Jun-08 14:29:15.599 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -r 3.2.0 --skip_tools haplotypecaller_filter,baserecalibrator,markduplicates -profile docker --input sample-sheet.csv --outdir sarek-test-jointVC --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 --vep_cache /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae --bwa /home/ubuntu/reproducible-sarek-error/bwa-index --igenomes_ignore --genome null --tools haplotypecaller,vep --vep_out_format tab --vep_include_fasta Jun-08 14:29:15.735 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 Jun-08 14:29:15.771 [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 Jun-08 14:29:15.788 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jun-08 14:29:15.789 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jun-08 14:29:15.795 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Jun-08 14:29:15.813 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jun-08 14:29:15.838 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ubuntu/.nextflow/scm Jun-08 14:29:17.862 [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 Jun-08 14:29:17.899 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Jun-08 14:29:17.913 [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 Jun-08 14:29:19.196 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config Jun-08 14:29:19.198 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config Jun-08 14:29:19.220 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker` Jun-08 14:29:23.220 [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, public_aws_ecr, 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] Jun-08 14:29:23.301 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Jun-08 14:29:23.303 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [soggy_albattani] DSL2 - revision: 71fac185a9 [3.2.0] Jun-08 14:29:23.304 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jun-08 14:29:23.304 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Jun-08 14:29:23.310 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/ubuntu/.nextflow/secrets/store.json Jun-08 14:29:23.315 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@430f0c63] - activable => nextflow.secret.LocalSecretsProvider@430f0c63 Jun-08 14:29:23.417 [main] DEBUG nextflow.Session - Session UUID: 00da3cee-c327-4b0a-8289-09746c6acc02 Jun-08 14:29:23.417 [main] DEBUG nextflow.Session - Run name: soggy_albattani Jun-08 14:29:23.418 [main] DEBUG nextflow.Session - Executor pool size: 64 Jun-08 14:29:23.435 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jun-08 14:29:23.476 [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 17.0.3-internal+0-adhoc..src Encoding: UTF-8 (UTF-8) Process: 4082788@bioinfosrv [10.252.254.98] CPUs: 64 - Mem: 251.7 GB (116.4 GB) - Swap: 0 (0) Jun-08 14:29:23.501 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/reproducible-sarek-error/work [ext2/ext3] Jun-08 14:29:23.502 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ubuntu/.nextflow/assets/nf-core/sarek/bin Jun-08 14:29:23.519 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jun-08 14:29:23.535 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jun-08 14:29:23.703 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jun-08 14:29:23.720 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000 Jun-08 14:29:23.826 [main] DEBUG nextflow.Session - Session start Jun-08 14:29:23.834 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ubuntu/reproducible-sarek-error/sarek-test-jointVC/pipeline_info/execution_trace_2023-06-08_14-29-20.txt Jun-08 14:29:23.849 [main] DEBUG nextflow.Session - Using default localLib path: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib Jun-08 14:29:23.855 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib Jun-08 14:29:23.856 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar Jun-08 14:29:25.319 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-08 14:29:25.404 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  ____  .´ _ `.  / |\`-_ \  __ __ ___   | | \ `-| |__` /\ |__) |__ |__/  \ | \ / .__| /¯¯\ | \ |___ | \  `|____\´  nf-core/sarek v3.2.0-g71fac18 ------------------------------------------------------ Core Nextflow options revision : 3.2.0 runName : soggy_albattani 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 skip_tools : haplotypecaller_filter,baserecalibrator,markduplicates Preprocessing save_mapped : 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 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 igenomes_base : s3://ngi-igenomes/igenomes igenomes_ignore : true Max job request options max_cpus : 64 max_memory : 256.GB max_time : 336.h !! Only displaying parameters that differ from the pipeline defaults !! Displaying all reference genome parameters ------------------------------------------------------ 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 ------------------------------------------------------ Jun-08 14:29:29.094 [main] WARN nextflow.Nextflow - If Haplotypecaller is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`. For more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches For more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator For more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- Jun-08 14:29:50.316 [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 Jun-08 14:29:50.323 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Jun-08 14:29:50.337 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.338 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.348 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Jun-08 14:29:50.355 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=251.7 GB; capacity=64; pollInterval=100ms; dumpInterval=5m Jun-08 14:29:50.475 [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 Jun-08 14:29:50.478 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Jun-08 14:29:50.483 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.498 [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 Jun-08 14:29:50.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Jun-08 14:29:50.506 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.506 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.517 [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 Jun-08 14:29:50.518 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Jun-08 14:29:50.522 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.522 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.535 [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 Jun-08 14:29:50.536 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Jun-08 14:29:50.540 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.540 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.552 [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 Jun-08 14:29:50.553 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Jun-08 14:29:50.558 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.558 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.582 [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 Jun-08 14:29:50.583 [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 Jun-08 14:29:50.584 [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 Jun-08 14:29:50.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jun-08 14:29:50.588 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.588 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.603 [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 Jun-08 14:29:50.604 [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 Jun-08 14:29:50.605 [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 Jun-08 14:29:50.605 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jun-08 14:29:50.610 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.610 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.623 [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 Jun-08 14:29:50.623 [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 Jun-08 14:29:50.624 [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 Jun-08 14:29:50.625 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jun-08 14:29:50.628 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.628 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.639 [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 Jun-08 14:29:50.640 [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 Jun-08 14:29:50.640 [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 Jun-08 14:29:50.641 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jun-08 14:29:50.644 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.644 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.654 [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 Jun-08 14:29:50.655 [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 Jun-08 14:29:50.655 [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 Jun-08 14:29:50.656 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jun-08 14:29:50.658 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.658 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.758 [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 Jun-08 14:29:50.763 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.763 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.774 [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 Jun-08 14:29:50.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Jun-08 14:29:50.776 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.777 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.823 [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 Jun-08 14:29:50.823 [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 Jun-08 14:29:50.824 [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 Jun-08 14:29:50.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jun-08 14:29:50.827 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.827 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.841 [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 Jun-08 14:29:50.841 [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 Jun-08 14:29:50.842 [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 Jun-08 14:29:50.844 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.844 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.878 [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 Jun-08 14:29:50.880 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Jun-08 14:29:50.884 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.884 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.897 [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 Jun-08 14:29:50.898 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Jun-08 14:29:50.903 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.903 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.915 [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 Jun-08 14:29:50.916 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Jun-08 14:29:50.919 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.919 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.928 [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 Jun-08 14:29:50.930 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Jun-08 14:29:50.933 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.934 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.963 [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 Jun-08 14:29:50.965 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Jun-08 14:29:50.967 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.967 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.976 [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 Jun-08 14:29:50.977 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Jun-08 14:29:50.979 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.979 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.984 [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 Jun-08 14:29:50.985 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Jun-08 14:29:50.987 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:50.987 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:50.997 [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 Jun-08 14:29:50.998 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Jun-08 14:29:51.000 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.000 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.018 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC Jun-08 14:29:51.019 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC Jun-08 14:29:51.022 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.022 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.034 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP Jun-08 14:29:51.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP Jun-08 14:29:51.037 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.037 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.059 [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 Jun-08 14:29:51.060 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jun-08 14:29:51.061 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jun-08 14:29:51.061 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jun-08 14:29:51.061 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jun-08 14:29:51.063 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.063 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.071 [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 Jun-08 14:29:51.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jun-08 14:29:51.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jun-08 14:29:51.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jun-08 14:29:51.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jun-08 14:29:51.074 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.074 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.081 [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 Jun-08 14:29:51.082 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jun-08 14:29:51.082 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jun-08 14:29:51.084 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.084 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.108 [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 Jun-08 14:29:51.109 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM Jun-08 14:29:51.110 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM Jun-08 14:29:51.111 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.112 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.121 [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 Jun-08 14:29:51.121 [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 Jun-08 14:29:51.122 [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 Jun-08 14:29:51.123 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.123 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.136 [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 Jun-08 14:29:51.137 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING Jun-08 14:29:51.137 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAM_TO_CRAM_MAPPING` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING Jun-08 14:29:51.139 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.139 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.189 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS Jun-08 14:29:51.190 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS Jun-08 14:29:51.193 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.193 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.220 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH Jun-08 14:29:51.221 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH Jun-08 14:29:51.224 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.224 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.245 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM Jun-08 14:29:51.246 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Jun-08 14:29:51.246 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Jun-08 14:29:51.247 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM Jun-08 14:29:51.248 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.248 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.303 [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 Jun-08 14:29:51.304 [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 Jun-08 14:29:51.306 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.306 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.328 [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 Jun-08 14:29:51.329 [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 Jun-08 14:29:51.329 [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 Jun-08 14:29:51.331 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.331 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.352 [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 Jun-08 14:29:51.352 [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 Jun-08 14:29:51.353 [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 Jun-08 14:29:51.353 [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 Jun-08 14:29:51.355 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.355 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.367 [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 Jun-08 14:29:51.367 [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 Jun-08 14:29:51.368 [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 Jun-08 14:29:51.368 [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 Jun-08 14:29:51.370 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.370 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Jun-08 14:29:51.428 [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:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Jun-08 14:29:51.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_STATS` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Jun-08 14:29:51.430 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.430 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.450 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Jun-08 14:29:51.450 [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:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Jun-08 14:29:51.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Jun-08 14:29:51.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_COUNT` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Jun-08 14:29:51.455 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.455 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Jun-08 14:29:51.489 [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:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Jun-08 14:29:51.489 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Jun-08 14:29:51.490 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_QUAL` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Jun-08 14:29:51.493 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.493 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.528 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Jun-08 14:29:51.528 [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:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Jun-08 14:29:51.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Jun-08 14:29:51.529 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_SUMMARY` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Jun-08 14:29:51.532 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.533 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.599 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP Jun-08 14:29:51.600 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ENSEMBLVEP_VEP` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP Jun-08 14:29:51.602 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.602 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.611 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX Jun-08 14:29:51.612 [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:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX Jun-08 14:29:51.613 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX Jun-08 14:29:51.614 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.615 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.654 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jun-08 14:29:51.656 [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:CUSTOM_DUMPSOFTWAREVERSIONS Jun-08 14:29:51.656 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jun-08 14:29:51.657 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.657 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.728 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC Jun-08 14:29:51.729 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC Jun-08 14:29:51.730 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-08 14:29:51.731 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-08 14:29:51.744 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKEGRAPH, CONTROLFREEC_MAKEGRAPH, SAMTOOLS_VIEW_MAP_MAP, SVDB_MERGE, MERGE_GENOTYPEGVCFS, SAMTOOLS_MERGE, BWA_MEM, GATK4_APPLYBQSR_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE, ADD_INFO_TO_VCF, FILTERVARIANTTRANCHES, BUILD_INTERVALS, SAMTOOLS_VIEW_UNMAP_UNMAP, CAT_FASTQ, CONTROLFREEC_FREEC2CIRCOS, SAMTOOLS_STATS, INDEX_MERGE_BAM, MUTECT2, GATK4_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX, TABIX_EXT_VCF, VCFTOOLS, NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX, TABIX_TABIX, FASTQC, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM, MULTIQC, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY, NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS, TABIX_GERMLINE_RESOURCE, ASSESS_SIGNIFICANCE, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT, CALLUMICONSENSUS, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER, TABIX_KNOWN_SNPS, CAT_CAT, NFCORE_SAREK:SAREK:FASTQC, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON, GATHERPILEUPSUMMARIES_NORMAL, SAMTOOLS_FAIDX, MERGE_BAM, STRELKA_GERMLINE, TIDDIT_SV, GETPILEUPSUMMARIES_TUMOR, STRELKA_SINGLE, SAMTOOLS_BAM2FQ, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP, BWAMEM2_MEM, VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE, UNZIP_ALLELES, BCFTOOLS_STATS, GATK4_GETPILEUPSUMMARIES, LEARNREADORIENTATIONMODEL, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM, GATK4_VARIANTRECALIBRATOR, FASTP, NFCORE_SAREK:SAREK:CRAM_TO_BAM, MERGE_FREEBAYES, MSISENSORPRO_SCAN, GATK4_MERGEVCFS, GATHERPILEUPSUMMARIES_TUMOR, TABIX_BGZIPTABIX_INTERVAL_SPLIT, UNTAR, MERGE_DEEPVARIANT_VCF, CNVKIT_REFERENCE, ENSEMBLVEP_VEP, FREEC2BED, UNZIP_LOCI, GATK4_FILTERVARIANTTRANCHES, TABIX_KNOWN_INDELS, SNPEFF_SNPEFF, CREATE_INTERVALS_BED, BAM_TO_CRAM, GROUPREADSBYUMI, NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN, BAM_TO_CRAM_MAPPING, FASTQTOBAM, CONTROLFREEC_FREEC, NFCORE_SAREK:SAREK:MULTIQC, CRAM_TO_BAM, GATK4_ESTIMATELIBRARYCOMPLEXITY, BWAMEM1_MEM, GATK4_APPLYVQSR_SNP, GATK4_BASERECALIBRATOR, GATK4_APPLYBQSR, VCFTOOLS_TSTV_QUAL, GERMLINE_VCFS_CONCAT, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM, NFCORE_SAREK:SAREK:FASTP, TABIX_DBSNP, FILTERMUTECTCALLS, CNNSCOREVARIANTS, SNPEFF_DOWNLOAD, BWA_INDEX, MANTA_GERMLINE, GATK4_LEARNREADORIENTATIONMODEL, INDEX_MARKDUPLICATES, MERGE_HAPLOTYPECALLER, GERMLINE_VCFS_CONCAT_SORT, STRELKA_SOMATIC, FREEC_SOMATIC, GATK4_MUTECT2, VARIANTRECALIBRATOR_INDEL, CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_MERGE_UNMAP, FGBIO_FASTQTOBAM, ENSEMBLVEP_DOWNLOAD, CRAM_TO_BAM_RECAL, GATK4_GATHERBQSRREPORTS, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL, TABIX_BGZIPTABIX, GATK4_MARKDUPLICATES_SPARK, GATK4_CREATESEQUENCEDICTIONARY, MERGE_DEEPVARIANT_GVCF, CALCULATECONTAMINATION, COLLATE_FASTQ_MAP, TABIX_VC_FREEBAYES, MOSDEPTH, MERGE_STRELKA_INDELS, UNZIP, COLLATE_FASTQ_UNMAP, UNZIP_GC, VCFTOOLS_TSTV_COUNT, GATK4_MERGEMUTECTSTATS, CAT_MPILEUP, CONTROLFREEC_ASSESSSIGNIFICANCE, MANTA_TUMORONLY, BWAMEM2_INDEX, MERGE_STRELKA_SNVS, SAMTOOLS_VIEW_MAP_UNMAP, MERGE_STRELKA, NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM, BCFTOOLS_CONCAT, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM, SAMTOOLS_INDEX, GATK4_CNNSCOREVARIANTS, MERGE_CRAM, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP, NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM, TABIX_BGZIP_TIDDIT_SV, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED, TABIX_PON, VARIANTRECALIBRATOR_SNP, TABIX_BGZIPTABIX_INTERVAL_COMBINED, UNTAR_CHR_DIR, FREEC_TUMORONLY, SAMBLASTER, FREEBAYES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP, GATHERPILEUPSUMMARIES, SAMTOOLS_MPILEUP, INDEX_CRAM, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ, BCFTOOLS_SORT, MANTA_SOMATIC, NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP, NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS, GATK4_FILTERMUTECTCALLS, MERGE_VQSR, MUTECT2_PAIRED, BWAMEM1_INDEX, GATK4_GATHERPILEUPSUMMARIES, DRAGMAP_HASHTABLE, CNVKIT_ANTITARGET, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN, NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX, GATK4_MARKDUPLICATES, SAMTOOLS_VIEW_UNMAP_MAP, SAMTOOLS_CONVERT, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS, TABIX_GERMLINE_VCFS_CONCAT_SORT, TABIX_VC_DEEPVARIANT_VCF, CONTROLFREEC_FREEC2BED, MERGE_STRELKA_GENOME, TABIX_VC_DEEPVARIANT_GVCF, NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP, BAM2FASTQ, UNZIP_RT, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT, SAMTOOLS_COLLATEFASTQ, MERGEMUTECTSTATS, GATK4_APPLYVQSR, GATK4_CALCULATECONTAMINATION, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS, DEEPVARIANT, GATK4_GENOTYPEGVCFS, MSISENSORPRO_MSI_SOMATIC, FREEC2CIRCOS, DRAGMAP_ALIGN, GATK4_INTERVALLISTTOBED, GATK4_APPLYVQSR_INDEL, FGBIO_GROUPREADSBYUMI, BCFTOOLS_MPILEUP, NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING, SAMTOOLS_VIEW, CNVKIT_BATCH, FGBIO_CALLMOLECULARCONSENSUSREADS, GETPILEUPSUMMARIES, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP, GETPILEUPSUMMARIES_NORMAL, GATK4_GENOMICSDBIMPORT, MERGE_MUTECT2, GATK4_BASERECALIBRATOR_SPARK, ASCAT Jun-08 14:29:51.817 [main] WARN nextflow.Session - There's no process matching config selector: NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS Jun-08 14:29:51.826 [main] DEBUG nextflow.Session - Igniting dataflow network (147) Jun-08 14:29:51.839 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX Jun-08 14:29:51.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX Jun-08 14:29:51.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE Jun-08 14:29:51.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS Jun-08 14:29:51.842 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON Jun-08 14:29:51.843 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS Jun-08 14:29:51.843 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED Jun-08 14:29:51.843 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT Jun-08 14:29:51.843 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED Jun-08 14:29:51.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP Jun-08 14:29:51.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN Jun-08 14:29:51.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM Jun-08 14:29:51.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM Jun-08 14:29:51.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING Jun-08 14:29:51.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS Jun-08 14:29:51.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH Jun-08 14:29:51.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM Jun-08 14:29:51.849 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER Jun-08 14:29:51.850 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER Jun-08 14:29:51.851 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM Jun-08 14:29:51.851 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM Jun-08 14:29:51.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS Jun-08 14:29:51.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT Jun-08 14:29:51.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL Jun-08 14:29:51.853 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY Jun-08 14:29:51.854 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP Jun-08 14:29:51.854 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX Jun-08 14:29:51.855 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS Jun-08 14:29:51.855 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC Jun-08 14:29:51.856 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Jun-08 14:29:51.856 [main] DEBUG nextflow.Session - Session await Jun-08 14:29:51.868 [Actor Thread 61] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Jun-08 14:29:52.129 [Actor Thread 55] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.003 s; external sort time: 0.028 s; total time: 0.031 s Jun-08 14:29:52.129 [Actor Thread 64] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.003 s; external sort time: 0.027 s; total time: 0.03 s Jun-08 14:29:52.143 [Actor Thread 64] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/6f7a145399bf4eef4a4a42e465beab09 Jun-08 14:29:52.143 [Actor Thread 55] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/8001fb17076ce2d2b46fbf4c8fc9fda6 Jun-08 14:29:52.160 [Actor Thread 64] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13792293372584868920 Jun-08 14:29:52.161 [Actor Thread 55] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-16604173403634962378 Jun-08 14:29:52.269 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:52.273 [Task submitter] INFO nextflow.Session - [54/cc2f84] Submitted process > NFCORE_SAREK:SAREK:FASTP (SRR9041541-1) Jun-08 14:29:52.293 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:52.294 [Task submitter] INFO nextflow.Session - [9a/b067df] Submitted process > NFCORE_SAREK:SAREK:FASTQC (SRR9041541-1) Jun-08 14:29:52.310 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:52.311 [Task submitter] INFO nextflow.Session - [1e/2f7046] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa]) Jun-08 14:29:52.324 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:52.325 [Task submitter] INFO nextflow.Session - [c9/3c287a] Submitted process > NFCORE_SAREK:SAREK:FASTQC (SRR9041540-1) Jun-08 14:29:52.333 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:52.333 [Task submitter] INFO nextflow.Session - [2a/a9b027] Submitted process > NFCORE_SAREK:SAREK:FASTP (SRR9041540-1) Jun-08 14:29:55.291 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa]); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1e/2f70462bb3c86e60251de085f070a5] Jun-08 14:29:55.337 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:55.338 [Task submitter] INFO nextflow.Session - [ad/233c4e] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED ([Saccharomyces_cerevisiae.R64-1-1-chr.fa]) Jun-08 14:29:55.339 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jun-08 14:29:55.346 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:55.347 [Task submitter] INFO nextflow.Session - [7b/a1ba63] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (Saccharomyces_cerevisiae.R64-1-1-chr.fa.bed) Jun-08 14:29:57.365 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED ([Saccharomyces_cerevisiae.R64-1-1-chr.fa]); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/ad/233c4e1ddc5b3695530c5647cbf4cc] Jun-08 14:29:57.526 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Jun-08 14:29:58.264 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (Saccharomyces_cerevisiae.R64-1-1-chr.fa.bed); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7b/a1ba63cf57d8be88a1df0a57a5bd44] Jun-08 14:29:58.303 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:29:58.304 [Task submitter] INFO nextflow.Session - [7c/696849] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (I_1-230218) Jun-08 14:29:59.793 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (I_1-230218); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7c/69684999c59f44484b65ee264e928c] Jun-08 14:29:59.801 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> Jun-08 14:30:17.268 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_SAREK:SAREK:FASTP (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/54/cc2f84050870d057f5507be2fbbfa1] Jun-08 14:30:17.304 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:30:17.304 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:30:17.347 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:17.348 [Task submitter] INFO nextflow.Session - [77/283969] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:30:28.842 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/77/283969859c3967f3a62c62c253b12a] Jun-08 14:30:28.851 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:28.852 [Task submitter] INFO nextflow.Session - [0d/ed8d48] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:30:28.858 [Actor Thread 50] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:30:33.673 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_SAREK:SAREK:FASTP (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/2a/a9b0276b736bdacbd165f3c85eb1fd] Jun-08 14:30:33.681 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:33.682 [Task submitter] INFO nextflow.Session - [c5/b754de] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:30:33.687 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:30:33.687 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:30:41.063 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/0d/ed8d48c716ffac4fb9c3bd00e10284] Jun-08 14:30:41.071 [Actor Thread 59] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:30:41.072 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:41.073 [Task submitter] INFO nextflow.Session - [60/b07cab] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:30:45.729 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c5/b754de3f7d92c80b6e0c8af4bfe833] Jun-08 14:30:45.734 [Actor Thread 59] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:30:45.738 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:45.739 [Task submitter] INFO nextflow.Session - [45/eba8c7] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:30:52.610 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/60/b07cabd91cbfcf9302dc7318ec1ebe] Jun-08 14:30:52.615 [Actor Thread 40] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:30:52.619 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:52.620 [Task submitter] INFO nextflow.Session - [7d/7cea45] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:30:56.150 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_SAREK:SAREK:FASTQC (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/9a/b067dfcca94d09a8cebe080bec5faf] Jun-08 14:30:58.450 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/45/eba8c781533aabcc3ed335685dc738] Jun-08 14:30:58.455 [Actor Thread 40] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:30:58.458 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:30:58.459 [Task submitter] INFO nextflow.Session - [5d/ef4f3f] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:31:05.280 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7d/7cea454d1cb90abc59da197e4640ef] Jun-08 14:31:05.285 [Actor Thread 29] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:05.290 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:05.291 [Task submitter] INFO nextflow.Session - [85/32384e] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:31:10.243 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/5d/ef4f3f8ff5b478ea43b8a4b835784c] Jun-08 14:31:10.248 [Actor Thread 40] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:10.249 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:10.250 [Task submitter] INFO nextflow.Session - [6d/57adbb] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:31:17.153 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/85/32384eaf902ffe2e39ebf48b46162c] Jun-08 14:31:17.158 [Actor Thread 29] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:17.160 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:17.161 [Task submitter] INFO nextflow.Session - [65/ea9bef] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:31:22.371 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/6d/57adbb60f0c08ab6157118657192b3] Jun-08 14:31:22.379 [Actor Thread 59] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:22.380 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:22.383 [Task submitter] INFO nextflow.Session - [e7/042f7a] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:31:29.316 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/65/ea9bef8cf324db3364eb04754f4b5e] Jun-08 14:31:29.322 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:29.326 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:29.328 [Task submitter] INFO nextflow.Session - [a4/73d162] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1) Jun-08 14:31:34.739 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/e7/042f7ae1e3f6511260ab8d8d59ca64] Jun-08 14:31:34.744 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:34.745 [Task submitter] INFO nextflow.Session - [be/c936ac] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:31:34.751 [Actor Thread 40] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:41.397 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/a4/73d162894dd5b66fbfe2495e535d8b] Jun-08 14:31:41.404 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:41.405 [Task submitter] INFO nextflow.Session - [fb/0d9dd1] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:31:41.407 [Actor Thread 52] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12 Jun-08 14:31:42.414 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:42.415 [Task submitter] INFO nextflow.Session - [d1/1be29a] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541) Jun-08 14:31:51.267 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/be/c936ac10c5830b7ec23114c5354ed9] Jun-08 14:31:51.272 [Actor Thread 51] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:31:51.275 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:51.277 [Task submitter] INFO nextflow.Session - [96/adf13c] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:31:55.472 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: NFCORE_SAREK:SAREK:FASTQC (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c9/3c287ab665e5f57200292bbe0a8eda] Jun-08 14:31:58.456 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fb/0d9dd1c330bc4b804968f21b75355e] Jun-08 14:31:58.461 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:31:58.461 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:31:58.462 [Task submitter] INFO nextflow.Session - [53/28d9d4] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:08.173 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/96/adf13c7bc9853b5e2dfb59fa6f30b5] Jun-08 14:32:08.179 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:08.180 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:08.181 [Task submitter] INFO nextflow.Session - [36/eaa8b7] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:15.079 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/53/28d9d4d5bc337ff588abb90365a859] Jun-08 14:32:15.086 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:15.087 [Task submitter] INFO nextflow.Session - [70/926dc7] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:15.087 [Actor Thread 59] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:25.112 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/36/eaa8b7de3a06980062c68aa9c26dfb] Jun-08 14:32:25.117 [Actor Thread 56] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:25.119 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:25.121 [Task submitter] INFO nextflow.Session - [7e/023d45] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:31.430 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/70/926dc75aab86c02dc63a0490d48357] Jun-08 14:32:31.435 [Actor Thread 56] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:31.437 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:31.438 [Task submitter] INFO nextflow.Session - [15/c326f2] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:41.668 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7e/023d45de2e31ed465475d338153e97] Jun-08 14:32:41.672 [Actor Thread 51] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:41.673 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:41.675 [Task submitter] INFO nextflow.Session - [6e/35717a] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:48.399 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/15/c326f27998ff6d02fae5390479dcae] Jun-08 14:32:48.405 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:48.406 [Task submitter] INFO nextflow.Session - [15/00c50a] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:32:48.407 [Actor Thread 59] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:58.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/6e/35717af68bcaf13d98902d437362f7] Jun-08 14:32:58.859 [Actor Thread 56] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:32:58.860 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:32:58.861 [Task submitter] INFO nextflow.Session - [06/989449] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:33:05.443 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/15/00c50a4d803bf6d15a6ed7f50ac12a] Jun-08 14:33:05.449 [Actor Thread 56] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:33:05.450 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:33:05.451 [Task submitter] INFO nextflow.Session - [cc/1f52e3] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1) Jun-08 14:33:16.344 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/06/989449d3ada857db5de354216872ec] Jun-08 14:33:16.349 [Actor Thread 40] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:33:22.566 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/cc/1f52e337c34055ad1d734077a6998a] Jun-08 14:33:22.571 [Actor Thread 58] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12 Jun-08 14:33:22.599 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:33:22.600 [Task submitter] INFO nextflow.Session - [41/589762] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540) Jun-08 14:33:33.686 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d1/1be29aac725d71421a42467ab2e09f] Jun-08 14:33:33.689 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541)` is unable to find [UnixPath]: `/home/ubuntu/reproducible-sarek-error/work/d1/1be29aac725d71421a42467ab2e09f/SRR9041541.sorted.cram` (pattern: `SRR9041541.sorted.cram`) Jun-08 14:33:33.693 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:33:33.693 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:33:33.710 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:33:33.712 [Task submitter] INFO nextflow.Session - [47/74deb3] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041541) Jun-08 14:33:43.671 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/47/74deb38a6542c8b7f39e79ab39878c] Jun-08 14:33:43.676 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:33:43.676 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:33:43.696 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:33:43.697 [Task submitter] INFO nextflow.Session - [f9/2cc780] Submitted process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041541) Jun-08 14:34:14.872 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/f9/2cc7804d5e8151e15ee783a1ced8dd] Jun-08 14:34:14.893 [Actor Thread 30] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.MemoryUnit Jun-08 14:34:14.894 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:34:14.895 [Task submitter] INFO nextflow.Session - [28/4c8f95] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041541) Jun-08 14:34:14.901 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:34:14.902 [Task submitter] INFO nextflow.Session - [15/e6c084] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041541) Jun-08 14:34:14.907 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:34:14.908 [Task submitter] INFO nextflow.Session - [85/2b4317] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541) Jun-08 14:34:21.431 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/15/e6c08446664ba82db790152b0bd4d3] Jun-08 14:34:21.445 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:34:21.445 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:34:21.445 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:34:21.445 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:34:21.445 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:34:21.446 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:34:21.446 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:34:46.446 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/28/4c8f95d9097ed6863c2579478a65d0] Jun-08 14:34:50.551 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[id: 88; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/41/58976297a3c758d81eb5151e546ac3] ~> TaskHandler[id: 93; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/85/2b43174a46675caf89e4c55720a221] Jun-08 14:36:23.104 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/41/58976297a3c758d81eb5151e546ac3] Jun-08 14:36:23.105 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540)` is unable to find [UnixPath]: `/home/ubuntu/reproducible-sarek-error/work/41/58976297a3c758d81eb5151e546ac3/SRR9041540.sorted.cram` (pattern: `SRR9041540.sorted.cram`) Jun-08 14:36:23.109 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:36:23.109 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:36:23.125 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:36:23.126 [Task submitter] INFO nextflow.Session - [d6/47c3c4] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041540) Jun-08 14:36:42.506 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d6/47c3c4f8ed495ccd3368b9424288b5] Jun-08 14:36:42.511 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:36:42.511 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:36:42.526 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:36:42.527 [Task submitter] INFO nextflow.Session - [9f/410c7d] Submitted process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041540) Jun-08 14:37:39.935 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/9f/410c7d71401862e88cf86891a8e62d] Jun-08 14:37:39.959 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:37:39.960 [Task submitter] INFO nextflow.Session - [0a/5da143] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041540) Jun-08 14:37:39.964 [Actor Thread 52] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.006 s; external sort time: 0.001 s; total time: 0.007 s Jun-08 14:37:39.965 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:37:39.967 [Task submitter] INFO nextflow.Session - [fb/a897a7] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540) Jun-08 14:37:39.972 [Actor Thread 52] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/d6ed3132c557a74240b58953c264b224 Jun-08 14:37:39.972 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:37:39.973 [Task submitter] INFO nextflow.Session - [d4/be0ce0] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041540) Jun-08 14:37:39.974 [Actor Thread 52] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-5509057384731980393 Jun-08 14:37:50.922 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d4/be0ce002029834dd85d0c1d8743177] Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:37:50.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:38:37.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/0a/5da1430d74ad374ef3732e57a58a38] Jun-08 14:38:58.733 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/85/2b43174a46675caf89e4c55720a221] Jun-08 14:38:58.738 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:38:58.759 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:38:58.760 [Task submitter] INFO nextflow.Session - [fe/a6cd08] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041541) Jun-08 14:38:58.771 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:38:58.772 [Task submitter] INFO nextflow.Session - [76/ffe06d] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041541) Jun-08 14:38:58.778 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:38:58.778 [Task submitter] INFO nextflow.Session - [74/45dac1] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041541) Jun-08 14:38:58.785 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:38:58.785 [Task submitter] INFO nextflow.Session - [3a/26e228] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041541) Jun-08 14:39:00.460 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fe/a6cd08665b966eec89eb95291b1e12] Jun-08 14:39:01.385 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/74/45dac1c3bc3aff6a923165bceaa183] Jun-08 14:39:01.429 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-08 14:39:01.429 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:39:01.429 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:39:01.429 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:39:01.429 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:39:01.429 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<17:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<19:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<20:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<21:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<22:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<23:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<24:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<25:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<26:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<27:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<28:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<29:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<30:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<31:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<32:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<33:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<34:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<35:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<36:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<37:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<38:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<39:1> Jun-08 14:39:01.430 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<40:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<41:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<42:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<43:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<44:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<45:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<46:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<47:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<48:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<49:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<50:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<51:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<52:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<53:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<54:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<55:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<56:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<57:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<58:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<59:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<60:1> Jun-08 14:39:01.431 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<61:1> Jun-08 14:39:01.476 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/76/ffe06d17444e323ee4cc75511df913] Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-08 14:39:01.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<17:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<18:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<20:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<21:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<22:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<23:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<24:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<25:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<26:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<27:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<28:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<29:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<30:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<31:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<32:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<33:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<34:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<35:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<36:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<37:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<38:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<39:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<40:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<41:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<42:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<43:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<44:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<45:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<46:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<47:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<48:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<49:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<50:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<51:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<52:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<53:1> Jun-08 14:39:01.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<54:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<55:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<56:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<57:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<58:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<59:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<60:1> Jun-08 14:39:01.522 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<61:1> Jun-08 14:39:01.748 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/3a/26e22818af4d504b8555b3cd60f4f8] Jun-08 14:39:01.784 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<18:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<19:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<20:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<21:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<22:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<23:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<24:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<25:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<26:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<27:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<28:1> Jun-08 14:39:01.785 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<29:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<30:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<31:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<32:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<33:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<34:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<35:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<36:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<37:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<38:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<39:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<40:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<41:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<42:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<43:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<44:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<45:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<46:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<47:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<48:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<49:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<50:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<51:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<52:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<53:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<54:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<55:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<56:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<57:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<58:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<59:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<60:1> Jun-08 14:39:01.786 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<61:1> Jun-08 14:39:50.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fb/a897a74859f0ac6ad4c89429f3c931] Jun-08 14:44:50.631 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fb/a897a74859f0ac6ad4c89429f3c931] Jun-08 14:46:39.887 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fb/a897a74859f0ac6ad4c89429f3c931] Jun-08 14:46:39.893 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:46:39.902 [Actor Thread 45] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s Jun-08 14:46:39.908 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/6a286de77221664ed76f05accf0a7284 Jun-08 14:46:39.909 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:46:39.910 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-1782274352974431706 Jun-08 14:46:39.910 [Task submitter] INFO nextflow.Session - [00/ce286c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041540) Jun-08 14:46:39.918 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:46:39.918 [Task submitter] INFO nextflow.Session - [11/34af07] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041540) Jun-08 14:46:39.925 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:46:39.926 [Task submitter] INFO nextflow.Session - [dc/13715c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041540) Jun-08 14:46:39.934 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:46:39.935 [Task submitter] INFO nextflow.Session - [4a/4c8c60] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041540) Jun-08 14:46:41.735 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/00/ce286cdc9cfd9dce6146948a830428] Jun-08 14:46:42.846 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/11/34af075e802b3117ef277c63cb6af9] Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<17:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<18:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<20:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<21:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<22:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<23:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<24:1> Jun-08 14:46:42.876 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<25:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<26:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<27:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<28:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<29:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<30:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<31:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<32:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<33:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<34:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<35:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<36:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<37:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<38:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<39:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<40:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<41:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<42:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<43:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<44:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<45:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<46:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<47:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<48:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<49:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<50:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<51:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<52:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<53:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<54:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<55:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<56:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<57:1> Jun-08 14:46:42.877 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<58:1> Jun-08 14:46:42.879 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<59:1> Jun-08 14:46:42.879 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<60:1> Jun-08 14:46:42.879 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<61:1> Jun-08 14:46:42.933 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/dc/13715ce9fa0a39e2269aadaf88734b] Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-08 14:46:42.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<17:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<19:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<20:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<21:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<22:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<23:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<24:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<25:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<26:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<27:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<28:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<29:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<30:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<31:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<32:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<33:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<34:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<35:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<36:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<37:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<38:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<39:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<40:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<41:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<42:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<43:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<44:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<45:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<46:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<47:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<48:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<49:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<50:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<51:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<52:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<53:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<54:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<55:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<56:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<57:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<58:1> Jun-08 14:46:42.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<59:1> Jun-08 14:46:42.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<60:1> Jun-08 14:46:42.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<61:1> Jun-08 14:46:43.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/4a/4c8c60fbf850ef26d0ea14ffc8b130] Jun-08 14:46:43.056 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-08 14:46:43.056 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-08 14:46:43.056 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<4:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<18:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<19:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<20:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<21:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<22:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<23:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<24:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<25:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<26:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<27:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<28:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<29:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<30:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<31:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<32:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<33:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<34:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<35:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<36:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<37:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<38:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<39:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<40:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<41:1> Jun-08 14:46:43.057 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<42:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<43:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<44:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<45:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<46:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<47:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<48:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<49:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<50:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<51:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<52:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<53:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<54:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<55:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<56:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<57:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<58:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<59:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<60:1> Jun-08 14:46:43.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<61:1> Jun-08 14:46:43.107 [Actor Thread 45] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 46; slices: 1; internal sort time: 0.038 s; external sort time: 0.007 s; total time: 0.045 s Jun-08 14:46:43.116 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/62b60cdfc0b133384add793bc5eb2797 Jun-08 14:46:43.118 [Actor Thread 45] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-14900597877699856045 Jun-08 14:46:43.208 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:46:43.209 [Task submitter] INFO nextflow.Session - [c3/648d4f] Submitted process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS (1) Jun-08 14:46:44.562 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS (1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c3/648d4f442e5034696aa6b6fffdac38] Jun-08 14:46:44.587 [Actor Thread 46] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/sarek/assets/multiqc_config.yml Jun-08 14:46:44.611 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-08 14:46:44.612 [Task submitter] INFO nextflow.Session - [b1/894ebd] Submitted process > NFCORE_SAREK:SAREK:MULTIQC Jun-08 14:47:20.326 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: NFCORE_SAREK:SAREK:MULTIQC; status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/b1/894ebd0532332d5090a6d8103c9149] Jun-08 14:47:20.334 [main] DEBUG nextflow.Session - Session await > all processes finished Jun-08 14:47:20.337 [main] DEBUG nextflow.Session - Session await > all barriers passed Jun-08 14:47:20.354 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Jun-08 14:47:20.359 [main] INFO nextflow.Nextflow - -[nf-core/sarek] Pipeline completed successfully- Jun-08 14:47:20.367 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=54; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3h 59m 9s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=6; peakCpus=56; peakMemory=82 GB; ] Jun-08 14:47:20.367 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jun-08 14:47:20.370 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jun-08 14:47:20.489 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":87.3,"min":87.3,"q1":87.3,"q2":87.3,"q3":87.3,"max":87.3,"minLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","maxLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","q1Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","q2Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","q3Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS 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Jun-08 14:47:21.319 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Jun-08 14:47:21.656 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jun-08 14:47:21.716 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Jun-08 14:47:21.719 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye