May-07 09:53:13.393 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -r dev -latest --input sample-sheet.csv --outdir sarek-test-jointVC -profile docker --max_time 336.h --max_cpus 64 --max_memory 256.GB --fasta /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa --fasta_fai /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa.fai --dict /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.dict --save_mapped --save_output_as_bam --vep_cache /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae --bwa /home/ubuntu/reproducible-sarek-error/bwa-index --igenomes_ignore --genome null --joint_germline --tools haplotypecaller,vep --dbsnp /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz --dbsnp_tbi /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz.tbi --dbsnp_vqsr '--resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz' --known_indels /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz --known_indels_tbi /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz.tbi --known_indels_vqsr '--resource:ensemblsnps,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_indels.vcf.gz' --known_snps /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz --known_snps_tbi /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz.tbi --known_snps_vqsr '--resource:ensemblindels,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_snps.vcf.gz' --vep_out_format tab --vep_include_fasta --email alex.mizeranschi@gmail.com May-07 09:53:13.520 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 May-07 09:53:13.556 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ubuntu/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2 May-07 09:53:13.574 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-07 09:53:13.575 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-07 09:53:13.581 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-07 09:53:13.599 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-07 09:53:13.625 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ubuntu/.nextflow/scm May-07 09:53:15.331 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git May-07 09:53:15.366 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] May-07 09:53:15.381 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git May-07 09:53:15.381 [main] INFO nextflow.cli.CmdRun - Pulling nf-core/sarek ... May-07 09:53:15.382 [main] DEBUG nextflow.scm.AssetManager - Pull pipeline nf-core/sarek -- Using local path: /home/ubuntu/.nextflow/assets/nf-core/sarek May-07 09:53:16.978 [main] INFO nextflow.cli.CmdRun - Already-up-to-date May-07 09:53:17.002 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config May-07 09:53:17.003 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config May-07 09:53:17.023 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker` May-07 09:53:21.021 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, uge, rosalind_uge, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, use_gatk_spark, eddie, medair, alignment_to_fastq, apptainer, bi, bigpurple, sbc_sharc, adcra, cedars, tools, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, targeted, icr_davros, ceres, save_bam_mapped, munin, arm, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, cheaha, xanadu, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, dkfz, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, psmn, umi, eva, markduplicates_bam, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac] May-07 09:53:21.108 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion May-07 09:53:21.109 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [gloomy_angela] DSL2 - revision: a36f952b3d [dev] May-07 09:53:21.110 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-07 09:53:21.110 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] May-07 09:53:21.116 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/ubuntu/.nextflow/secrets/store.json May-07 09:53:21.121 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3a7d6976] - activable => nextflow.secret.LocalSecretsProvider@3a7d6976 May-07 09:53:21.241 [main] DEBUG nextflow.Session - Session UUID: 27fa913c-1dd9-420a-b736-9da6d9b1bc95 May-07 09:53:21.242 [main] DEBUG nextflow.Session - Run name: gloomy_angela May-07 09:53:21.243 [main] DEBUG nextflow.Session - Executor pool size: 64 May-07 09:53:21.263 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-07 09:53:21.304 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.1 build 5866 Created: 15-04-2023 06:51 UTC (09:51 EEST) System: Linux 5.15.0-69-generic Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS Encoding: UTF-8 (UTF-8) Process: 861827@bioinfosrv [10.252.254.98] CPUs: 64 - Mem: 251.7 GB (54.1 GB) - Swap: 0 (0) May-07 09:53:21.336 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/reproducible-sarek-error/work [ext2/ext3] May-07 09:53:21.337 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ubuntu/.nextflow/assets/nf-core/sarek/bin May-07 09:53:21.362 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-07 09:53:21.385 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-07 09:53:21.552 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-07 09:53:21.575 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000 May-07 09:53:21.704 [main] DEBUG nextflow.Session - Session start May-07 09:53:21.714 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ubuntu/reproducible-sarek-error/sarek-test-jointVC/pipeline_info/execution_trace_2023-05-07_09-53-18.txt May-07 09:53:21.730 [main] DEBUG nextflow.Session - Using default localLib path: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib May-07 09:53:21.735 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib May-07 09:53:21.736 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar May-07 09:53:23.478 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-07 09:53:23.563 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  ____  .´ _ `.  / |\`-_ \  __ __ ___   | | \ `-| |__` /\ |__) |__ |__/  \ | \ / .__| /¯¯\ | \ |___ | \  `|____\´  nf-core/sarek v3.2dev-ga36f952 ------------------------------------------------------ Core Nextflow options revision : dev runName : gloomy_angela containerEngine : docker launchDir : /home/ubuntu/reproducible-sarek-error workDir : /home/ubuntu/reproducible-sarek-error/work projectDir : /home/ubuntu/.nextflow/assets/nf-core/sarek userName : ubuntu profile : docker configFiles : /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config Input/output options input : sample-sheet.csv outdir : sarek-test-jointVC Main options tools : haplotypecaller,vep Preprocessing save_mapped : true save_output_as_bam: true Variant Calling joint_germline : true Annotation vep_include_fasta : true vep_cache : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae vep_out_format : tab Reference genome options genome : null bwa : /home/ubuntu/reproducible-sarek-error/bwa-index dbsnp : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz dbsnp_tbi : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz.tbi dbsnp_vqsr : --resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz dict : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.dict fasta : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa fasta_fai : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa.fai known_indels : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz known_indels_tbi : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz.tbi known_indels_vqsr : --resource:ensemblsnps,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_indels.vcf.gz known_snps : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz known_snps_tbi : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz.tbi known_snps_vqsr : --resource:ensemblindels,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_snps.vcf.gz igenomes_base : s3://ngi-igenomes/igenomes igenomes_ignore : true Max job request options max_cpus : 64 max_memory : 256.GB max_time : 336.h Generic options email : alex.mizeranschi@gmail.com !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/sarek for your analysis please cite: * The pipeline https://doi.org/10.12688/f1000research.16665.2 https://doi.org/10.5281/zenodo.4468605 * 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 ------------------------------------------------------ May-07 09:53:50.791 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX May-07 09:53:50.799 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX May-07 09:53:50.815 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:50.815 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:50.826 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-07 09:53:50.836 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=251.7 GB; capacity=64; pollInterval=100ms; dumpInterval=5m May-07 09:53:50.978 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX May-07 09:53:50.979 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX May-07 09:53:50.985 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:50.985 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:50.995 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE May-07 09:53:50.995 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE May-07 09:53:51.000 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.000 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.012 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY May-07 09:53:51.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY May-07 09:53:51.017 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.023 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.044 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN May-07 09:53:51.045 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN May-07 09:53:51.050 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.050 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.064 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX May-07 09:53:51.067 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX May-07 09:53:51.071 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.071 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.093 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP May-07 09:53:51.094 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP May-07 09:53:51.095 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP May-07 09:53:51.095 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP May-07 09:53:51.099 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.099 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.113 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE May-07 09:53:51.114 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE May-07 09:53:51.115 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE May-07 09:53:51.115 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE May-07 09:53:51.119 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.119 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.133 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS May-07 09:53:51.133 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS May-07 09:53:51.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS May-07 09:53:51.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS May-07 09:53:51.137 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.137 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.146 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS May-07 09:53:51.147 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS May-07 09:53:51.148 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS May-07 09:53:51.148 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS May-07 09:53:51.150 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.151 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.162 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON May-07 09:53:51.163 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON May-07 09:53:51.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON May-07 09:53:51.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON May-07 09:53:51.167 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.167 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.332 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS May-07 09:53:51.336 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.336 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.345 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED May-07 09:53:51.345 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED May-07 09:53:51.347 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.347 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.390 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT May-07 09:53:51.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT May-07 09:53:51.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT May-07 09:53:51.392 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT May-07 09:53:51.394 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.394 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED May-07 09:53:51.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED May-07 09:53:51.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED May-07 09:53:51.408 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.408 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.439 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP May-07 09:53:51.441 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP May-07 09:53:51.446 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.446 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP May-07 09:53:51.460 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP May-07 09:53:51.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP May-07 09:53:51.471 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP May-07 09:53:51.474 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.474 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP May-07 09:53:51.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP May-07 09:53:51.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.507 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP May-07 09:53:51.508 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP May-07 09:53:51.510 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.510 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP May-07 09:53:51.519 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP May-07 09:53:51.521 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.521 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.526 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP May-07 09:53:51.527 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP May-07 09:53:51.529 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.529 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.539 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ May-07 09:53:51.539 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ May-07 09:53:51.541 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.541 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.564 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC May-07 09:53:51.565 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC May-07 09:53:51.568 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.568 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.580 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP May-07 09:53:51.580 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP May-07 09:53:51.586 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.586 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.607 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM May-07 09:53:51.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM May-07 09:53:51.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM May-07 09:53:51.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM May-07 09:53:51.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM May-07 09:53:51.610 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.610 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM May-07 09:53:51.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM May-07 09:53:51.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM May-07 09:53:51.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM May-07 09:53:51.620 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM May-07 09:53:51.621 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.621 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.629 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN May-07 09:53:51.630 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN May-07 09:53:51.630 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN May-07 09:53:51.632 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.632 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.657 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:51.658 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:51.658 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:51.659 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.659 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:51.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:51.670 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:51.671 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.671 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.683 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING May-07 09:53:51.683 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING May-07 09:53:51.684 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAM_TO_CRAM_MAPPING` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING May-07 09:53:51.686 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.686 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.727 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES May-07 09:53:51.728 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES May-07 09:53:51.728 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES May-07 09:53:51.730 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.730 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES May-07 09:53:51.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES May-07 09:53:51.739 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:INDEX_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES May-07 09:53:51.741 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.741 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.751 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS May-07 09:53:51.752 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS May-07 09:53:51.753 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.754 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.776 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH May-07 09:53:51.776 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH May-07 09:53:51.779 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.779 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.801 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM May-07 09:53:51.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM May-07 09:53:51.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM May-07 09:53:51.803 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM May-07 09:53:51.804 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.804 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR May-07 09:53:51.825 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR May-07 09:53:51.825 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR May-07 09:53:51.827 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.827 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS May-07 09:53:51.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS May-07 09:53:51.838 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS May-07 09:53:51.839 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.839 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.864 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR May-07 09:53:51.865 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR May-07 09:53:51.865 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR May-07 09:53:51.866 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.867 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.879 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM May-07 09:53:51.880 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM May-07 09:53:51.881 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.881 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.889 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM May-07 09:53:51.890 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM May-07 09:53:51.890 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM May-07 09:53:51.891 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.891 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.909 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS May-07 09:53:51.910 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS May-07 09:53:51.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.925 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH May-07 09:53:51.925 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH May-07 09:53:51.925 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH May-07 09:53:51.927 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.927 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.944 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL May-07 09:53:51.944 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL May-07 09:53:51.945 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM_RECAL` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL May-07 09:53:51.946 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.946 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:51.982 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER May-07 09:53:51.983 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_HAPLOTYPECALLER` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER May-07 09:53:51.984 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:51.984 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.005 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER May-07 09:53:52.005 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER May-07 09:53:52.006 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_HAPLOTYPECALLER` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER May-07 09:53:52.007 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.007 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.024 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:52.025 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:52.025 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:52.026 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM May-07 09:53:52.026 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.027 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:52.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:52.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:52.036 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM May-07 09:53:52.036 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.036 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.068 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS May-07 09:53:52.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CNNSCOREVARIANTS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS May-07 09:53:52.070 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.079 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES May-07 09:53:52.080 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FILTERVARIANTTRANCHES` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES May-07 09:53:52.081 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.081 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.106 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT May-07 09:53:52.106 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GENOMICSDBIMPORT` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT May-07 09:53:52.107 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.107 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.116 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS May-07 09:53:52.116 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GENOTYPEGVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS May-07 09:53:52.117 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.117 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.123 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT May-07 09:53:52.123 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT May-07 09:53:52.123 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_SORT` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT May-07 09:53:52.123 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT May-07 09:53:52.124 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.124 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.133 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS May-07 09:53:52.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS May-07 09:53:52.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_GENOTYPEGVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS May-07 09:53:52.135 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-07 09:53:52.135 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-07 09:53:52.150 [main] DEBUG nextflow.Session - Session aborted -- Cause: Missing process or function mix([--resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz]) May-07 09:53:52.200 [main] DEBUG nextflow.Session - The following nodes are still active: [operator] splitCsv [operator] map [operator] splitCsv [operator] map [operator] groupTuple [operator] map [operator] transpose [operator] map [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect [operator] map [operator] map [operator] flatten [operator] map [operator] flatten [operator] map [operator] flatten [operator] map [operator] flatten [operator] map [operator] flatten [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] map [operator] collect [operator] map [operator] collect [operator] map [operator] collect [operator] map [operator] collect [operator] map [operator] map [operator] collect [operator] map [operator] collect [operator] map [operator] collect [operator] map [operator] map [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect [operator] collect [operator] concat [operator] collect [operator] concat [operator] collect [operator] concat [operator] collect [operator] concat [operator] collect [operator] map [operator] map [operator] mix [operator] mix [operator] flatten [operator] map [operator] toSortedList [operator] flatten [operator] collate [operator] map [operator] collect [operator] map [operator] transpose [operator] map [operator] map [operator] toList [operator] map [operator] transpose [operator] mix [operator] mix [operator] map [operator] collect [operator] map [operator] collect [operator] map [operator] map [operator] mix [operator] mix [operator] branch [operator] join [operator] join [operator] map [operator] join [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] collect [operator] mix [operator] mix [operator] collect [operator] mix [operator] collect [operator] mix [operator] map [operator] transpose [operator] mix [operator] map [operator] map [operator] map [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] map [operator] groupTuple [operator] branch [operator] mix [operator] join [operator] mix [operator] mix [operator] collectFile [operator] mix [operator] mix [operator] mix [operator] mix [operator] join [operator] map [operator] combine [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] collect [operator] mix [operator] mix [operator] mix [operator] map [operator] mix [operator] collectFile [operator] mix [operator] map [operator] combine [operator] map [operator] map [operator] groupTuple [operator] branch [operator] map [operator] mix [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] collect [operator] mix [operator] join [operator] join [operator] collectFile [operator] combine [operator] map [operator] map [operator] groupTuple [operator] branch [operator] mix [operator] join [operator] mix [operator] mix [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] map [operator] combine [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] collect [operator] mix [operator] mix [operator] mix [operator] collectFile [operator] branch [operator] map [operator] map [operator] groupTuple [operator] join [operator] filter [operator] transpose [operator] map [operator] cross [operator] map [operator] combine [operator] map [operator] join [operator] join [operator] map [operator] branch [operator] branch [operator] branch [operator] map [operator] groupTuple [operator] map [operator] mix [operator] mix [operator] map [operator] groupTuple [operator] mix [operator] branch [operator] mix [operator] join [operator] mix [operator] mix [operator] join [operator] concat [operator] flatten [operator] unique [operator] collect [operator] concat [operator] flatten [operator] unique [operator] collect [operator] combine [operator] map [operator] join [operator] combine [operator] map [operator] mix [operator] mix [operator] mix [operator] mix [operator] mix [operator] map [operator] mix [operator] map [operator] groupTuple [operator] map [operator] map [operator] map [operator] groupTuple [operator] map [operator] join May-07 09:53:52.375 [Actor Thread 20] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-07 09:53:52.379 [Actor Thread 196] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-07 09:53:52.379 [Actor Thread 176] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-07 09:53:52.382 [Actor Thread 172] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-07 09:53:52.394 [main] ERROR nextflow.cli.Launcher - @unknown nextflow.exception.MissingProcessException: Missing process or function mix([--resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz]) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:191) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171) at Script_4af0f42a$_runScript_closure1$_closure2.doCall(Script_4af0f42a:134) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:406) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171) at Script_44fa9e61$_runScript_closure8$_closure12.doCall(Script_44fa9e61:917) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:406) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at Script_c05744b2$_runScript_closure1$_closure3.doCall(Script_c05744b2:83) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:406) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176) at Script_c05744b2$_runScript_closure2$_closure4.doCall(Script_c05744b2:95) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:406) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.IterableDef$invoke_a.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at nextflow.script.BaseScript.run0(BaseScript.groovy:183) at nextflow.script.BaseScript.run(BaseScript.groovy:192) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:229) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:224) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:130) at nextflow.cli.CmdRun.run(CmdRun.groovy:368) at nextflow.cli.Launcher.run(Launcher.groovy:494) at nextflow.cli.Launcher.main(Launcher.groovy:653) Caused by: groovy.lang.MissingMethodException: No signature of method: java.lang.String.mix() is applicable for argument types: (String) values: [--resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz] Possible solutions: md5(), is(java.lang.Object), wait(), trim(), next(), find() at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:70) at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:46) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at Script_9640c075$_runScript_closure1$_closure2.doCall(Script_9640c075:59) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:406) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) ... 99 common frames omitted