForks=0; fair=false; array=0 Mar-17 19:23:09.564 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS Mar-17 19:23:09.565 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:FILTERMUTECTCALLS.*` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS Mar-17 19:23:09.568 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.568 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.569 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS': maxForks=0; fair=false; array=0 Mar-17 19:23:09.615 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Mar-17 19:23:09.615 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Mar-17 19:23:09.616 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:BCFTOOLS_STATS` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Mar-17 19:23:09.619 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.619 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.619 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS': maxForks=0; fair=false; array=0 Mar-17 19:23:09.631 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Mar-17 19:23:09.631 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Mar-17 19:23:09.632 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Mar-17 19:23:09.632 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:VCFTOOLS_TSTV_COUNT` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Mar-17 19:23:09.635 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.635 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.635 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT': maxForks=0; fair=false; array=0 Mar-17 19:23:09.664 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Mar-17 19:23:09.665 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Mar-17 19:23:09.665 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Mar-17 19:23:09.666 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:VCFTOOLS_TSTV_QUAL` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Mar-17 19:23:09.669 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.669 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.669 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL': maxForks=0; fair=false; array=0 Mar-17 19:23:09.695 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Mar-17 19:23:09.696 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Mar-17 19:23:09.697 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Mar-17 19:23:09.697 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:VCFTOOLS_SUMMARY` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Mar-17 19:23:09.700 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.700 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.700 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY': maxForks=0; fair=false; array=0 Mar-17 19:23:09.842 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC Mar-17 19:23:09.842 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC Mar-17 19:23:09.845 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Mar-17 19:23:09.845 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Mar-17 19:23:09.846 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_SAREK:SAREK:MULTIQC': maxForks=0; fair=false; array=0 Mar-17 19:23:09.869 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Mar-17 19:23:09.923 [main] DEBUG nextflow.Session - Igniting dataflow network (178) Mar-17 19:23:09.938 [PathVisitor-3] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz; options: [:] Mar-17 19:23:09.938 [PathVisitor-5] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/; pattern: {Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi; options: [:] Mar-17 19:23:09.946 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Mar-17 19:23:09.947 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Mar-17 19:23:09.947 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Mar-17 19:23:09.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS Mar-17 19:23:09.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH Mar-17 19:23:09.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP Mar-17 19:23:09.953 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2 Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MERGEMUTECTSTATS Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:LEARNREADORIENTATIONMODEL Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GETPILEUPSUMMARIES Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:GATHERPILEUPSUMMARIES Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:CALCULATECONTAMINATION Mar-17 19:23:10.012 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:FILTERMUTECTCALLS Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:LEARNREADORIENTATIONMODEL Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION Mar-17 19:23:10.018 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:FILTERMUTECTCALLS Mar-17 19:23:10.019 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Mar-17 19:23:10.019 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Mar-17 19:23:10.019 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Mar-17 19:23:10.019 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Mar-17 19:23:10.019 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC Mar-17 19:23:10.029 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_d3865926248d0c08: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/samtools/stats/main.nf Script_c8d59298afea0bfb: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/controlfreec/freec2circos/main.nf Script_16777475677f32d8: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/cnnscorevariants/main.nf Script_9e61b79b569950a4: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/fastqc/main.nf Script_e32e42ae4de921ec: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/fgbio/groupreadsbyumi/main.nf Script_e3adf9ad2f2912db: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/calculatecontamination/main.nf Script_9c2e978ff49f2509: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_variant_calling_tumor_only_all/main.nf Script_da5079923d83b72c: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/mutect2/main.nf Script_cd9de50525435b88: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_variant_calling_tumor_only_lofreq/main.nf Script_ee8970a3b78d31c2: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/fastp/main.nf Script_8ff83fc63a22c8fb: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/local/samtools/reindex_bam/main.nf Script_a2aa0d1ede76c3e4: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/cat/cat/main.nf Script_213f65daf02ad325: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_convert_samtools/main.nf Script_1831c72c96b04171: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/multiqc/main.nf Script_1e06434ac317a579: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/genomicsdbimport/main.nf Script_8fc82b9520076c78: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/sentieon/tnscope/main.nf Script_129045cbcec43290: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/goleft/indexcov/main.nf Script_1f0a1eb4bf79a7fd: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_sentieon_dedup/main.nf Script_4da5e6231058e316: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/markduplicates/main.nf Script_55d562cd46880324: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/sentieon/dnamodelapply/main.nf Script_fff8e472d2832414: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/snpsift/annmem/main.nf Script_9f4b705a218210c4: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/prepare_reference_cnvkit/main.nf Script_62f899b12a250fec: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/vcf_variant_filtering_gatk/main.nf Script_47c9e5087123dd2b: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/bcftools/mpileup/main.nf Script_09d762bbddf624de: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf Script_3ff925592f3c771c: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/bwamem2/index/main.nf Script_057d3de35ec771e9: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_markduplicates_spark/main.nf Script_94903505569de6f7: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/bcftools/stats/main.nf Script_f635d70ccf3f5f7c: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4spark/markduplicates/main.nf Script_10693a2faf538ce1: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_variant_calling_somatic_tnscope/main.nf Script_881607023f7cda54: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/samtools/convert/main.nf Script_2aaa99b284400807: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/baserecalibrator/main.nf Script_ca1602e337ab4f2a: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/cnvkit/genemetrics/main.nf Script_e5fccee2ba9a7b56: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/samtools/merge/main.nf Script_5977f542cd315b9b: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/nf-core/utils_nfcore_pipeline/main.nf Script_470736e50691adf4: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/sentieon/bwamem/main.nf Script_b51e866816de7307: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/samtools/bam2fq/main.nf Script_5a1ee4df50ceb976: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/channel_markduplicates_create_csv/main.nf Script_699b096599f2ee18: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/varlociraptor/preprocess/main.nf Script_31c41c03e5d4f489: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/controlfreec/makegraph2/main.nf Script_4779b6382e5427ab: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/cat/fastq/main.nf Script_c752e59174411c9b: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/sentieon/dedup/main.nf Script_0edb32c316733e34: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_applybqsr_spark/main.nf Script_7882589d2e2ef368: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/vcf_annotate_all/main.nf Script_d11b5c79ea543e09: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf Script_12f1b0cba653bc40: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_variant_calling_somatic_ascat/main.nf Script_a44e2ae5dde189b4: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/varlociraptor/estimatealignmentproperties/main.nf Script_3fb35437a373c5f5: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/haplotypecaller/main.nf Script_dedbba5968c49a0d: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/samtools/faidx/main.nf Script_6ec5d65e462b3741: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/bwa/index/main.nf Script_57ee94b0d1ea8856: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/channel_variant_calling_create_csv/main.nf Script_aa9f615e74edb2bb: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/local/consensus_from_sites/main.nf Script_020aec49db5802b2: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/ngscheckmate/ncm/main.nf Script_3ff1656b1d66c1f2: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/samtools/index/main.nf Script_458c0092a1c22da3: /home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf Script_e1b15902bafd2763: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/muse/call/main.nf Script_96bfb03e094f76ad: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/bbmap/bbsplit/main.nf Script_05df603030fed9db: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/snpsift/annmemcreate/main.nf Script_2a3123de5fac596c: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/untar/main.nf Script_815be9f6135ccf61: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/deepvariant/rundeepvariant/main.nf Script_5062712f72bf0720: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/gatk4/filtervarianttranches/main.nf 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/home/vkanch/.nextflow/assets/nf-core/sarek/subworkflows/nf-core/bam_ngscheckmate/main.nf Script_f526ea333b3ea25e: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/freebayes/main.nf Script_8b560cf26a0f6f39: /home/vkanch/.nextflow/assets/nf-core/sarek/modules/nf-core/unzip/main.nf Mar-17 19:23:10.030 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Mar-17 19:23:10.030 [main] DEBUG nextflow.Session - Session await Mar-17 19:23:10.178 [Actor Thread 28] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.015 s; total time: 0.017 s Mar-17 19:23:10.178 [Actor Thread 34] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.015 s; total time: 0.017 s Mar-17 19:23:10.191 [Actor Thread 34] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/collect-file/ee6c4cac8930d3df663b054307bedc78 Mar-17 19:23:10.191 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/collect-file/040e78744217c0986ad404b8937531d3 Mar-17 19:23:10.236 [Actor Thread 34] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-12025122085999600765 Mar-17 19:23:10.236 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8722180084742171026 Mar-17 19:23:10.697 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/4c/fcae8ac0089137f4710ff7d6f98ebb/wgs_calling_regions_noseconds.hg38.bed Mar-17 19:23:10.698 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/9b/f477d371486f9d159d6ad93bf9c842/Homo_sapiens_assembly38.fasta Mar-17 19:23:10.748 [FileTransfer-1] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/4c/fcae8ac0089137f4710ff7d6f98ebb/wgs_calling_regions_noseconds.hg38.bed size=8263 Mar-17 19:23:10.749 [FileTransfer-2] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/9b/f477d371486f9d159d6ad93bf9c842/Homo_sapiens_assembly38.fasta size=3249912778 Mar-17 19:23:10.758 [FileTransfer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'S3TransferManager' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Mar-17 19:23:10.944 [FileTransfer-1] DEBUG nextflow.cloud.aws.AwsClientFactory - No AWS credentials available - falling back to anonymous access Mar-17 19:23:11.865 [Actor Thread 34] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/gawk:5.3.0; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/depot.galaxyproject.org-singularity-gawk-5.3.0.img Mar-17 19:23:11.865 [Actor Thread 4] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-92-92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd-data.img Mar-17 19:23:12.096 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed) > jobId: 1744859; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a9/70b6a69536f4c7cc2aaae8f8cf12b4 Mar-17 19:23:12.097 [Task submitter] INFO nextflow.Session - [a9/70b6a6] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed) Mar-17 19:23:12.697 [Actor Thread 14] INFO nextflow.file.FilePorter - Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Mar-17 19:23:14.042 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38) > jobId: 1744860; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8a/077945fb99f31d7da0fd485637c8bb Mar-17 19:23:14.042 [Task submitter] INFO nextflow.Session - [8a/077945] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38) Mar-17 19:23:29.559 [Actor Thread 12] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/depot.galaxyproject.org-singularity-samtools-1.21--h50ea8bc_0.img Mar-17 19:23:29.559 [Actor Thread 9] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mosdepth:0.3.10--h4e814b3_1; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/depot.galaxyproject.org-singularity-mosdepth-0.3.10--h4e814b3_1.img Mar-17 19:23:29.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_5TT6TT4K) > jobId: 1744861; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e3/7b8f9a9bb0817b94d37eea5befc8ec Mar-17 19:23:29.778 [Task submitter] INFO nextflow.Session - [e3/7b8f9a] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_5TT6TT4K) Mar-17 19:23:31.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_2VB8649B) > jobId: 1744862; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/99/a05839dcfb464d7537e28b863b9168 Mar-17 19:23:31.777 [Task submitter] INFO nextflow.Session - [99/a05839] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_2VB8649B) Mar-17 19:23:34.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_CW6NWAWQ) > jobId: 1744863; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/83/68e038c4b773957d5e4f473c230d07 Mar-17 19:23:34.774 [Task submitter] INFO nextflow.Session - [83/68e038] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_CW6NWAWQ) Mar-17 19:23:37.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B) > jobId: 1744864; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c Mar-17 19:23:37.775 [Task submitter] INFO nextflow.Session - [ec/7c3774] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B) Mar-17 19:23:39.035 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744859; id: 2; name: NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (wgs_calling_regions_noseconds.hg38.bed); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a9/70b6a69536f4c7cc2aaae8f8cf12b4 started: 1773771818980; exited: 2026-03-17T18:23:15.455279603Z; ] Mar-17 19:23:39.036 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Mar-17 19:23:40.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ) > jobId: 1744865; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 Mar-17 19:23:40.787 [Task submitter] INFO nextflow.Session - [ad/d6fb4e] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ) Mar-17 19:23:43.783 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K) > jobId: 1744867; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d Mar-17 19:23:43.783 [Task submitter] INFO nextflow.Session - [c1/f25f34] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K) Mar-17 19:23:47.418 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_10001-1429358) > jobId: 1744868; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/96/eca2238e09cb73d473367139632f13 Mar-17 19:23:47.418 [Task submitter] INFO nextflow.Session - [96/eca223] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_10001-1429358) Mar-17 19:23:47.938 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/d7/18f7588869c28af7a9488b97b814fc/Homo_sapiens_assembly38.fasta.fai Mar-17 19:23:47.938 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/a2/679734cc24e7a26876077b3f8d78d2/Homo_sapiens_assembly38.dict Mar-17 19:23:47.938 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/27/82af8b42c4eaa3c76666316d87ad81/af-only-gnomad.hg38.vcf.gz Mar-17 19:23:47.939 [FileTransfer-6] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/86/058c6db815c450c86f68b39906b5fe/af-only-gnomad.hg38.vcf.gz.tbi Mar-17 19:23:48.071 [FileTransfer-3] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/d7/18f7588869c28af7a9488b97b814fc/Homo_sapiens_assembly38.fasta.fai size=160928 Mar-17 19:23:48.085 [FileTransfer-4] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/a2/679734cc24e7a26876077b3f8d78d2/Homo_sapiens_assembly38.dict size=581712 Mar-17 19:23:48.086 [FileTransfer-5] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/27/82af8b42c4eaa3c76666316d87ad81/af-only-gnomad.hg38.vcf.gz size=3184275189 Mar-17 19:23:48.168 [FileTransfer-6] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/86/058c6db815c450c86f68b39906b5fe/af-only-gnomad.hg38.vcf.gz.tbi size=2443190 Mar-17 19:23:48.252 [FileTransfer-7] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/91/e70ae00a642de5752b18c125ed4ac7/1000g_pon.hg38.vcf.gz Mar-17 19:23:48.252 [FileTransfer-8] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi to work dir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/b7/4e0acb2b9c90dea0662836f3e82bcf/1000g_pon.hg38.vcf.gz.tbi Mar-17 19:23:48.303 [FileTransfer-8] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/b7/4e0acb2b9c90dea0662836f3e82bcf/1000g_pon.hg38.vcf.gz.tbi size=1534802 Mar-17 19:23:48.306 [FileTransfer-7] DEBUG n.cloud.aws.nio.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz to=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/stage-860707c1-a589-4f14-b77b-b9d0c051aa9f/91/e70ae00a642de5752b18c125ed4ac7/1000g_pon.hg38.vcf.gz size=17273497 Mar-17 19:23:49.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr12_37235253-37240944) > jobId: 1744869; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4e/a181fe7835fe2e60f145c50ba0884a Mar-17 19:23:49.776 [Task submitter] INFO nextflow.Session - [4e/a181fe] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr12_37235253-37240944) Mar-17 19:23:50.621 [Actor Thread 57] INFO nextflow.file.FilePorter - Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz Mar-17 19:23:52.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_16146120-32867130) > jobId: 1744870; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/66/669606f2ac2573c3d0f43b6ba22bcc Mar-17 19:23:52.772 [Task submitter] INFO nextflow.Session - [66/669606] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_16146120-32867130) Mar-17 19:23:55.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr7_58169654-60828234) > jobId: 1744871; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/60/28265df69e459a3db3b1058a0e7730 Mar-17 19:23:55.777 [Task submitter] INFO nextflow.Session - [60/28265d] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr7_58169654-60828234) Mar-17 19:23:58.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_190173122-190204555) > jobId: 1744872; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0b/07c44ee5fdc7f9c1ff8d7ab87cee1c Mar-17 19:23:58.772 [Task submitter] INFO nextflow.Session - [0b/07c44e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_190173122-190204555) Mar-17 19:24:01.762 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr6_95070791-167591393) > jobId: 1744873; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/96/72396fc62b1301bdc38335968429cb Mar-17 19:24:01.763 [Task submitter] INFO nextflow.Session - [96/72396f] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr6_95070791-167591393) Mar-17 19:24:04.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr8_44033745-45877265) > jobId: 1744874; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/ad412d8dda25134ced96b3437613cd Mar-17 19:24:04.777 [Task submitter] INFO nextflow.Session - [25/ad412d] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr8_44033745-45877265) Mar-17 19:24:07.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr20_36314720-64334167) > jobId: 1744875; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/53/b73204ea25ac6efcaaf4ae1b1d60ac Mar-17 19:24:07.777 [Task submitter] INFO nextflow.Session - [53/b73204] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr20_36314720-64334167) Mar-17 19:24:07.837 [Actor Thread 22] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-b2-b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98-data.img Mar-17 19:24:09.009 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744860; id: 1; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8a/077945fb99f31d7da0fd485637c8bb started: 1773771848978; exited: 2026-03-17T18:23:44.833277693Z; ] Mar-17 19:24:09.169 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:10.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr17_60001-448188) > jobId: 1744876; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/80516f8fab5d3caf6b63b0321b149a Mar-17 19:24:10.777 [Task submitter] INFO nextflow.Session - [62/80516f] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr17_60001-448188) Mar-17 19:24:13.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr10_39590436-39593013) > jobId: 1744877; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/61/d3b00be48ac24bba91d9f6d65c1901 Mar-17 19:24:13.773 [Task submitter] INFO nextflow.Session - [61/d3b00b] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr10_39590436-39593013) Mar-17 19:24:16.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrX_37285838-49348394) > jobId: 1744878; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/312ebfa7502577e33315a255f9eb5f Mar-17 19:24:16.772 [Task submitter] INFO nextflow.Session - [c2/312ebf] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrX_37285838-49348394) Mar-17 19:24:19.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr15_20729747-21193490) > jobId: 1744879; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6a/34215c97108289f0c7aac729b71d7d Mar-17 19:24:19.772 [Task submitter] INFO nextflow.Session - [6a/34215c] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr15_20729747-21193490) Mar-17 19:24:22.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_238904048-242183529) > jobId: 1744880; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8d/8f63bed6b65ce3e00b6405967d6817 Mar-17 19:24:22.772 [Task submitter] INFO nextflow.Session - [8d/8f63be] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_238904048-242183529) Mar-17 19:24:25.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr5_139453660-155760324) > jobId: 1744881; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c6/739a0da438e288dc4f4a997b0cdaca Mar-17 19:24:25.774 [Task submitter] INFO nextflow.Session - [c6/739a0d] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr5_139453660-155760324) Mar-17 19:24:28.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_10001-207666) > jobId: 1744882; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ef/e618dba64473cbf20465499effc715 Mar-17 19:24:28.775 [Task submitter] INFO nextflow.Session - [ef/e618db] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_10001-207666) Mar-17 19:24:31.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr11_51078349-54425074) > jobId: 1744883; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/33/1d9a8aad0042dc688b3f5d6a7acef8 Mar-17 19:24:31.771 [Task submitter] INFO nextflow.Session - [33/1d9a8a] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr11_51078349-54425074) Mar-17 19:24:34.905 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr18_47019913-54536574) > jobId: 1744884; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5d/b4ee836e93f169b0f1bd17012d659c Mar-17 19:24:34.905 [Task submitter] INFO nextflow.Session - [5d/b4ee83] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr18_47019913-54536574) Mar-17 19:24:37.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_122026460-124977944) > jobId: 1744885; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/7f/06147132fd2270dc3f87b5234512bb Mar-17 19:24:37.771 [Task submitter] INFO nextflow.Session - [7f/061471] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_122026460-124977944) Mar-17 19:24:39.016 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744868; id: 14; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_10001-1429358); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/96/eca2238e09cb73d473367139632f13 started: 1773771878990; exited: 2026-03-17T18:24:14.590360542Z; ] Mar-17 19:24:39.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744869; id: 15; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr12_37235253-37240944); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4e/a181fe7835fe2e60f145c50ba0884a started: 1773771879021; exited: 2026-03-17T18:24:14.945385581Z; ] Mar-17 19:24:39.059 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.086 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.088 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744870; id: 12; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_16146120-32867130); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/66/669606f2ac2573c3d0f43b6ba22bcc started: 1773771879060; exited: 2026-03-17T18:24:14.697073654Z; ] Mar-17 19:24:39.122 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.141 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744871; id: 17; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr7_58169654-60828234); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/60/28265df69e459a3db3b1058a0e7730 started: 1773771879094; exited: 2026-03-17T18:24:14.490059335Z; ] Mar-17 19:24:39.178 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744872; id: 44; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_190173122-190204555); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0b/07c44ee5fdc7f9c1ff8d7ab87cee1c started: 1773771879148; exited: 2026-03-17T18:24:16.748077261Z; ] Mar-17 19:24:39.238 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744873; id: 50; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr6_95070791-167591393); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/96/72396fc62b1301bdc38335968429cb started: 1773771879194; exited: 2026-03-17T18:24:17.400121796Z; ] Mar-17 19:24:39.260 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744874; id: 19; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr8_44033745-45877265); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/ad412d8dda25134ced96b3437613cd started: 1773771879243; exited: 2026-03-17T18:24:16.841083614Z; ] Mar-17 19:24:39.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744875; id: 20; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr20_36314720-64334167); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/53/b73204ea25ac6efcaaf4ae1b1d60ac started: 1773771879264; exited: 2026-03-17T18:24:15.54368996Z; ] Mar-17 19:24:39.318 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.327 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744876; id: 51; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr17_60001-448188); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/80516f8fab5d3caf6b63b0321b149a started: 1773771879290; exited: 2026-03-17T18:24:15.618695141Z; ] Mar-17 19:24:39.356 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744877; id: 18; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr10_39590436-39593013); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/61/d3b00be48ac24bba91d9f6d65c1901 started: 1773771879332; exited: 2026-03-17T18:24:15.245638778Z; ] Mar-17 19:24:39.359 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.391 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.498 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:39.874 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:40.109 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:24:40.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr13_86252980-111703855) > jobId: 1744886; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b5/ad352f80a42d5c0baab93c17018b0c Mar-17 19:24:40.773 [Task submitter] INFO nextflow.Session - [b5/ad352f] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr13_86252980-111703855) Mar-17 19:24:43.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrY_9055175-9057608) > jobId: 1744887; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4b/a764e7bdee2bfa580a6380fb8fe8aa Mar-17 19:24:43.772 [Task submitter] INFO nextflow.Session - [4b/a764e7] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrY_9055175-9057608) Mar-17 19:24:46.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr9_41229379-41237752) > jobId: 1744888; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/b504fd45ce1158be6036e7ac220992 Mar-17 19:24:46.774 [Task submitter] INFO nextflow.Session - [08/b504fd] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr9_41229379-41237752) Mar-17 19:24:50.252 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744890; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/1cfdcc09536d5d286b55ddf2a827d2 Mar-17 19:24:50.252 [Task submitter] INFO nextflow.Session - [9a/1cfdcc] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:24:52.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744891; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 Mar-17 19:24:52.775 [Task submitter] INFO nextflow.Session - [ce/7e47c1] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:24:55.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744892; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2d/4b1791eaebdcfa6757c17eff698fbb Mar-17 19:24:55.773 [Task submitter] INFO nextflow.Session - [2d/4b1791] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:24:58.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744893; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba Mar-17 19:24:58.772 [Task submitter] INFO nextflow.Session - [36/5ea8fe] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:25:01.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744894; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c8/289458982d040f21a618fc05e85003 Mar-17 19:25:01.772 [Task submitter] INFO nextflow.Session - [c8/289458] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:25:04.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744895; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/88/08d7f604403b6fa7ef01f2d879edb3 Mar-17 19:25:04.776 [Task submitter] INFO nextflow.Session - [88/08d7f6] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:07.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744896; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/60/13802159ec9e838c7d039f75c34196 Mar-17 19:25:07.776 [Task submitter] INFO nextflow.Session - [60/138021] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:25:09.045 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744878; id: 54; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrX_37285838-49348394); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/312ebfa7502577e33315a255f9eb5f started: 1773771908981; exited: 2026-03-17T18:24:44.769488948Z; ] Mar-17 19:25:09.072 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744879; id: 16; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr15_20729747-21193490); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6a/34215c97108289f0c7aac729b71d7d started: 1773771909049; exited: 2026-03-17T18:24:44.654480837Z; ] Mar-17 19:25:09.083 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.106 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.127 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744880; id: 13; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_238904048-242183529); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8d/8f63bed6b65ce3e00b6405967d6817 started: 1773771909077; exited: 2026-03-17T18:24:45.043173159Z; ] Mar-17 19:25:09.166 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.166 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744881; id: 45; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr5_139453660-155760324); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c6/739a0da438e288dc4f4a997b0cdaca started: 1773771909133; exited: 2026-03-17T18:24:44.780154958Z; ] Mar-17 19:25:09.184 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744882; id: 55; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_10001-207666); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ef/e618dba64473cbf20465499effc715 started: 1773771909171; exited: 2026-03-17T18:24:44.808994398Z; ] Mar-17 19:25:09.197 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.285 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744883; id: 56; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr11_51078349-54425074); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/33/1d9a8aad0042dc688b3f5d6a7acef8 started: 1773771909187; exited: 2026-03-17T18:24:44.859997884Z; ] Mar-17 19:25:09.467 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744884; id: 53; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr18_47019913-54536574); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5d/b4ee836e93f169b0f1bd17012d659c started: 1773771909291; exited: 2026-03-17T18:24:44.641982984Z; ] Mar-17 19:25:09.541 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.568 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744885; id: 52; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_122026460-124977944); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/7f/06147132fd2270dc3f87b5234512bb started: 1773771909473; exited: 2026-03-17T18:24:44.725705817Z; ] Mar-17 19:25:09.585 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744886; id: 57; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr13_86252980-111703855); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b5/ad352f80a42d5c0baab93c17018b0c started: 1773771909573; exited: 2026-03-17T18:24:45.19173801Z; ] Mar-17 19:25:09.602 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.615 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744887; id: 59; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrY_9055175-9057608); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4b/a764e7bdee2bfa580a6380fb8fe8aa started: 1773771909589; exited: 2026-03-17T18:24:44.969633098Z; ] Mar-17 19:25:09.620 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.645 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:09.666 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:10.008 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744897; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/4313970a98d1ea731bd7568b727c05 Mar-17 19:25:10.773 [Task submitter] INFO nextflow.Session - [11/431397] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:25:13.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744898; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/42/d1a227050a811af63d674fe7fc863c Mar-17 19:25:13.774 [Task submitter] INFO nextflow.Session - [42/d1a227] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:16.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744899; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/60abc7c9e10504ca16adbc7be90c1d Mar-17 19:25:16.773 [Task submitter] INFO nextflow.Session - [62/60abc7] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:19.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744900; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8b/e1c4cb0b2f7d798e3d8cb8fb6e86d0 Mar-17 19:25:19.774 [Task submitter] INFO nextflow.Session - [8b/e1c4cb] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:23.489 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744901; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/1f/7b3908a7d1e7e8f7d339bb41bbf140 Mar-17 19:25:23.489 [Task submitter] INFO nextflow.Session - [1f/7b3908] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:25.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744902; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a0/54f5b5e63a024ac0b746beda24f4e6 Mar-17 19:25:25.775 [Task submitter] INFO nextflow.Session - [a0/54f5b5] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:25:28.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744903; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/19/4409177384f07536120e9d4f98d041 Mar-17 19:25:28.775 [Task submitter] INFO nextflow.Session - [19/440917] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:31.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744904; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/38/6203d4a6b9e75dd2056ff5c8984db5 Mar-17 19:25:31.774 [Task submitter] INFO nextflow.Session - [38/6203d4] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:25:35.131 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744905; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/03a94690a66780ebb8bbb4f9361423 Mar-17 19:25:35.131 [Task submitter] INFO nextflow.Session - [5e/03a946] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:25:37.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744906; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d Mar-17 19:25:37.774 [Task submitter] INFO nextflow.Session - [86/852185] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:25:39.006 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744888; id: 58; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr9_41229379-41237752); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/b504fd45ce1158be6036e7ac220992 started: 1773771938977; exited: 2026-03-17T18:25:15.302642321Z; ] Mar-17 19:25:39.053 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Mar-17 19:25:40.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744907; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 Mar-17 19:25:40.774 [Task submitter] INFO nextflow.Session - [ea/cf5884] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:25:43.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744908; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 Mar-17 19:25:43.772 [Task submitter] INFO nextflow.Session - [3a/962b19] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:25:46.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744909; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 Mar-17 19:25:46.772 [Task submitter] INFO nextflow.Session - [d5/d923fa] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:25:49.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744910; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 Mar-17 19:25:49.774 [Task submitter] INFO nextflow.Session - [5a/91284c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:25:52.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744911; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 Mar-17 19:25:52.775 [Task submitter] INFO nextflow.Session - [0c/452742] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:25:55.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744912; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 Mar-17 19:25:55.775 [Task submitter] INFO nextflow.Session - [92/6f5a29] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:25:58.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744913; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 Mar-17 19:25:58.777 [Task submitter] INFO nextflow.Session - [c2/06a1e5] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:26:01.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744914; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/d2f143f40fa4e60bd513c897cff119 Mar-17 19:26:01.773 [Task submitter] INFO nextflow.Session - [cc/d2f143] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:04.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744915; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/22/14ae995e705fb1cdbbffa5a79b092f Mar-17 19:26:04.774 [Task submitter] INFO nextflow.Session - [22/14ae99] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:26:07.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744916; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8a/7a21839e9c251ff17535293572b631 Mar-17 19:26:07.774 [Task submitter] INFO nextflow.Session - [8a/7a2183] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:26:10.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744917; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6d/af294fc765c6790a8933965d0a972e Mar-17 19:26:10.774 [Task submitter] INFO nextflow.Session - [6d/af294f] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:26:13.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744918; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/f9/c8dc9320ff25b49db3efc38a5920a6 Mar-17 19:26:13.773 [Task submitter] INFO nextflow.Session - [f9/c8dc93] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:16.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744919; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/31/1d83dd83657b6d5dc980ca3f03b591 Mar-17 19:26:16.773 [Task submitter] INFO nextflow.Session - [31/1d83dd] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:19.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744921; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/bb/65120146b171a68a33df4791622b2b Mar-17 19:26:19.775 [Task submitter] INFO nextflow.Session - [bb/651201] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:22.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744922; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/77/2bc81926563f46d725cbe5ccc200a1 Mar-17 19:26:22.774 [Task submitter] INFO nextflow.Session - [77/2bc819] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:25.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744923; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9e/8b772fded01172fec60af0e64ef293 Mar-17 19:26:25.772 [Task submitter] INFO nextflow.Session - [9e/8b772f] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:26:28.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744924; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e7/70f5800c998d4bed5c0a80e5a60379 Mar-17 19:26:28.775 [Task submitter] INFO nextflow.Session - [e7/70f580] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:26:31.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744925; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9f/f64eca8a048d4d264c1d8d8eb9b5d1 Mar-17 19:26:31.772 [Task submitter] INFO nextflow.Session - [9f/f64eca] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:26:35.127 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744926; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2d/4a9992d2475c99da6595b57b19b9e4 Mar-17 19:26:35.128 [Task submitter] INFO nextflow.Session - [2d/4a9992] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:26:37.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744927; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/e70e321a4bbe5a8d2aba2cdbaf86e7 Mar-17 19:26:37.773 [Task submitter] INFO nextflow.Session - [94/e70e32] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:40.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744928; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/30/8e999c11293f704301c4a70eb089da Mar-17 19:26:40.773 [Task submitter] INFO nextflow.Session - [30/8e999c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:43.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744929; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/59/c11da4c7d8accd4856ac428970707a Mar-17 19:26:43.774 [Task submitter] INFO nextflow.Session - [59/c11da4] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:26:46.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744930; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/13/afddeba437cf3d91e148fb423b87e0 Mar-17 19:26:46.774 [Task submitter] INFO nextflow.Session - [13/afddeb] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:26:49.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744931; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/54/8f4ba5a563b957ce42ef8092b5cbe9 Mar-17 19:26:49.775 [Task submitter] INFO nextflow.Session - [54/8f4ba5] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:26:52.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744932; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4b/f30f16b287cfc9920aa69bda36e7a9 Mar-17 19:26:52.775 [Task submitter] INFO nextflow.Session - [4b/f30f16] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:26:55.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744933; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/09/3a8c34f10f8d4b8e253022181bdc62 Mar-17 19:26:55.772 [Task submitter] INFO nextflow.Session - [09/3a8c34] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:26:58.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744934; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/af/ae53a2dea331b26033bcc5ce23cc2e Mar-17 19:26:58.773 [Task submitter] INFO nextflow.Session - [af/ae53a2] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:28:38.979 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744861; id: 11; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e3/7b8f9a9bb0817b94d37eea5befc8ec started: 1773771849012; exited: -; ] ~> TaskHandler[jobId: 1744862; id: 10; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/99/a05839dcfb464d7537e28b863b9168 started: 1773771849015; exited: -; ] ~> TaskHandler[jobId: 1744863; id: 5; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/83/68e038c4b773957d5e4f473c230d07 started: 1773771849018; exited: -; ] ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744890; id: 37; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/1cfdcc09536d5d286b55ddf2a827d2 started: 1773771939007; exited: -; ] ~> TaskHandler[jobId: 1744891; id: 40; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 started: 1773771969013; exited: -; ] ~> TaskHandler[jobId: 1744892; id: 47; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2d/4b1791eaebdcfa6757c17eff698fbb started: 1773771939011; exited: -; ] ~> TaskHandler[jobId: 1744893; id: 36; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba started: 1773771939013; exited: -; ] .. remaining tasks omitted. Mar-17 19:29:38.986 [Task monitor] DEBUG nextflow.file.FileHelper - FS path type (false): /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work Mar-17 19:31:39.036 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744863; id: 5; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/83/68e038c4b773957d5e4f473c230d07 started: 1773771849018; exited: 2026-03-17T18:31:13.434557338Z; ] Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Mar-17 19:31:39.067 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Mar-17 19:31:39.074 [TaskFinalizer-5] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Mar-17 19:31:40.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744936; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/1acf6442e232261550a8f9ee69b973 Mar-17 19:31:40.776 [Task submitter] INFO nextflow.Session - [5e/1acf64] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:32:09.069 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744927; id: 73; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/e70e321a4bbe5a8d2aba2cdbaf86e7 started: 1773772029046; exited: 2026-03-17T18:31:55.10171741Z; ] Mar-17 19:32:09.103 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:32:10.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744937; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/57/d48193e62d5661307cc3ade388a74e Mar-17 19:32:10.774 [Task submitter] INFO nextflow.Session - [57/d48193] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:33:38.991 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744861; id: 11; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e3/7b8f9a9bb0817b94d37eea5befc8ec started: 1773771849012; exited: -; ] ~> TaskHandler[jobId: 1744862; id: 10; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/99/a05839dcfb464d7537e28b863b9168 started: 1773771849015; exited: 2026-03-17T18:33:20.664951174Z; ] ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744890; id: 37; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/1cfdcc09536d5d286b55ddf2a827d2 started: 1773771939007; exited: -; ] ~> TaskHandler[jobId: 1744891; id: 40; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 started: 1773771969013; exited: -; ] ~> TaskHandler[jobId: 1744892; id: 47; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2d/4b1791eaebdcfa6757c17eff698fbb started: 1773771939011; exited: -; ] ~> TaskHandler[jobId: 1744893; id: 36; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba started: 1773771939013; exited: -; ] ~> TaskHandler[jobId: 1744894; id: 39; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c8/289458982d040f21a618fc05e85003 started: 1773771939015; exited: -; ] .. remaining tasks omitted. Mar-17 19:33:39.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744862; id: 10; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/99/a05839dcfb464d7537e28b863b9168 started: 1773771849015; exited: 2026-03-17T18:33:20.664951174Z; ] Mar-17 19:33:39.054 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744891; id: 40; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 started: 1773771969013; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270024 Current queue status: > job: 1744927: DONE > job: 1744863: DONE > job: 1744937: ERROR > job: 1744936: ERROR > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744921: RUNNING > job: 1744922: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744925: RUNNING > job: 1744926: RUNNING > job: 1744928: RUNNING > job: 1744929: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744918: RUNNING > job: 1744900: RUNNING > job: 1744901: RUNNING > job: 1744902: RUNNING > job: 1744903: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744892: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744895: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744898: RUNNING > job: 1744867: RUNNING > job: 1744861: RUNNING > job: 1744862: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 null Mar-17 19:33:39.054 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744891; id: 40; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 started: 1773771969013; exited: -; ] Mar-17 19:33:39.057 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744899; id: 35; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/60abc7c9e10504ca16adbc7be90c1d started: 1773771969015; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270025 Current queue status: > job: 1744927: DONE > job: 1744863: DONE > job: 1744937: ERROR > job: 1744936: ERROR > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744921: RUNNING > job: 1744922: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744925: RUNNING > job: 1744926: RUNNING > job: 1744928: RUNNING > job: 1744929: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744918: RUNNING > job: 1744900: RUNNING > job: 1744901: RUNNING > job: 1744902: RUNNING > job: 1744903: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744892: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744895: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744898: RUNNING > job: 1744867: RUNNING > job: 1744861: RUNNING > job: 1744862: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/60abc7c9e10504ca16adbc7be90c1d null Mar-17 19:33:39.057 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744899; id: 35; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/60abc7c9e10504ca16adbc7be90c1d started: 1773771969015; exited: -; ] Mar-17 19:33:39.062 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ce/7e47c18bf4b8088b9137aaef77ff19 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:33:39.062 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/62/60abc7c9e10504ca16adbc7be90c1d error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:33:39.075 [TaskFinalizer-10] INFO nextflow.processor.TaskProcessor - [ce/7e47c1] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:33:39.075 [TaskFinalizer-7] INFO nextflow.processor.TaskProcessor - [62/60abc7] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Mar-17 19:33:39.085 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Mar-17 19:33:40.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744939; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/cb71cb1bfb4853821cb9e1d902ca13 Mar-17 19:33:40.776 [Task submitter] INFO nextflow.Session - [d1/cb71cb] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:33:43.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744940; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0f/6575f9b154a2dcaf8322eb891fc660 Mar-17 19:33:43.774 [Task submitter] INFO nextflow.Session - [0f/6575f9] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:33:46.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744941; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/22/68cd14e1a25b8dd6f15cfdcc460a84 Mar-17 19:33:46.772 [Task submitter] INFO nextflow.Session - [22/68cd14] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:34:39.008 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744861; id: 11; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e3/7b8f9a9bb0817b94d37eea5befc8ec started: 1773771849012; exited: 2026-03-17T18:34:26.706530196Z; ] Mar-17 19:34:39.102 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 19:34:39.103 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Mar-17 19:34:39.103 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Mar-17 19:34:39.103 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Mar-17 19:34:39.103 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Mar-17 19:34:39.103 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Mar-17 19:34:39.103 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Mar-17 19:34:40.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744943; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/16/7a7911fef5701c03abb71e1c90b00c Mar-17 19:34:40.776 [Task submitter] INFO nextflow.Session - [16/7a7911] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:35:09.050 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744914; id: 49; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/d2f143f40fa4e60bd513c897cff119 started: 1773772029027; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 300010 Current queue status: > job: 1744927: DONE > job: 1744861: DONE > job: 1744862: DONE > job: 1744863: DONE > job: 1744943: ERROR > job: 1744939: ERROR > job: 1744937: ERROR > job: 1744936: ERROR > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744921: RUNNING > job: 1744922: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744925: RUNNING > job: 1744926: RUNNING > job: 1744928: RUNNING > job: 1744929: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744918: RUNNING > job: 1744900: RUNNING > job: 1744901: RUNNING > job: 1744902: RUNNING > job: 1744903: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744892: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744895: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744898: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/d2f143f40fa4e60bd513c897cff119 null Mar-17 19:35:09.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744914; id: 49; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/d2f143f40fa4e60bd513c897cff119 started: 1773772029027; exited: -; ] Mar-17 19:35:09.053 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744919; id: 62; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/31/1d83dd83657b6d5dc980ca3f03b591 started: 1773772029030; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 300012 Current queue status: > job: 1744927: DONE > job: 1744861: DONE > job: 1744862: DONE > job: 1744863: DONE > job: 1744943: ERROR > job: 1744939: ERROR > job: 1744937: ERROR > job: 1744936: ERROR > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744921: RUNNING > job: 1744922: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744925: RUNNING > job: 1744926: RUNNING > job: 1744928: RUNNING > job: 1744929: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744918: RUNNING > job: 1744900: RUNNING > job: 1744901: RUNNING > job: 1744902: RUNNING > job: 1744903: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744892: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744895: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744898: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/31/1d83dd83657b6d5dc980ca3f03b591 null Mar-17 19:35:09.053 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744919; id: 62; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/31/1d83dd83657b6d5dc980ca3f03b591 started: 1773772029030; exited: -; ] Mar-17 19:35:09.053 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/d2f143f40fa4e60bd513c897cff119 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:35:09.054 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [cc/d2f143] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:35:09.055 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/31/1d83dd83657b6d5dc980ca3f03b591 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:35:09.057 [TaskFinalizer-9] INFO nextflow.processor.TaskProcessor - [31/1d83dd] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:35:10.779 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744945; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0f/2d66519f96e07be91361e63a578a57 Mar-17 19:35:10.780 [Task submitter] INFO nextflow.Session - [0f/2d6651] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:35:13.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744947; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/c1e97e1ed609deb80d8a3312551af7 Mar-17 19:35:13.773 [Task submitter] INFO nextflow.Session - [d1/c1e97e] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:36:09.338 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744898; id: 46; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/42/d1a227050a811af63d674fe7fc863c started: 1773771939023; exited: 2026-03-17T18:36:01.527164962Z; ] Mar-17 19:36:09.549 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744918; id: 69; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/f9/c8dc9320ff25b49db3efc38a5920a6 started: 1773771999001; exited: 2026-03-17T18:35:44.70757486Z; ] Mar-17 19:36:09.555 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744930; id: 71; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/13/afddeba437cf3d91e148fb423b87e0 started: 1773772089036; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 300512 Current queue status: > job: 1744927: DONE > job: 1744918: DONE > job: 1744898: DONE > job: 1744861: DONE > job: 1744862: DONE > job: 1744863: DONE > job: 1744947: ERROR > job: 1744943: ERROR > job: 1744939: ERROR > job: 1744937: ERROR > job: 1744936: ERROR > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744921: RUNNING > job: 1744922: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744925: RUNNING > job: 1744926: RUNNING > job: 1744928: RUNNING > job: 1744929: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744900: RUNNING > job: 1744901: RUNNING > job: 1744902: RUNNING > job: 1744903: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744892: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744895: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744945: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/13/afddeba437cf3d91e148fb423b87e0 null Mar-17 19:36:09.555 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744930; id: 71; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/13/afddeba437cf3d91e148fb423b87e0 started: 1773772089036; exited: -; ] Mar-17 19:36:09.558 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/13/afddeba437cf3d91e148fb423b87e0 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:36:09.559 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [13/afddeb] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:36:10.087 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:36:10.438 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:36:10.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744948; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/99/4e2c8cdf5795fe4ffb9b5131db284b Mar-17 19:36:10.776 [Task submitter] INFO nextflow.Session - [99/4e2c8c] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:36:13.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744949; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/fb/f36c568eb0d2c49b95985981585f72 Mar-17 19:36:13.774 [Task submitter] INFO nextflow.Session - [fb/f36c56] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:36:16.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744950; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6a/b5891eef40046010c18a104c08ce0f Mar-17 19:36:16.772 [Task submitter] INFO nextflow.Session - [6a/b5891e] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:36:39.314 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744892; id: 47; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2d/4b1791eaebdcfa6757c17eff698fbb started: 1773771939011; exited: 2026-03-17T18:36:32.618868868Z; ] Mar-17 19:36:39.840 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:36:40.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744951; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/4bf236c16f0ec903783e140a1fc0b1 Mar-17 19:36:40.773 [Task submitter] INFO nextflow.Session - [86/4bf236] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:37:09.184 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744901; id: 48; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/1f/7b3908a7d1e7e8f7d339bb41bbf140 started: 1773771969019; exited: 2026-03-17T18:37:07.047341383Z; ] Mar-17 19:37:09.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744922; id: 70; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/77/2bc81926563f46d725cbe5ccc200a1 started: 1773772029034; exited: 2026-03-17T18:36:56.223375117Z; ] Mar-17 19:37:09.214 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:37:09.286 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744928; id: 68; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/30/8e999c11293f704301c4a70eb089da started: 1773772029048; exited: 2026-03-17T18:37:04.888798713Z; ] Mar-17 19:37:09.529 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:37:09.601 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:37:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744952; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cd/d538f2fb009706fcb9bac0cdf794b9 Mar-17 19:37:10.772 [Task submitter] INFO nextflow.Session - [cd/d538f2] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:37:13.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744953; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d6/463eefec9d2840bdc352a5909e7229 Mar-17 19:37:13.773 [Task submitter] INFO nextflow.Session - [d6/463eef] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:37:16.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744954; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/24/aca4f3033db9fe32f8d1e46cd9ce87 Mar-17 19:37:16.773 [Task submitter] INFO nextflow.Session - [24/aca4f3] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:38:39.003 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744890; id: 37; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/1cfdcc09536d5d286b55ddf2a827d2 started: 1773771939007; exited: -; ] ~> TaskHandler[jobId: 1744893; id: 36; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba started: 1773771939013; exited: -; ] ~> TaskHandler[jobId: 1744894; id: 39; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c8/289458982d040f21a618fc05e85003 started: 1773771939015; exited: -; ] ~> TaskHandler[jobId: 1744895; id: 29; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/88/08d7f604403b6fa7ef01f2d879edb3 started: 1773771939017; exited: -; ] ~> TaskHandler[jobId: 1744896; id: 41; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/60/13802159ec9e838c7d039f75c34196 started: 1773771939019; exited: -; ] ~> TaskHandler[jobId: 1744897; id: 38; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/4313970a98d1ea731bd7568b727c05 started: 1773771939021; exited: -; ] ~> TaskHandler[jobId: 1744900; id: 27; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8b/e1c4cb0b2f7d798e3d8cb8fb6e86d0 started: 1773771969017; exited: -; ] .. remaining tasks omitted. Mar-17 19:39:39.041 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744903; id: 33; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/19/4409177384f07536120e9d4f98d041 started: 1773771969023; exited: 2026-03-17T18:39:36.768353492Z; ] Mar-17 19:39:39.065 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744929; id: 67; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/59/c11da4c7d8accd4856ac428970707a started: 1773772029050; exited: 2026-03-17T18:39:24.882347857Z; ] Mar-17 19:39:39.070 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744936; id: 110; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/1acf6442e232261550a8f9ee69b973 started: 1773772329074; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270009 Current queue status: > job: 1744922: DONE > job: 1744928: DONE > job: 1744918: DONE > job: 1744901: DONE > job: 1744892: DONE > job: 1744898: DONE > job: 1744861: DONE > job: 1744947: ERROR > job: 1744943: ERROR > job: 1744939: ERROR > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744921: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744925: RUNNING > job: 1744926: RUNNING > job: 1744929: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744900: RUNNING > job: 1744902: RUNNING > job: 1744903: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744895: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744951: RUNNING > job: 1744948: RUNNING > job: 1744949: RUNNING > job: 1744950: RUNNING > job: 1744945: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/1acf6442e232261550a8f9ee69b973 null Mar-17 19:39:39.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744936; id: 110; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/1acf6442e232261550a8f9ee69b973 started: 1773772329074; exited: -; ] Mar-17 19:39:39.075 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/1acf6442e232261550a8f9ee69b973 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:39:39.076 [TaskFinalizer-9] INFO nextflow.processor.TaskProcessor - [5e/1acf64] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:39:39.083 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:39:40.604 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:39:40.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744963; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/66/66a46f1f95e393ea0aaa984c1e7c9e Mar-17 19:39:40.775 [Task submitter] INFO nextflow.Session - [66/66a46f] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:39:43.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744964; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/bb/62e7541f4e26a3259f77df8eb6cea7 Mar-17 19:39:43.773 [Task submitter] INFO nextflow.Session - [bb/62e754] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:39:46.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744965; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/21/698eaae7ca03ddc11abd3a287908d2 Mar-17 19:39:46.774 [Task submitter] INFO nextflow.Session - [21/698eaa] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:40:09.338 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744895; id: 29; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/88/08d7f604403b6fa7ef01f2d879edb3 started: 1773771939017; exited: 2026-03-17T18:39:55.441950759Z; ] Mar-17 19:40:09.791 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744925; id: 64; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9f/f64eca8a048d4d264c1d8d8eb9b5d1 started: 1773772029041; exited: 2026-03-17T18:39:47.156001198Z; ] Mar-17 19:40:10.620 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:40:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744966; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c3/70e448223dc3c05c537b3ae6e741ee Mar-17 19:40:10.773 [Task submitter] INFO nextflow.Session - [c3/70e448] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:40:10.834 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:40:13.770 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744967; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/06c9bd0dc4077a8a0d1460b55bbeb0 Mar-17 19:40:13.770 [Task submitter] INFO nextflow.Session - [5a/06c9bd] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:40:39.287 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744921; id: 65; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/bb/65120146b171a68a33df4791622b2b started: 1773772029032; exited: 2026-03-17T18:40:26.383623871Z; ] Mar-17 19:40:39.795 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:40:40.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744970; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/208f17db20e9bedfcab8d9a7dc2f86 Mar-17 19:40:40.776 [Task submitter] INFO nextflow.Session - [9a/208f17] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:41:09.059 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744937; id: 126; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/57/d48193e62d5661307cc3ade388a74e started: 1773772389047; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 299500 Current queue status: > job: 1744921: DONE > job: 1744922: DONE > job: 1744925: DONE > job: 1744928: DONE > job: 1744929: DONE > job: 1744918: DONE > job: 1744901: DONE > job: 1744903: DONE > job: 1744892: DONE > job: 1744895: DONE > job: 1744898: DONE > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744926: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744900: RUNNING > job: 1744902: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744970: RUNNING > job: 1744966: RUNNING > job: 1744967: RUNNING > job: 1744963: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744951: RUNNING > job: 1744948: RUNNING > job: 1744949: RUNNING > job: 1744950: RUNNING > job: 1744945: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/57/d48193e62d5661307cc3ade388a74e null Mar-17 19:41:09.059 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744937; id: 126; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/57/d48193e62d5661307cc3ade388a74e started: 1773772389047; exited: -; ] Mar-17 19:41:09.062 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/57/d48193e62d5661307cc3ade388a74e error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:41:09.063 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [57/d48193] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:41:10.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1744971; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/12/e80bf1bd7b93bf5f5e87901d3947ce Mar-17 19:41:10.774 [Task submitter] INFO nextflow.Session - [12/e80bf1] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:41:39.034 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744939; id: 89; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/cb71cb1bfb4853821cb9e1d902ca13 started: 1773772449065; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 299707 Current queue status: > job: 1744921: DONE > job: 1744922: DONE > job: 1744925: DONE > job: 1744928: DONE > job: 1744929: DONE > job: 1744918: DONE > job: 1744901: DONE > job: 1744903: DONE > job: 1744892: DONE > job: 1744895: DONE > job: 1744898: DONE > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744926: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744915: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744900: RUNNING > job: 1744902: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744970: RUNNING > job: 1744966: RUNNING > job: 1744967: RUNNING > job: 1744963: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744951: RUNNING > job: 1744948: RUNNING > job: 1744949: RUNNING > job: 1744950: RUNNING > job: 1744945: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/cb71cb1bfb4853821cb9e1d902ca13 null Mar-17 19:41:39.034 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744939; id: 89; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/cb71cb1bfb4853821cb9e1d902ca13 started: 1773772449065; exited: -; ] Mar-17 19:41:39.037 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/cb71cb1bfb4853821cb9e1d902ca13 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:41:39.039 [TaskFinalizer-7] INFO nextflow.processor.TaskProcessor - [d1/cb71cb] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:41:40.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1744973; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ed/1c967088d20c8a707634e92f567a6c Mar-17 19:41:40.778 [Task submitter] INFO nextflow.Session - [ed/1c9670] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:42:09.095 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744915; id: 43; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/22/14ae995e705fb1cdbbffa5a79b092f started: 1773771998995; exited: 2026-03-17T18:41:43.01545419Z; ] Mar-17 19:42:09.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744926; id: 72; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2d/4a9992d2475c99da6595b57b19b9e4 started: 1773772029043; exited: 2026-03-17T18:42:01.017047336Z; ] Mar-17 19:42:09.602 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:42:09.842 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:42:10.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1744996; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b3/0ccb5acc2c63f13c0b387181e4e85c Mar-17 19:42:10.773 [Task submitter] INFO nextflow.Session - [b3/0ccb5a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:42:13.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1744997; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9c/62f469b9c581b4a1322fa63f5d2b7d Mar-17 19:42:13.773 [Task submitter] INFO nextflow.Session - [9c/62f469] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:42:39.133 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744916; id: 63; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8a/7a21839e9c251ff17535293572b631 started: 1773771998997; exited: 2026-03-17T18:42:13.98525659Z; ] Mar-17 19:42:39.135 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744943; id: 105; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/16/7a7911fef5701c03abb71e1c90b00c started: 1773772509063; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270078 Current queue status: > job: 1744921: DONE > job: 1744922: DONE > job: 1744925: DONE > job: 1744926: DONE > job: 1744928: DONE > job: 1744929: DONE > job: 1744915: DONE > job: 1744901: DONE > job: 1744903: DONE > job: 1744895: DONE > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744916: RUNNING > job: 1744917: RUNNING > job: 1744900: RUNNING > job: 1744902: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744896: RUNNING > job: 1744897: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744973: RUNNING > job: 1744971: RUNNING > job: 1744970: RUNNING > job: 1744966: RUNNING > job: 1744967: RUNNING > job: 1744963: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744951: RUNNING > job: 1744948: RUNNING > job: 1744949: RUNNING > job: 1744950: RUNNING > job: 1744945: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/16/7a7911fef5701c03abb71e1c90b00c null Mar-17 19:42:39.136 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744943; id: 105; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/16/7a7911fef5701c03abb71e1c90b00c started: 1773772509063; exited: -; ] Mar-17 19:42:39.139 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/16/7a7911fef5701c03abb71e1c90b00c error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:42:39.140 [TaskFinalizer-1] INFO nextflow.processor.TaskProcessor - [16/7a7911] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:42:39.828 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:42:40.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1744999; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c0/c78b7672db1a29be373facbbc340bb Mar-17 19:42:40.775 [Task submitter] INFO nextflow.Session - [c0/c78b76] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:42:43.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745000; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f Mar-17 19:42:43.771 [Task submitter] INFO nextflow.Session - [6e/a0c4b7] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:43:09.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744896; id: 41; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/60/13802159ec9e838c7d039f75c34196 started: 1773771939019; exited: 2026-03-17T18:42:53.317048632Z; ] Mar-17 19:43:09.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744900; id: 27; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8b/e1c4cb0b2f7d798e3d8cb8fb6e86d0 started: 1773771969017; exited: 2026-03-17T18:42:54.464507979Z; ] Mar-17 19:43:10.497 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:43:10.569 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:43:10.780 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745011; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 Mar-17 19:43:10.780 [Task submitter] INFO nextflow.Session - [4a/c0be13] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:43:13.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745012; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5b/f1c345f3736c9e46450b553a39a06a Mar-17 19:43:13.774 [Task submitter] INFO nextflow.Session - [5b/f1c345] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:43:39.021 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744890; id: 37; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/1cfdcc09536d5d286b55ddf2a827d2 started: 1773771939007; exited: -; ] ~> TaskHandler[jobId: 1744893; id: 36; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba started: 1773771939013; exited: -; ] ~> TaskHandler[jobId: 1744894; id: 39; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c8/289458982d040f21a618fc05e85003 started: 1773771939015; exited: -; ] ~> TaskHandler[jobId: 1744897; id: 38; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/4313970a98d1ea731bd7568b727c05 started: 1773771939021; exited: -; ] ~> TaskHandler[jobId: 1744902; id: 42; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a0/54f5b5e63a024ac0b746beda24f4e6 started: 1773771969021; exited: -; ] ~> TaskHandler[jobId: 1744904; id: 31; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/38/6203d4a6b9e75dd2056ff5c8984db5 started: 1773771969025; exited: -; ] ~> TaskHandler[jobId: 1744905; id: 34; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/03a94690a66780ebb8bbb4f9361423 started: 1773771969027; exited: -; ] .. remaining tasks omitted. Mar-17 19:44:09.073 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1744947; id: 121; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/c1e97e1ed609deb80d8a3312551af7 started: 1773772569563; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 300008 Current queue status: > job: 1744921: DONE > job: 1744925: DONE > job: 1744926: DONE > job: 1744929: DONE > job: 1744915: DONE > job: 1744916: DONE > job: 1744900: DONE > job: 1744903: DONE > job: 1744895: DONE > job: 1744896: DONE > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744923: RUNNING > job: 1744924: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744917: RUNNING > job: 1744902: RUNNING > job: 1744904: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744890: RUNNING > job: 1744893: RUNNING > job: 1744894: RUNNING > job: 1744897: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1744999: RUNNING > job: 1745000: RUNNING > job: 1745011: RUNNING > job: 1745012: RUNNING > job: 1744996: RUNNING > job: 1744997: RUNNING > job: 1744973: RUNNING > job: 1744971: RUNNING > job: 1744970: RUNNING > job: 1744966: RUNNING > job: 1744967: RUNNING > job: 1744963: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744951: RUNNING > job: 1744948: RUNNING > job: 1744949: RUNNING > job: 1744950: RUNNING > job: 1744945: RUNNING > job: 1744940: RUNNING > job: 1744941: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/c1e97e1ed609deb80d8a3312551af7 null Mar-17 19:44:09.073 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744947; id: 121; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/c1e97e1ed609deb80d8a3312551af7 started: 1773772569563; exited: -; ] Mar-17 19:44:09.076 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d1/c1e97e1ed609deb80d8a3312551af7 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:44:09.077 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [d1/c1e97e] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:44:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745113; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/75/edbc89ead57372767d448197fb2288 Mar-17 19:44:10.773 [Task submitter] INFO nextflow.Session - [75/edbc89] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:45:09.104 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744950; id: 142; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6a/b5891eef40046010c18a104c08ce0f started: 1773772599363; exited: 2026-03-17T18:45:08.31652851Z; ] Mar-17 19:45:09.131 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:45:10.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745115; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/b0becb228b527c4732ff8c786b0eeb Mar-17 19:45:10.773 [Task submitter] INFO nextflow.Session - [94/b0becb] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:45:39.067 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744890; id: 37; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/1cfdcc09536d5d286b55ddf2a827d2 started: 1773771939007; exited: 2026-03-17T18:45:21.749572456Z; ] Mar-17 19:45:39.375 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744894; id: 39; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c8/289458982d040f21a618fc05e85003 started: 1773771939015; exited: 2026-03-17T18:45:19.646594129Z; ] Mar-17 19:45:40.059 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:45:40.194 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:45:40.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745116; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0b/4affd6480c8adcb17f993e3b4258d4 Mar-17 19:45:40.773 [Task submitter] INFO nextflow.Session - [0b/4affd6] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:45:43.820 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745117; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/49/2b241ef6c0a503fd3a4c7174dabd3c Mar-17 19:45:43.821 [Task submitter] INFO nextflow.Session - [49/2b241e] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:46:09.352 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744948; id: 140; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/99/4e2c8cdf5795fe4ffb9b5131db284b started: 1773772599328; exited: 2026-03-17T18:46:07.966876725Z; ] Mar-17 19:46:09.382 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:46:10.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745118; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/47/b5e18ce52b5441f9b8220935f78f0b Mar-17 19:46:10.997 [Task submitter] INFO nextflow.Session - [47/b5e18c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:46:39.025 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744917; id: 60; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6d/af294fc765c6790a8933965d0a972e started: 1773771998999; exited: 2026-03-17T18:46:19.844593048Z; ] Mar-17 19:46:39.030 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:46:39.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744949; id: 141; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/fb/f36c568eb0d2c49b95985981585f72 started: 1773772599331; exited: 2026-03-17T18:46:29.25736387Z; ] Mar-17 19:46:39.804 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:46:40.777 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745119; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a9/c446f2b989f68776e074c9e9e6e137 Mar-17 19:46:40.777 [Task submitter] INFO nextflow.Session - [a9/c446f2] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:46:43.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745120; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4f/b2f963c6dd75494cc6ce8dc20786ae Mar-17 19:46:43.773 [Task submitter] INFO nextflow.Session - [4f/b2f963] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:47:09.279 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744904; id: 31; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/38/6203d4a6b9e75dd2056ff5c8984db5 started: 1773771969025; exited: 2026-03-17T18:46:53.809345412Z; ] Mar-17 19:47:09.400 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744924; id: 61; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e7/70f5800c998d4bed5c0a80e5a60379 started: 1773772029039; exited: 2026-03-17T18:46:52.135955035Z; ] Mar-17 19:47:09.453 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744941; id: 93; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/22/68cd14e1a25b8dd6f15cfdcc460a84 started: 1773772449071; exited: 2026-03-17T18:46:59.996951439Z; ] Mar-17 19:47:09.751 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744951; id: 84; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/4bf236c16f0ec903783e140a1fc0b1 started: 1773772629293; exited: 2026-03-17T18:46:55.542565801Z; ] Mar-17 19:47:10.052 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744967; id: 109; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/06c9bd0dc4077a8a0d1460b55bbeb0 started: 1773772839302; exited: 2026-03-17T18:46:47.211131079Z; ] Mar-17 19:47:10.110 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:47:10.223 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:47:10.330 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:47:10.603 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:47:10.685 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:47:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745121; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/897883adcfff52aa5dbece2563d1c2 Mar-17 19:47:10.773 [Task submitter] INFO nextflow.Session - [25/897883] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:47:13.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745122; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/9198fae663a188afdd86494521ba6e Mar-17 19:47:13.771 [Task submitter] INFO nextflow.Session - [11/9198fa] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:47:16.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745123; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/adb57b7f6368a672038b922f828948 Mar-17 19:47:16.773 [Task submitter] INFO nextflow.Session - [5a/adb57b] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:47:19.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745124; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/e347855875f8a5b1f8eadcd3a32b47 Mar-17 19:47:19.776 [Task submitter] INFO nextflow.Session - [6e/e34785] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:47:22.770 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745125; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/15/f161dc3aacabe44c55845d7c8f6d06 Mar-17 19:47:22.771 [Task submitter] INFO nextflow.Session - [15/f161dc] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:48:39.028 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744893; id: 36; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba started: 1773771939013; exited: -; ] ~> TaskHandler[jobId: 1744897; id: 38; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/4313970a98d1ea731bd7568b727c05 started: 1773771939021; exited: -; ] ~> TaskHandler[jobId: 1744902; id: 42; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a0/54f5b5e63a024ac0b746beda24f4e6 started: 1773771969021; exited: -; ] ~> TaskHandler[jobId: 1744905; id: 34; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/03a94690a66780ebb8bbb4f9361423 started: 1773771969027; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] .. remaining tasks omitted. Mar-17 19:48:39.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744940; id: 87; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0f/6575f9b154a2dcaf8322eb891fc660 started: 1773772449067; exited: 2026-03-17T18:48:23.871044219Z; ] Mar-17 19:48:39.806 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:48:40.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745127; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2e/da9f0f58b20a3b1a0ee9f6c783d37b Mar-17 19:48:40.774 [Task submitter] INFO nextflow.Session - [2e/da9f0f] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:49:09.102 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744897; id: 38; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/4313970a98d1ea731bd7568b727c05 started: 1773771939021; exited: 2026-03-17T18:49:04.488986127Z; ] Mar-17 19:49:09.268 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:49:09.286 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744902; id: 42; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a0/54f5b5e63a024ac0b746beda24f4e6 started: 1773771969021; exited: 2026-03-17T18:48:39.47275642Z; ] Mar-17 19:49:09.840 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:49:10.770 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745128; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c0/b604a5f90688ec35975ebf185aae0f Mar-17 19:49:10.771 [Task submitter] INFO nextflow.Session - [c0/b604a5] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:49:13.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745129; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/6cb17cf3efa0f982cdade4852a1d4f Mar-17 19:49:13.775 [Task submitter] INFO nextflow.Session - [08/6cb17c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:49:39.037 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745124; id: 127; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/e347855875f8a5b1f8eadcd3a32b47 started: 1773773259045; exited: 2026-03-17T18:49:17.116838298Z; ] Mar-17 19:49:39.042 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:49:40.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1745131; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3c/2676a449ea6a8eb05f6b25b95df5d2 Mar-17 19:49:40.775 [Task submitter] INFO nextflow.Session - [3c/2676a4] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:50:09.330 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745125; id: 130; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/15/f161dc3aacabe44c55845d7c8f6d06 started: 1773773259055; exited: 2026-03-17T18:49:50.502560585Z; ] Mar-17 19:50:09.686 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:50:10.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745132; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/72/2a42ad8f713da6f09e9724056f49d1 Mar-17 19:50:10.772 [Task submitter] INFO nextflow.Session - [72/2a42ad] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:51:39.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744893; id: 36; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5ea8fef877d0dc00c63bfdecdad1ba started: 1773771939013; exited: 2026-03-17T18:51:14.169968568Z; ] Mar-17 19:51:39.654 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744996; id: 88; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b3/0ccb5acc2c63f13c0b387181e4e85c started: 1773772959144; exited: 2026-03-17T18:51:13.490444465Z; ] Mar-17 19:51:39.912 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:51:40.191 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:51:40.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745133; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b7/33f470a8fa0f4bdb351ee0e3cc432c Mar-17 19:51:40.775 [Task submitter] INFO nextflow.Session - [b7/33f470] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:51:43.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745134; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/06/46b3bb76c500fd2450806de91b10e2 Mar-17 19:51:43.774 [Task submitter] INFO nextflow.Session - [06/46b3bb] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:52:09.155 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744966; id: 107; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c3/70e448223dc3c05c537b3ae6e741ee started: 1773772839295; exited: 2026-03-17T18:51:55.781244418Z; ] Mar-17 19:52:10.232 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:52:10.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745135; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cf/e7ac5bb54ea551295e7288100f1def Mar-17 19:52:10.871 [Task submitter] INFO nextflow.Session - [cf/e7ac5b] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:53:39.043 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744905; id: 34; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/03a94690a66780ebb8bbb4f9361423 started: 1773771969027; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] .. remaining tasks omitted. Mar-17 19:54:09.444 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744973; id: 144; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ed/1c967088d20c8a707634e92f567a6c started: 1773772929195; exited: 2026-03-17T18:53:59.033470754Z; ] Mar-17 19:54:10.266 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:54:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745136; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/82/1b38ee1335a2ae0aa0a9c289a6c7cc Mar-17 19:54:10.772 [Task submitter] INFO nextflow.Session - [82/1b38ee] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:55:09.464 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744923; id: 66; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9e/8b772fded01172fec60af0e64ef293 started: 1773772029037; exited: 2026-03-17T18:55:01.935755041Z; ] Mar-17 19:55:09.554 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744997; id: 91; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9c/62f469b9c581b4a1322fa63f5d2b7d started: 1773772959152; exited: 2026-03-17T18:55:08.971848843Z; ] Mar-17 19:55:09.560 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1745120; id: 95; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4f/b2f963c6dd75494cc6ce8dc20786ae started: 1773773230060; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 300470 Current queue status: > job: 1744923: DONE > job: 1744893: DONE > job: 1745125: DONE > job: 1744996: DONE > job: 1744997: DONE > job: 1744973: DONE > job: 1744966: DONE > job: 1745135: PENDING > job: 1745134: PENDING > job: 1745133: PENDING > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1745129: RUNNING > job: 1745123: RUNNING > job: 1745136: RUNNING > job: 1745128: RUNNING > job: 1745113: RUNNING > job: 1745132: RUNNING > job: 1745131: RUNNING > job: 1745119: RUNNING > job: 1745122: RUNNING > job: 1745117: RUNNING > job: 1745118: RUNNING > job: 1745116: RUNNING > job: 1745115: RUNNING > job: 1744999: RUNNING > job: 1745000: RUNNING > job: 1745011: RUNNING > job: 1745012: RUNNING > job: 1744971: RUNNING > job: 1744970: RUNNING > job: 1744963: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744945: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4f/b2f963c6dd75494cc6ce8dc20786ae null Mar-17 19:55:09.561 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745120; id: 95; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4f/b2f963c6dd75494cc6ce8dc20786ae started: 1773773230060; exited: -; ] Mar-17 19:55:09.563 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4f/b2f963c6dd75494cc6ce8dc20786ae error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:55:09.564 [TaskFinalizer-6] INFO nextflow.processor.TaskProcessor - [4f/b2f963] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:55:09.590 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:55:10.288 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:55:10.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745138; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9b/834787c4db35786d861f970bce8f98 Mar-17 19:55:10.774 [Task submitter] INFO nextflow.Session - [9b/834787] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 19:55:13.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1745139; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c7/2ab39f4580d57c1d3fe87ea7dfe6c2 Mar-17 19:55:13.771 [Task submitter] INFO nextflow.Session - [c7/2ab39f] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:55:16.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745140; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b7/796bf05557c4a95af8fc8d1b681d93 Mar-17 19:55:16.773 [Task submitter] INFO nextflow.Session - [b7/796bf0] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:56:09.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744905; id: 34; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5e/03a94690a66780ebb8bbb4f9361423 started: 1773771969027; exited: 2026-03-17T18:55:39.231536669Z; ] Mar-17 19:56:09.182 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1745121; id: 120; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/897883adcfff52aa5dbece2563d1c2 started: 1773773289079; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 300095 Current queue status: > job: 1744923: DONE > job: 1744893: DONE > job: 1745125: DONE > job: 1744996: DONE > job: 1744997: DONE > job: 1744973: DONE > job: 1744966: DONE > job: 1745135: PENDING > job: 1745134: PENDING > job: 1745133: PENDING > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744905: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1745129: RUNNING > job: 1745123: RUNNING > job: 1745136: RUNNING > job: 1745128: RUNNING > job: 1745113: RUNNING > job: 1745132: RUNNING > job: 1745131: RUNNING > job: 1745119: RUNNING > job: 1745122: RUNNING > job: 1745117: RUNNING > job: 1745118: RUNNING > job: 1745116: RUNNING > job: 1745115: RUNNING > job: 1744999: RUNNING > job: 1745000: RUNNING > job: 1745011: RUNNING > job: 1745012: RUNNING > job: 1744971: RUNNING > job: 1744970: RUNNING > job: 1744963: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744945: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/897883adcfff52aa5dbece2563d1c2 null Mar-17 19:56:09.182 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745121; id: 120; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/897883adcfff52aa5dbece2563d1c2 started: 1773773289079; exited: -; ] Mar-17 19:56:09.186 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/25/897883adcfff52aa5dbece2563d1c2 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:56:09.187 [TaskFinalizer-10] INFO nextflow.processor.TaskProcessor - [25/897883] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:56:09.912 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:56:10.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745143; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a5/162ed51d59bcc7134d510ddd58d871 Mar-17 19:56:10.776 [Task submitter] INFO nextflow.Session - [a5/162ed5] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:56:13.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745144; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 Mar-17 19:56:13.777 [Task submitter] INFO nextflow.Session - [28/a46f51] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 19:56:39.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744963; id: 94; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/66/66a46f1f95e393ea0aaa984c1e7c9e started: 1773772809804; exited: 2026-03-17T18:56:20.873748195Z; ] Mar-17 19:56:39.401 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 1745127; id: 108; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2e/da9f0f58b20a3b1a0ee9f6c783d37b started: 1773773349309; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 299724 Current queue status: > job: 1744923: DONE > job: 1744905: DONE > job: 1744997: DONE > job: 1744973: DONE > job: 1744966: DONE > job: 1744963: DONE > job: 1745135: PENDING > job: 1745134: PENDING > job: 1745144: PENDING > job: 1745143: PENDING > job: 1745138: PENDING > job: 1744931: RUNNING > job: 1744932: RUNNING > job: 1744933: RUNNING > job: 1744934: RUNNING > job: 1744909: RUNNING > job: 1744910: RUNNING > job: 1744911: RUNNING > job: 1744912: RUNNING > job: 1744913: RUNNING > job: 1744906: RUNNING > job: 1744907: RUNNING > job: 1744908: RUNNING > job: 1744867: RUNNING > job: 1744864: RUNNING > job: 1744865: RUNNING > job: 1744857: RUNNING > job: 1745129: RUNNING > job: 1745133: RUNNING > job: 1745123: RUNNING > job: 1745136: RUNNING > job: 1745128: RUNNING > job: 1745113: RUNNING > job: 1745139: RUNNING > job: 1745140: RUNNING > job: 1745132: RUNNING > job: 1745131: RUNNING > job: 1745119: RUNNING > job: 1745122: RUNNING > job: 1745117: RUNNING > job: 1745118: RUNNING > job: 1745116: RUNNING > job: 1745115: RUNNING > job: 1744999: RUNNING > job: 1745000: RUNNING > job: 1745011: RUNNING > job: 1745012: RUNNING > job: 1744971: RUNNING > job: 1744970: RUNNING > job: 1744964: RUNNING > job: 1744965: RUNNING > job: 1744952: RUNNING > job: 1744953: RUNNING > job: 1744954: RUNNING > job: 1744945: RUNNING Content of workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2e/da9f0f58b20a3b1a0ee9f6c783d37b null Mar-17 19:56:39.401 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745127; id: 108; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2e/da9f0f58b20a3b1a0ee9f6c783d37b started: 1773773349309; exited: -; ] Mar-17 19:56:39.404 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); work-dir=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2e/da9f0f58b20a3b1a0ee9f6c783d37b error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system Mar-17 19:56:39.405 [TaskFinalizer-8] INFO nextflow.processor.TaskProcessor - [2e/da9f0f] NOTE: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K)` terminated for an unknown reason -- Likely it has been terminated by the external system -- Execution is retried (1) Mar-17 19:56:40.432 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 19:56:40.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745145; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/61af734ebd17ae2aae8876f5d4e7f5 Mar-17 19:56:40.771 [Task submitter] INFO nextflow.Session - [94/61af73] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 19:56:43.774 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745146; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8d/b559aaac464d0079383c4b7a75966d Mar-17 19:56:43.774 [Task submitter] INFO nextflow.Session - [8d/b559aa] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:57:09.082 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745115; id: 123; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/b0becb228b527c4732ff8c786b0eeb started: 1773773139400; exited: 2026-03-17T18:57:01.176874925Z; ] Mar-17 19:57:09.668 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:57:10.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1745147; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/f7/716aa5521d8728a0ffd404dd5d0b8a Mar-17 19:57:10.775 [Task submitter] INFO nextflow.Session - [f7/716aa5] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 19:58:39.053 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] .. remaining tasks omitted. Mar-17 19:59:09.305 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745122; id: 125; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/11/9198fae663a188afdd86494521ba6e started: 1773773259043; exited: 2026-03-17T18:58:58.828456556Z; ] Mar-17 19:59:09.476 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745131; id: 74; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3c/2676a449ea6a8eb05f6b25b95df5d2 started: 1773773409338; exited: 2026-03-17T18:58:41.420242451Z; ] Mar-17 19:59:10.776 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745149; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/f2/73bf03a4e0b8694ef5a6f4ac1bab72 Mar-17 19:59:10.786 [Task submitter] INFO nextflow.Session - [f2/73bf03] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 19:59:10.796 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 19:59:10.900 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 19:59:13.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745150; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b7/208e8db0cb1c46e09aedade55248e0 Mar-17 19:59:13.773 [Task submitter] INFO nextflow.Session - [b7/208e8d] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:01:09.666 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744970; id: 124; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9a/208f17db20e9bedfcab8d9a7dc2f86 started: 1773772869067; exited: 2026-03-17T19:00:42.688367481Z; ] Mar-17 20:01:10.696 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:01:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745156; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a0/ec7b7592421fedcde4d71af06f8b18 Mar-17 20:01:10.773 [Task submitter] INFO nextflow.Session - [a0/ec7b75] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 20:02:39.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745132; id: 111; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/72/2a42ad8f713da6f09e9724056f49d1 started: 1773773439036; exited: 2026-03-17T19:02:36.103946972Z; ] Mar-17 20:02:39.074 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:02:39.283 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745140; id: 143; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b7/796bf05557c4a95af8fc8d1b681d93 started: 1773773739070; exited: 2026-03-17T19:02:37.27316456Z; ] Mar-17 20:02:39.318 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:02:40.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745160; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a6/9ecdbd4253800df994741a7bb87e37 Mar-17 20:02:40.773 [Task submitter] INFO nextflow.Session - [a6/9ecdbd] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 20:02:43.770 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745161; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/78/0ba2587dbf82e99e03b702ec370330 Mar-17 20:02:43.770 [Task submitter] INFO nextflow.Session - [78/0ba258] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:03:39.067 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] .. remaining tasks omitted. Mar-17 20:03:43.753 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor slurm > tasks in the submission queue: 11 -- tasks to be submitted are shown below ~> TaskHandler[jobId: null; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 90; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3e/be057296329305efa826b6822ce3e3 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 106; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/64/be6a548ed0e48a0c3bdae37b1e0635 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 101; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/02/aaae97c6be2538485fa571cba1724e started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 112; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 119; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/87/31e75eaab0c5ad83a4bec4e1bc2577 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 146; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4e/c5ce87fe3c07b9251ce50f182074aa started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 147; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/05/1c367fb14b04adb2c1fe93ae5d223a started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 148; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/5091dfec3681cf2d1fbddaad00625b started: -; exited: -; ] Mar-17 20:06:09.203 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745147; id: 145; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/f7/716aa5521d8728a0ffd404dd5d0b8a started: 1773773859123; exited: 2026-03-17T19:05:39.422580673Z; ] Mar-17 20:06:10.787 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 20:06:10.820 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745167; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 Mar-17 20:06:10.820 [Task submitter] INFO nextflow.Session - [36/5c227d] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 20:07:09.735 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745139; id: 139; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c7/2ab39f4580d57c1d3fe87ea7dfe6c2 started: 1773773739064; exited: 2026-03-17T19:06:59.268001156Z; ] Mar-17 20:07:10.770 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745191; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/02/aaae97c6be2538485fa571cba1724e Mar-17 20:07:10.771 [Task submitter] INFO nextflow.Session - [02/aaae97] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 20:07:11.722 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 20:07:39.259 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745128; id: 136; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c0/b604a5f90688ec35975ebf185aae0f started: 1773773649474; exited: 2026-03-17T19:07:29.106654197Z; ] Mar-17 20:07:40.878 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745194; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e Mar-17 20:07:40.878 [Task submitter] INFO nextflow.Session - [6f/f27510] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 20:07:45.053 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:07:45.054 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:07:45.055 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:08:09.482 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745012; id: 117; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5b/f1c345f3736c9e46450b553a39a06a started: 1773773019043; exited: 2026-03-17T19:07:49.905876174Z; ] Mar-17 20:08:10.771 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745195; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4e/c5ce87fe3c07b9251ce50f182074aa Mar-17 20:08:10.771 [Task submitter] INFO nextflow.Session - [4e/c5ce87] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 20:08:14.164 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:08:14.165 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:08:14.165 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:08:39.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] .. remaining tasks omitted. Mar-17 20:09:01.728 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor slurm > tasks in the submission queue: 7 -- tasks to be submitted are shown below ~> TaskHandler[jobId: null; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 90; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3e/be057296329305efa826b6822ce3e3 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 106; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/64/be6a548ed0e48a0c3bdae37b1e0635 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 119; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/87/31e75eaab0c5ad83a4bec4e1bc2577 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 147; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/05/1c367fb14b04adb2c1fe93ae5d223a started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 148; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/5091dfec3681cf2d1fbddaad00625b started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 150; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ef/d20d1af88f55ca3e30ba2edffb9c15 started: -; exited: -; ] Mar-17 20:11:39.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745146; id: 86; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/8d/b559aaac464d0079383c4b7a75966d started: 1773773829099; exited: 2026-03-17T19:11:10.63310372Z; ] Mar-17 20:11:40.102 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:11:40.770 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745204; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/87/31e75eaab0c5ad83a4bec4e1bc2577 Mar-17 20:11:40.770 [Task submitter] INFO nextflow.Session - [87/31e75e] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:13:09.293 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745145; id: 85; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/61af734ebd17ae2aae8876f5d4e7f5 started: 1773773829091; exited: 2026-03-17T19:12:39.209574311Z; ] Mar-17 20:13:09.813 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:13:10.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745215; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/64/be6a548ed0e48a0c3bdae37b1e0635 Mar-17 20:13:10.772 [Task submitter] INFO nextflow.Session - [64/be6a54] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:13:39.079 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 50 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] .. remaining tasks omitted. Mar-17 20:13:39.156 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745156; id: 149; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a0/ec7b7592421fedcde4d71af06f8b18 started: 1773774099150; exited: 2026-03-17T19:13:37.110633653Z; ] Mar-17 20:13:39.180 [Actor Thread 45] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:13:40.773 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1745216; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3e/be057296329305efa826b6822ce3e3 Mar-17 20:13:40.773 [Task submitter] INFO nextflow.Session - [3e/be0572] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 20:14:13.728 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor slurm > tasks in the submission queue: 4 -- tasks to be submitted are shown below ~> TaskHandler[jobId: null; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 147; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/05/1c367fb14b04adb2c1fe93ae5d223a started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 148; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/5091dfec3681cf2d1fbddaad00625b started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 150; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ef/d20d1af88f55ca3e30ba2edffb9c15 started: -; exited: -; ] Mar-17 20:14:39.168 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745149; id: 75; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/f2/73bf03a4e0b8694ef5a6f4ac1bab72 started: 1773773979132; exited: 2026-03-17T19:14:21.007812688Z; ] Mar-17 20:14:40.517 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:14:40.802 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745217; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 Mar-17 20:14:40.802 [Task submitter] INFO nextflow.Session - [08/4f1e43] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 20:15:09.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745216; id: 90; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3e/be057296329305efa826b6822ce3e3 started: 1773774849088; exited: 2026-03-17T19:15:07.827272957Z; ] Mar-17 20:15:09.205 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, contamination:null, num_intervals:21] size=21 Mar-17 20:15:10.787 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745218; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/05/1c367fb14b04adb2c1fe93ae5d223a Mar-17 20:15:10.787 [Task submitter] INFO nextflow.Session - [05/1c367f] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:16:39.089 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744865; id: 3; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ad/d6fb4e4128aaeda47473ee95404dc8 started: 1773771849033; exited: 2026-03-17T19:16:28.926268257Z; ] Mar-17 20:16:40.783 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) > jobId: 1745222; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/39/e03e35dd166e7d3cf6e6694aaa338e Mar-17 20:16:40.783 [Task submitter] INFO nextflow.Session - [39/e03e35] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ) Mar-17 20:17:09.285 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745136; id: 138; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/82/1b38ee1335a2ae0aa0a9c289a6c7cc started: 1773773679091; exited: 2026-03-17T19:16:45.582411901Z; ] Mar-17 20:17:09.543 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745150; id: 92; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b7/208e8db0cb1c46e09aedade55248e0 started: 1773773979141; exited: 2026-03-17T19:16:41.630796683Z; ] Mar-17 20:17:09.813 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:17:10.104 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:17:10.775 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745223; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ef/d20d1af88f55ca3e30ba2edffb9c15 Mar-17 20:17:10.775 [Task submitter] INFO nextflow.Session - [ef/d20d1a] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:17:13.772 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745224; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/5091dfec3681cf2d1fbddaad00625b Mar-17 20:17:13.773 [Task submitter] INFO nextflow.Session - [94/5091df] Re-submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 20:18:09.128 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745222; id: 151; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_NORMAL (BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/39/e03e35dd166e7d3cf6e6694aaa338e started: 1773775029546; exited: 2026-03-17T19:17:58.043693772Z; ] Mar-17 20:18:39.090 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 49 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] .. remaining tasks omitted. Mar-17 20:18:39.460 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745123; id: 118; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/adb57b7f6368a672038b922f828948 started: 1773773499674; exited: 2026-03-17T19:18:31.683726513Z; ] Mar-17 20:18:39.591 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745161; id: 104; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/78/0ba2587dbf82e99e03b702ec370330 started: 1773774219121; exited: 2026-03-17T19:18:15.590107224Z; ] Mar-17 20:18:40.346 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:18:44.399 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:18:44.400 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:18:44.400 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:19:09.201 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745129; id: 137; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/6cb17cf3efa0f982cdade4852a1d4f started: 1773773709568; exited: 2026-03-17T19:19:02.256147822Z; ] Mar-17 20:19:18.760 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:19:18.762 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:19:18.762 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:20:39.153 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745195; id: 146; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4e/c5ce87fe3c07b9251ce50f182074aa started: 1773774519090; exited: 2026-03-17T19:20:28.810281994Z; ] Mar-17 20:20:40.322 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:23:39.096 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 45 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] .. remaining tasks omitted. Mar-17 20:24:39.177 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745204; id: 119; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/87/31e75eaab0c5ad83a4bec4e1bc2577 started: 1773774729079; exited: 2026-03-17T19:24:27.413165714Z; ] Mar-17 20:24:40.370 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:28:39.106 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 44 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: -; ] ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] .. remaining tasks omitted. Mar-17 20:28:39.543 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745218; id: 147; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/05/1c367fb14b04adb2c1fe93ae5d223a started: 1773774939185; exited: 2026-03-17T19:28:12.747702163Z; ] Mar-17 20:28:40.891 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:29:09.486 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745215; id: 106; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/64/be6a548ed0e48a0c3bdae37b1e0635 started: 1773774819159; exited: 2026-03-17T19:28:51.405674787Z; ] Mar-17 20:29:09.980 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745224; id: 148; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/94/5091dfec3681cf2d1fbddaad00625b started: 1773775089135; exited: 2026-03-17T19:29:02.827859942Z; ] Mar-17 20:29:10.272 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:29:10.800 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:29:11.088 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR (BS_2VB8649B) > jobId: 1745551; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/3c2b8ef94aa1499afd0ffb672fbf4d Mar-17 20:29:11.089 [Task submitter] INFO nextflow.Session - [cc/3c2b8e] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR (BS_2VB8649B) Mar-17 20:31:39.263 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744864; id: 4; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ec/7c377457d75071a66f0d350c13424c started: 1773771849025; exited: 2026-03-17T19:31:16.20954563Z; ] Mar-17 20:31:39.557 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745551; id: 152; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR (BS_2VB8649B); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cc/3c2b8ef94aa1499afd0ffb672fbf4d started: 1773775839163; exited: 2026-03-17T19:31:13.844817302Z; ] Mar-17 20:31:41.219 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745568; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e3/793dfc434da91ad729ead132f96e8c Mar-17 20:31:41.219 [Task submitter] INFO nextflow.Session - [e3/793dfc] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 20:32:39.468 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744934; id: 79; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/af/ae53a2dea331b26033bcc5ce23cc2e started: 1773772058991; exited: 2026-03-17T19:32:25.478225923Z; ] Mar-17 20:32:40.210 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744952; id: 99; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cd/d538f2fb009706fcb9bac0cdf794b9 started: 1773772659006; exited: 2026-03-17T19:32:26.109631836Z; ] Mar-17 20:32:40.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745223; id: 150; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ef/d20d1af88f55ca3e30ba2edffb9c15 started: 1773775059143; exited: 2026-03-17T19:32:36.222684029Z; ] Mar-17 20:32:40.448 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:32:41.078 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) > jobId: 1745570; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/51/84134c9275016c988167bb8cfa3136 Mar-17 20:32:41.078 [Task submitter] INFO nextflow.Session - [51/84134c] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K) Mar-17 20:32:43.896 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:32:43.897 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:32:43.897 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:32:44.600 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:32:44.601 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:32:44.601 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:33:39.116 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 39 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744931; id: 32; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/54/8f4ba5a563b957ce42ef8092b5cbe9 started: 1773772058983; exited: -; ] .. remaining tasks omitted. Mar-17 20:34:09.275 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745570; id: 154; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GATHERPILEUPSUMMARIES_TUMOR (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/51/84134c9275016c988167bb8cfa3136 started: 1773775989144; exited: 2026-03-17T19:33:42.23280929Z; ] Mar-17 20:34:12.244 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745571; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c5/8441edd07aa9b8fe89cf47881c3495 Mar-17 20:34:12.244 [Task submitter] INFO nextflow.Session - [c5/8441ed] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 20:36:39.337 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744965; id: 97; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/21/698eaae7ca03ddc11abd3a287908d2 started: 1773772809815; exited: 2026-03-17T19:36:33.681663566Z; ] Mar-17 20:36:45.885 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:36:45.886 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:36:45.886 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:38:39.124 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 38 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744931; id: 32; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/54/8f4ba5a563b957ce42ef8092b5cbe9 started: 1773772058983; exited: -; ] .. remaining tasks omitted. Mar-17 20:39:39.446 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745116; id: 134; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0b/4affd6480c8adcb17f993e3b4258d4 started: 1773773169358; exited: 2026-03-17T19:39:19.951392432Z; ] Mar-17 20:39:45.275 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:39:45.275 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:39:45.276 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:41:39.582 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744971; id: 128; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/12/e80bf1bd7b93bf5f5e87901d3947ce started: 1773772899051; exited: 2026-03-17T19:41:24.05091945Z; ] Mar-17 20:41:45.652 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:41:45.653 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:41:45.653 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:43:39.138 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 36 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744931; id: 32; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/54/8f4ba5a563b957ce42ef8092b5cbe9 started: 1773772058983; exited: -; ] .. remaining tasks omitted. Mar-17 20:43:39.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745568; id: 153; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/e3/793dfc434da91ad729ead132f96e8c started: 1773775929141; exited: 2026-03-17T19:43:32.309897219Z; ] Mar-17 20:44:09.280 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744945; id: 115; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0f/2d66519f96e07be91361e63a578a57 started: 1773772539027; exited: 2026-03-17T19:43:55.151315296Z; ] Mar-17 20:44:09.313 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745113; id: 81; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/75/edbc89ead57372767d448197fb2288 started: 1773773079048; exited: 2026-03-17T19:44:06.817447388Z; ] Mar-17 20:44:09.431 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:44:09.431 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:44:09.432 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:44:14.542 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:44:14.543 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:44:14.543 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:44:39.475 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744932; id: 78; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4b/f30f16b287cfc9920aa69bda36e7a9 started: 1773772058985; exited: 2026-03-17T19:44:30.584987821Z; ] Mar-17 20:44:39.944 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744953; id: 100; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d6/463eefec9d2840bdc352a5909e7229 started: 1773772659008; exited: 2026-03-17T19:44:11.348032628Z; ] Mar-17 20:44:45.737 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:44:45.738 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:44:45.738 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:44:48.099 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:44:48.100 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:44:48.100 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:45:09.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745571; id: 155; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:CALCULATECONTAMINATION (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c5/8441edd07aa9b8fe89cf47881c3495 started: 1773776079191; exited: 2026-03-17T19:45:04.161515651Z; ] Mar-17 20:45:39.181 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744999; id: 103; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c0/c78b7672db1a29be373facbbc340bb started: 1773773019032; exited: 2026-03-17T19:45:37.703719515Z; ] Mar-17 20:45:40.093 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:45:40.094 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:45:40.094 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:48:39.146 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 29 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: -; ] ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744931; id: 32; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/54/8f4ba5a563b957ce42ef8092b5cbe9 started: 1773772058983; exited: -; ] .. remaining tasks omitted. Mar-17 20:49:09.218 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744867; id: 6; name: NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (BS_5TT6TT4K); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c1/f25f34d5f2e39a60670aef4205475d started: 1773771878982; exited: 2026-03-17T19:48:55.812529434Z; ] Mar-17 20:50:09.664 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745118; id: 77; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/47/b5e18ce52b5441f9b8220935f78f0b started: 1773773199189; exited: 2026-03-17T19:49:52.60692156Z; ] Mar-17 20:50:16.701 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:50:16.702 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:50:16.702 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:51:39.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744908; id: 25; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/3a/962b19810e1d1a84bb32d2a29bd133 started: 1773771969032; exited: 2026-03-17T19:51:35.692900426Z; ] Mar-17 20:51:39.868 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744931; id: 32; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/54/8f4ba5a563b957ce42ef8092b5cbe9 started: 1773772058983; exited: 2026-03-17T19:51:29.829280345Z; ] Mar-17 20:51:40.197 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:51:40.198 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:51:40.198 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:51:47.502 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:51:47.503 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:51:47.503 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:53:39.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 25 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744933; id: 76; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/09/3a8c34f10f8d4b8e253022181bdc62 started: 1773772058988; exited: -; ] ~> TaskHandler[jobId: 1744954; id: 96; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/24/aca4f3033db9fe32f8d1e46cd9ce87 started: 1773772659010; exited: -; ] ~> TaskHandler[jobId: 1744964; id: 83; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/bb/62e7541f4e26a3259f77df8eb6cea7 started: 1773772809812; exited: 2026-03-17T19:53:21.997505979Z; ] .. remaining tasks omitted. Mar-17 20:53:39.237 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744964; id: 83; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/bb/62e7541f4e26a3259f77df8eb6cea7 started: 1773772809812; exited: 2026-03-17T19:53:21.997505979Z; ] Mar-17 20:53:39.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745117; id: 135; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/49/2b241ef6c0a503fd3a4c7174dabd3c started: 1773773199184; exited: 2026-03-17T19:53:29.45420195Z; ] Mar-17 20:53:43.944 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:53:43.944 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:53:43.945 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 20:53:47.232 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:53:47.233 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:53:47.233 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:58:39.208 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 23 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744933; id: 76; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/09/3a8c34f10f8d4b8e253022181bdc62 started: 1773772058988; exited: 2026-03-17T19:58:36.864960896Z; ] ~> TaskHandler[jobId: 1744954; id: 96; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/24/aca4f3033db9fe32f8d1e46cd9ce87 started: 1773772659010; exited: -; ] ~> TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: -; ] .. remaining tasks omitted. Mar-17 20:58:39.281 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744933; id: 76; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/09/3a8c34f10f8d4b8e253022181bdc62 started: 1773772058988; exited: 2026-03-17T19:58:36.864960896Z; ] Mar-17 20:58:39.388 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 20:58:39.389 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 20:58:39.390 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:00:09.293 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745134; id: 131; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/06/46b3bb76c500fd2450806de91b10e2 started: 1773773949482; exited: 2026-03-17T19:59:56.631322105Z; ] Mar-17 21:00:15.189 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:00:15.190 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:00:15.190 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:02:39.290 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745119; id: 102; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a9/c446f2b989f68776e074c9e9e6e137 started: 1773773349306; exited: 2026-03-17T20:02:19.145882937Z; ] Mar-17 21:02:44.628 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:02:44.629 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:02:44.630 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:03:39.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 20 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744954; id: 96; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/24/aca4f3033db9fe32f8d1e46cd9ce87 started: 1773772659010; exited: -; ] ~> TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: -; ] ~> TaskHandler[jobId: 1745011; id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 started: 1773773019041; exited: -; ] .. remaining tasks omitted. Mar-17 21:05:39.417 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745133; id: 129; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b7/33f470a8fa0f4bdb351ee0e3cc432c started: 1773773769192; exited: 2026-03-17T20:05:38.637577233Z; ] Mar-17 21:05:39.929 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:05:39.930 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:05:39.930 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:08:39.340 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 19 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1744954; id: 96; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/24/aca4f3033db9fe32f8d1e46cd9ce87 started: 1773772659010; exited: 2026-03-17T20:08:15.543507458Z; ] ~> TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: -; ] ~> TaskHandler[jobId: 1745011; id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 started: 1773773019041; exited: -; ] .. remaining tasks omitted. Mar-17 21:08:39.351 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744954; id: 96; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/24/aca4f3033db9fe32f8d1e46cd9ce87 started: 1773772659010; exited: 2026-03-17T20:08:15.543507458Z; ] Mar-17 21:08:45.971 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:08:45.972 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:08:45.972 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:09:09.524 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744907; id: 28; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/ea/cf58848de3a0f70cc7081fd3a45035 started: 1773771969031; exited: 2026-03-17T20:09:03.203906983Z; ] Mar-17 21:09:17.265 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:09:17.266 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:09:17.266 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:13:39.349 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 17 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: -; ] ~> TaskHandler[jobId: 1745011; id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 started: 1773773019041; exited: -; ] ~> TaskHandler[jobId: 1745135; id: 82; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cf/e7ac5bb54ea551295e7288100f1def started: 1773774489494; exited: -; ] ~> TaskHandler[jobId: 1745138; id: 133; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9b/834787c4db35786d861f970bce8f98 started: 1773774519081; exited: -; ] .. remaining tasks omitted. Mar-17 21:14:09.481 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745135; id: 82; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/cf/e7ac5bb54ea551295e7288100f1def started: 1773774489494; exited: 2026-03-17T20:13:48.914138855Z; ] Mar-17 21:14:14.106 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:14:14.106 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:14:14.106 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:14:39.380 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745143; id: 122; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a5/162ed51d59bcc7134d510ddd58d871 started: 1773775149208; exited: 2026-03-17T20:14:34.887820138Z; ] Mar-17 21:14:44.279 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:14:44.280 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:14:44.280 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:18:39.355 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 15 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: -; ] ~> TaskHandler[jobId: 1745011; id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 started: 1773773019041; exited: -; ] ~> TaskHandler[jobId: 1745138; id: 133; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9b/834787c4db35786d861f970bce8f98 started: 1773774519081; exited: -; ] ~> TaskHandler[jobId: 1745144; id: 132; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 started: 1773775179107; exited: -; ] .. remaining tasks omitted. Mar-17 21:20:09.434 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745138; id: 133; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/9b/834787c4db35786d861f970bce8f98 started: 1773774519081; exited: 2026-03-17T20:20:01.428503827Z; ] Mar-17 21:20:20.481 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:20:20.482 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:20:20.482 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:23:39.365 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 14 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: -; ] ~> TaskHandler[jobId: 1745011; id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 started: 1773773019041; exited: -; ] ~> TaskHandler[jobId: 1745144; id: 132; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 started: 1773775179107; exited: -; ] ~> TaskHandler[jobId: 1745160; id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a6/9ecdbd4253800df994741a7bb87e37 started: 1773775989136; exited: -; ] .. remaining tasks omitted. Mar-17 21:24:39.573 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745000; id: 114; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6e/a0c4b7d967053d69a79f84a856f62f started: 1773773019037; exited: 2026-03-17T20:24:28.279026063Z; ] Mar-17 21:24:48.797 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:24:48.797 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:24:48.797 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:28:10.396 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745011; id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/4a/c0be1319eeaba791cb5ca5f19dcbd6 started: 1773773019041; exited: 2026-03-17T20:27:59.181875405Z; ] Mar-17 21:28:30.866 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:28:30.866 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:28:30.866 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:28:39.373 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 12 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745144; id: 132; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 started: 1773775179107; exited: -; ] ~> TaskHandler[jobId: 1745160; id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a6/9ecdbd4253800df994741a7bb87e37 started: 1773775989136; exited: -; ] ~> TaskHandler[jobId: 1745167; id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 started: 1773775989141; exited: -; ] ~> TaskHandler[jobId: 1745191; id: 101; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/02/aaae97c6be2538485fa571cba1724e started: 1773776229126; exited: -; ] .. remaining tasks omitted. Mar-17 21:29:40.197 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745191; id: 101; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/02/aaae97c6be2538485fa571cba1724e started: 1773776229126; exited: 2026-03-17T20:29:28.182468551Z; ] Mar-17 21:29:59.188 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:29:59.189 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:29:59.189 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:33:39.384 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 11 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745144; id: 132; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 started: 1773775179107; exited: -; ] ~> TaskHandler[jobId: 1745160; id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a6/9ecdbd4253800df994741a7bb87e37 started: 1773775989136; exited: -; ] ~> TaskHandler[jobId: 1745167; id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 started: 1773775989141; exited: -; ] ~> TaskHandler[jobId: 1745194; id: 112; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e started: 1773776409136; exited: -; ] Mar-17 21:36:39.445 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744910; id: 30; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/5a/91284c4625e5958d8e09583f2b5f42 started: 1773771998986; exited: 2026-03-17T20:36:27.604079782Z; ] Mar-17 21:36:49.064 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:36:49.065 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:36:49.065 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:38:11.041 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745160; id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/a6/9ecdbd4253800df994741a7bb87e37 started: 1773775989136; exited: 2026-03-17T20:37:44.465375197Z; ] Mar-17 21:38:19.215 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:38:19.218 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:38:19.219 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:38:39.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 9 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745144; id: 132; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 started: 1773775179107; exited: -; ] ~> TaskHandler[jobId: 1745167; id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 started: 1773775989141; exited: -; ] ~> TaskHandler[jobId: 1745194; id: 112; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e started: 1773776409136; exited: -; ] ~> TaskHandler[jobId: 1745217; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: 1773776529140; exited: -; ] Mar-17 21:39:12.142 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745144; id: 132; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/28/a46f5150fb67671ddd7df2b07722b9 started: 1773775179107; exited: 2026-03-17T20:39:01.161084849Z; ] Mar-17 21:39:26.511 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:39:26.512 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:39:26.512 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:40:10.576 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744909; id: 23; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d5/d923facb6b973b87b4d60301e19f66 started: 1773771998983; exited: 2026-03-17T20:39:52.848677473Z; ] Mar-17 21:40:23.913 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:40:23.914 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:40:23.914 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:43:39.414 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 7 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: -; ] ~> TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: -; ] ~> TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: -; ] ~> TaskHandler[jobId: 1745167; id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 started: 1773775989141; exited: -; ] ~> TaskHandler[jobId: 1745194; id: 112; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e started: 1773776409136; exited: -; ] ~> TaskHandler[jobId: 1745217; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: 1773776529140; exited: -; ] Mar-17 21:44:09.458 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744912; id: 26; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/92/6f5a294cdff3618d48eb3075d9d436 started: 1773771998990; exited: 2026-03-17T20:44:04.633433438Z; ] Mar-17 21:44:28.496 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:44:28.497 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:44:28.497 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:45:09.462 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745167; id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/36/5c227dc149a0ae362e6836360d5d13 started: 1773775989141; exited: 2026-03-17T20:45:07.591416804Z; ] Mar-17 21:45:12.259 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:45:12.261 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:45:12.261 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:47:11.308 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744913; id: 24; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/c2/06a1e5d13c586158a23eb904321aa2 started: 1773771998993; exited: 2026-03-17T20:46:49.445306092Z; ] Mar-17 21:47:26.338 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:47:26.339 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:47:26.339 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:48:10.028 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744911; id: 21; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/0c/45274288da0eef9c1ffbd361d7ce85 started: 1773771998988; exited: 2026-03-17T20:47:47.189353538Z; ] Mar-17 21:48:22.244 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:48:22.245 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:48:22.245 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null, num_intervals:21] size=21 Mar-17 21:48:22.319 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745823; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2a/0181333d491b3d53f61c0709a8d376 Mar-17 21:48:22.319 [Task submitter] INFO nextflow.Session - [2a/018133] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 21:48:24.314 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_2VB8649B_vs_BS_CW6NWAWQ) > jobId: 1745824; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/78/0e163d7f4fff15f32830c70879e10c Mar-17 21:48:24.314 [Task submitter] INFO nextflow.Session - [78/0e163d] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_2VB8649B_vs_BS_CW6NWAWQ) Mar-17 21:48:39.428 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 5 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1745194; id: 112; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e started: 1773776409136; exited: -; ] ~> TaskHandler[jobId: 1745217; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: 1773776529140; exited: -; ] ~> TaskHandler[jobId: 1745823; id: 156; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_2VB8649B_vs_BS_CW6NWAWQ); status: SUBMITTED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2a/0181333d491b3d53f61c0709a8d376 started: -; exited: -; ] ~> TaskHandler[jobId: 1745824; id: 157; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_2VB8649B_vs_BS_CW6NWAWQ); status: SUBMITTED; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/78/0e163d7f4fff15f32830c70879e10c started: -; exited: -; ] Mar-17 21:49:09.503 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745823; id: 156; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/2a/0181333d491b3d53f61c0709a8d376 started: 1773780549468; exited: 2026-03-17T20:48:57.050178384Z; ] Mar-17 21:49:39.460 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745824; id: 157; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_2VB8649B_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/78/0e163d7f4fff15f32830c70879e10c started: 1773780549504; exited: 2026-03-17T20:49:15.434421356Z; ] Mar-17 21:50:39.490 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745194; id: 112; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/6f/f275108100405244dd2087cfc68e9e started: 1773776409136; exited: 2026-03-17T20:50:34.487942838Z; ] Mar-17 21:50:58.759 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:50:58.760 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:50:58.760 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:53:39.433 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] ~> TaskHandler[jobId: 1745217; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: 1773776529140; exited: -; ] Mar-17 21:57:41.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745217; id: 80; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/08/4f1e43574cc5ddac0b31fa5a37f860 started: 1773776529140; exited: 2026-03-17T20:57:32.124887044Z; ] Mar-17 21:58:02.317 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 21:58:02.318 [Actor Thread 8] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:58:02.318 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 21:58:39.441 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] Mar-17 22:03:39.443 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: RUNNING; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: -; ] Mar-17 22:05:42.360 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1744906; id: 22; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/86/85218568b2f68963af1667e967589d started: 1773771969029; exited: 2026-03-17T21:05:16.05648649Z; ] Mar-17 22:05:57.359 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Mar-17 22:05:57.360 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 22:05:57.361 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null, num_intervals:21] size=21 Mar-17 22:05:57.433 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745997; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b2/25d2f144265e94144e19c9dfa3817d Mar-17 22:05:57.433 [Task submitter] INFO nextflow.Session - [b2/25d2f1] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 22:05:59.427 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_5TT6TT4K_vs_BS_CW6NWAWQ) > jobId: 1745998; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/32/10866b824a13ed34e8fabf9b5bfc45 Mar-17 22:05:59.428 [Task submitter] INFO nextflow.Session - [32/10866b] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_5TT6TT4K_vs_BS_CW6NWAWQ) Mar-17 22:06:39.488 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745997; id: 158; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGEMUTECTSTATS (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/b2/25d2f144265e94144e19c9dfa3817d started: 1773781569448; exited: 2026-03-17T21:06:32.364561279Z; ] Mar-17 22:07:09.475 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 1745998; id: 159; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MERGE_MUTECT2 (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: COMPLETED; exit: 0; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/32/10866b824a13ed34e8fabf9b5bfc45 started: 1773781599497; exited: 2026-03-17T21:06:49.052738923Z; ] Mar-17 22:07:09.639 [Actor Thread 59] ERROR nextflow.extension.OperatorImpl - @unknown nextflow.exception.AbortOperationException: Join mismatch for the following entries: - key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null] values= - key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null] values= at nextflow.extension.JoinOp.checkForMismatch(JoinOp.groovy:290) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1339) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1094) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82) at nextflow.extension.JoinOp$_handler_closure2.doCall(JoinOp.groovy:135) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) 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.DataflowHelper$3.afterStop(DataflowHelper.groovy:257) at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324) at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1339) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1094) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:633) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:624) at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369) at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320) at groovyx.gpars.actor.AbstractLoopingActor.terminate(AbstractLoopingActor.java:204) at groovyx.gpars.dataflow.operator.DataflowProcessor.terminate(DataflowProcessor.java:147) at groovyx.gpars.dataflow.operator.DataflowProcessorActor.checkPoison(DataflowProcessorActor.java:115) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:83) 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$1.handleMessage(AbstractLoopingActor.java:93) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) Mar-17 22:07:09.657 [Actor Thread 66] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-5a-5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0-data.img Mar-17 22:07:09.762 [Actor Thread 61] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.002 s; external sort time: 0.001 s; total time: 0.003 s Mar-17 22:07:10.036 [Actor Thread 59] DEBUG nextflow.Session - Session aborted -- Cause: Join mismatch for the following entries: - key=[id:BS_2VB8649B_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_2VB8649B, contamination:null] values= - key=[id:BS_5TT6TT4K_vs_BS_CW6NWAWQ, normal_id:BS_CW6NWAWQ, patient:C90159, sex:NA, tumor_id:BS_5TT6TT4K, contamination:null] values= Mar-17 22:07:10.045 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor slurm > tasks in the submission queue: 2 -- tasks to be submitted are shown below ~> TaskHandler[jobId: null; id: 162; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (BS_5TT6TT4K_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/d4/4744ebfb36a5a03e781d81951bf943 started: -; exited: -; ] ~> TaskHandler[jobId: null; id: 160; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (BS_2VB8649B_vs_BS_CW6NWAWQ); status: NEW; exit: -; error: -; workDir: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/43/8a04d59d1916343dc331e29dbdea04 started: -; exited: -; ] Mar-17 22:07:10.051 [Actor Thread 61] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/work/collect-file/d8073411e23d3bb8ddb0115ab8b53506 Mar-17 22:07:10.052 [Actor Thread 37] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4; path=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache/depot.galaxyproject.org-singularity-vcftools-0.1.16--he513fc3_4.img Mar-17 22:07:10.083 [Actor Thread 61] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6188524292644678334 Mar-17 22:07:10.095 [Actor Thread 59] DEBUG nextflow.Session - The following nodes are still active: [process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT status=ACTIVE port 0: (queue) closed; channel: - port 1: (value) bound ; channel: bed port 2: (value) bound ; channel: diff_variant_file port 3: (cntrl) - ; channel: $ [process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL status=ACTIVE port 0: (queue) closed; channel: - port 1: (value) bound ; channel: bed port 2: (value) bound ; channel: diff_variant_file port 3: (cntrl) - ; channel: $ [process] NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY status=ACTIVE port 0: (queue) closed; channel: - port 1: (value) bound ; channel: bed port 2: (value) bound ; channel: diff_variant_file port 3: (cntrl) - ; channel: $ [process] NFCORE_SAREK:SAREK: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: $ Mar-17 22:07:10.101 [Actor Thread 59] INFO nextflow.Nextflow - -[nf-core/sarek] Pipeline completed with errors- Mar-17 22:07:10.536 [Actor Thread 59] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=143; failedCount=13; ignoredCount=0; cachedCount=0; pendingCount=8; submittedCount=0; runningCount=0; retriesCount=13; abortedCount=0; succeedDuration=20d 14h 1m 47s; failedDuration=6h 44m; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=50; peakCpus=307; peakMemory=2.5 TB; ] Mar-17 22:07:11.429 [Actor Thread 59] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Mar-17 22:07:12.036 [Actor Thread 59] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Mar-17 22:07:12.098 [Actor Thread 59] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Mar-17 22:07:12.102 [Actor Thread 59] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting Mar-17 22:07:12.162 [main] DEBUG nextflow.Session - Session await > all processes finished Mar-17 22:07:12.162 [main] DEBUG nextflow.Session - Session await > all barriers passed Mar-17 22:07:12.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Mar-17 22:07:12.164 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=143; failedCount=13; ignoredCount=0; cachedCount=0; pendingCount=8; submittedCount=0; runningCount=0; retriesCount=13; abortedCount=0; succeedDuration=20d 14h 1m 47s; failedDuration=6h 44m; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=50; peakCpus=307; peakMemory=2.5 TB; ] Mar-17 22:07:12.167 [Actor Thread 57] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Mar-17 22:07:12.223 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Mar-17 22:07:12.773 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Mar-17 22:07:12.831 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Mar-17 22:07:12.840 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Mar-17 22:07:13.621 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@3.4.4' Mar-17 22:07:13.622 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon Mar-17 22:07:13.622 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.6.1' Mar-17 22:07:13.622 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema Mar-17 22:07:13.622 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-prov@1.2.2' Mar-17 22:07:13.622 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-prov Mar-17 22:07:13.622 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-fgbio@1.0.0' Mar-17 22:07:13.622 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-fgbio Mar-17 22:07:13.622 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-core-utils@0.4.0' Mar-17 22:07:13.622 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-core-utils Mar-17 22:07:13.625 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye