Jan-30 13:16:10.390 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -profile docker --fasta /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta --bwa /home/ec2-user/SageMaker/Nextflow/references/BWAIndex --igenomes_ignore true --input /home/ec2-user/SageMaker/Nextflow/samplesheet.csv --outdir /home/ec2-user/SageMaker/Nextflow/results --step mapping variant_calling annotate --aligner bwa-mem --tools haplotypecaller,snpeff --dbsnp /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz --dbsnp_tbi /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi --snpeff_db GRCh38.105 --snpeff_cache /home/ec2-user/anaconda3/envs/JupyterSystemEnv/share/snpeff-5.2-1/data -c nextflow.config -resume
Jan-30 13:16:10.443 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.10.4
Jan-30 13:16:10.462 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ec2-user/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4
Jan-30 13:16:10.474 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-30 13:16:10.475 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-30 13:16:10.477 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jan-30 13:16:10.486 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jan-30 13:16:10.498 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ec2-user/.nextflow/scm
Jan-30 13:16:11.204 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ec2-user/.nextflow/assets/nf-core/sarek/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/sarek.git
Jan-30 13:16:11.226 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jan-30 13:16:11.232 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ec2-user/.nextflow/assets/nf-core/sarek/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/sarek.git
Jan-30 13:16:11.764 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ec2-user/.nextflow/assets/nf-core/sarek/nextflow.config
Jan-30 13:16:11.764 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/ec2-user/SageMaker/Nextflow/nextflow.config
Jan-30 13:16:11.766 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/ec2-user/SageMaker/Nextflow/nextflow.config
Jan-30 13:16:11.766 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ec2-user/.nextflow/assets/nf-core/sarek/nextflow.config
Jan-30 13:16:11.766 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ec2-user/SageMaker/Nextflow/nextflow.config
Jan-30 13:16:11.767 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ec2-user/SageMaker/Nextflow/nextflow.config
Jan-30 13:16:11.771 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/ec2-user/.nextflow/secrets/store.json
Jan-30 13:16:11.773 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@11c88cca] - activable => nextflow.secret.LocalSecretsProvider@11c88cca
Jan-30 13:16:11.781 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jan-30 13:16:13.649 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jan-30 13:16:13.664 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jan-30 13:16:13.668 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, giga, incliva, ilifu, ki_luria, uge, rosalind_uge, tools_germline_deepvariant, lugh, mccleary, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, roslin, ccga_med, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, ceci_nic5, use_gatk_spark, alignment_from_everything, stjude, daisybio, eddie, alignment_to_fastq, medair, biowulf, apptainer, bi, bigpurple, adcra, tools, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, spark, utd_ganymede, charliecloud, targeted, icr_davros, save_bam_mapped, ceres, arm, munin, rosalind, annotation, hasta, cfc, test_full_aws, split_fastq, uzh, shu_bmrc, ebi_codon_slurm, ebc, variantcalling_channels, ccga_dx, crick, recalibrate_bam, ku_sund_danhead, marvin, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, test_aws, awsbatch, wustl_htcf, test_full_germline_ncbench_agilent, arcc, ceci_dragon2, imperial, maestro, skip_bqsr, software_license, genotoul, nci_gadi, skip_markduplicates, abims, test_full_germline_aws, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, mpcdf, leicester, vsc_ugent, trimming, create, sage, cambridge, tools_tumoronly, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, prepare_recalibration_bam, marjorie, tools_germline, computerome, ucd_sonic, seg_globe, sanger, tools_somatic_ascat, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, test_azure, test_full_azure, umi, engaging, gis, hypatia, psmn, eva, unity, nygc, markduplicates_bam, fgcz, conda, crg, singularity, sentieon_dedup_bam, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, sentieon_dedup_cram, debug, tools_somatic, genouest, cbe, markduplicates_cram, unsw_katana, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, gitpod, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, test_full_germline_azure, binac]
Jan-30 13:16:13.673 [main] WARN  nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option `-resume` is ignored
Jan-30 13:16:13.714 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jan-30 13:16:13.715 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [mad_kirch] DSL2 - revision: ae4dd11acc [master]
Jan-30 13:16:13.716 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1, nf-prov@1.2.2]
Jan-30 13:16:13.716 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-30 13:16:13.717 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1, nf-prov@1.2.2]
Jan-30 13:16:13.717 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1
Jan-30 13:16:13.720 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved
Jan-30 13:16:13.721 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1'
Jan-30 13:16:13.725 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1
Jan-30 13:16:13.725 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-prov version: 1.2.2
Jan-30 13:16:13.726 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-prov@1.2.2' resolved
Jan-30 13:16:13.726 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-prov@1.2.2'
Jan-30 13:16:13.727 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-prov@1.2.2
Jan-30 13:16:13.775 [main] DEBUG nextflow.Session - Session UUID: 97700fa3-c7a8-4fcc-bc70-df5621e232a5
Jan-30 13:16:13.776 [main] DEBUG nextflow.Session - Run name: mad_kirch
Jan-30 13:16:13.776 [main] DEBUG nextflow.Session - Executor pool size: 32
Jan-30 13:16:13.783 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jan-30 13:16:13.787 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-30 13:16:13.804 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.10.4 build 5934
  Created: 20-01-2025 16:47 UTC 
  System: Linux 5.10.230-223.885.amzn2.x86_64
  Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 11.0.9.1-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 15539@ip-172-16-8-1.eu-west-1.compute.internal [172.16.8.1]
  CPUs: 32 - Mem: 123.8 GB (35 GB) - Swap: 0 (0)
Jan-30 13:16:13.816 [main] DEBUG nextflow.Session - Work-dir: /home/ec2-user/SageMaker/Nextflow/work [ext2/ext3]
Jan-30 13:16:13.832 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jan-30 13:16:13.842 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-30 13:16:13.859 [main] DEBUG nextflow.Session - Observer factory: ProvObserverFactory
Jan-30 13:16:13.896 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jan-30 13:16:13.905 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jan-30 13:16:13.959 [main] DEBUG nextflow.Session - Session start
Jan-30 13:16:13.961 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ec2-user/SageMaker/Nextflow/results/pipeline_info/execution_trace_2025-01-30_13-16-12.txt
Jan-30 13:16:14.335 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-30 13:16:14.937 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Jan-30 13:16:15.543 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
Jan-30 13:16:15.544 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
Jan-30 13:16:15.547 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Jan-30 13:16:15.547 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
Jan-30 13:16:26.814 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
Jan-30 13:16:26.814 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
Jan-30 13:16:26.816 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
Jan-30 13:16:26.817 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
Jan-30 13:16:27.542 [main] INFO  nextflow.Nextflow - 
------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input          : /home/ec2-user/SageMaker/Nextflow/samplesheet.csv
  outdir         : /home/ec2-user/SageMaker/Nextflow/results

Main options
  tools          : haplotypecaller,snpeff

General reference genome options
  igenomes_ignore: true

Reference genome options
  bwa            : /home/ec2-user/SageMaker/Nextflow/references/BWAIndex
  dbsnp          : /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi      : /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  fasta          : /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  snpeff_cache   : /home/ec2-user/anaconda3/envs/JupyterSystemEnv/share/snpeff-5.2-1/data
  snpeff_db      : GRCh38.105

Core Nextflow options
  revision       : master
  runName        : mad_kirch
  containerEngine: docker
  launchDir      : /home/ec2-user/SageMaker/Nextflow
  workDir        : /home/ec2-user/SageMaker/Nextflow/work
  projectDir     : /home/ec2-user/.nextflow/assets/nf-core/sarek
  userName       : ec2-user
  profile        : docker
  configFiles    : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.12688/f1000research.16665.2
    https://doi.org/10.1093/nargab/lqae031
    https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/sarek/blob/master/CITATIONS.md

Jan-30 13:16:27.544 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation
Jan-30 13:16:27.691 [main] DEBUG nextflow.validation.SchemaEvaluator - Started validating /home/ec2-user/SageMaker/Nextflow/samplesheet.csv
Jan-30 13:16:27.738 [main] DEBUG nextflow.validation.SchemaEvaluator - Validation of file '/home/ec2-user/SageMaker/Nextflow/samplesheet.csv' passed!
Jan-30 13:16:27.739 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://ngi-igenomes/igenomes/'
Jan-30 13:16:27.740 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://annotation-cache/vep_cache/'
Jan-30 13:16:27.740 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation
Jan-30 13:16:27.743 [main] WARN  nextflow.Nextflow - nf-core pipelines do not accept positional arguments. The positional argument `variant_calling` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.

Jan-30 13:16:27.867 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jan-30 13:16:27.873 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jan-30 13:16:27.888 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:27.888 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:27.893 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-30 13:16:27.899 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=123.8 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Jan-30 13:16:27.901 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jan-30 13:16:27.941 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jan-30 13:16:27.943 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jan-30 13:16:27.948 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:27.948 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:27.954 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jan-30 13:16:27.955 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jan-30 13:16:27.960 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:27.960 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:27.966 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jan-30 13:16:27.967 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jan-30 13:16:27.972 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:27.972 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:27.978 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jan-30 13:16:27.978 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jan-30 13:16:27.982 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:27.982 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:27.989 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jan-30 13:16:27.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jan-30 13:16:27.994 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:27.994 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS
Jan-30 13:16:28.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS
Jan-30 13:16:28.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS
Jan-30 13:16:28.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BCFTOOLS_ANNOTATIONS` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS
Jan-30 13:16:28.013 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.013 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.020 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP
Jan-30 13:16:28.021 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP
Jan-30 13:16:28.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP
Jan-30 13:16:28.022 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP
Jan-30 13:16:28.025 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.025 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.034 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jan-30 13:16:28.034 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jan-30 13:16:28.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jan-30 13:16:28.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jan-30 13:16:28.038 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.038 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.048 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jan-30 13:16:28.049 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jan-30 13:16:28.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jan-30 13:16:28.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jan-30 13:16:28.058 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.059 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.070 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jan-30 13:16:28.071 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jan-30 13:16:28.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jan-30 13:16:28.073 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jan-30 13:16:28.079 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.079 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.088 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_GENOME:TABIX_PON
Jan-30 13:16:28.088 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_PON
Jan-30 13:16:28.089 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_PON
Jan-30 13:16:28.090 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:PREPARE_GENOME:TABIX_PON
Jan-30 13:16:28.092 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.092 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.163 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
Jan-30 13:16:28.164 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
Jan-30 13:16:28.165 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BUILD_INTERVALS` matches process NFCORE_SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
Jan-30 13:16:28.168 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.168 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.175 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jan-30 13:16:28.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jan-30 13:16:28.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jan-30 13:16:28.179 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.180 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.211 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jan-30 13:16:28.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jan-30 13:16:28.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jan-30 13:16:28.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT|TABIX_BGZIPTABIX_INTERVAL_COMBINED` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jan-30 13:16:28.216 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.216 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jan-30 13:16:28.228 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jan-30 13:16:28.229 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jan-30 13:16:28.229 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT|TABIX_BGZIPTABIX_INTERVAL_COMBINED` matches process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jan-30 13:16:28.232 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.232 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.293 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_FQ_PAIR
Jan-30 13:16:28.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_.*` matches process NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_FQ_PAIR
Jan-30 13:16:28.299 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.299 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.305 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R1_FQ
Jan-30 13:16:28.306 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_.*` matches process NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R1_FQ
Jan-30 13:16:28.308 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.308 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.313 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R2_FQ
Jan-30 13:16:28.314 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_.*` matches process NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R2_FQ
Jan-30 13:16:28.316 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.316 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.332 [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
Jan-30 13:16:28.333 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jan-30 13:16:28.336 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.336 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.343 [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
Jan-30 13:16:28.344 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jan-30 13:16:28.347 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.347 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.354 [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
Jan-30 13:16:28.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jan-30 13:16:28.358 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.358 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.366 [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
Jan-30 13:16:28.367 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jan-30 13:16:28.370 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.370 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.386 [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
Jan-30 13:16:28.387 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jan-30 13:16:28.390 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.390 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.399 [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
Jan-30 13:16:28.402 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jan-30 13:16:28.405 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.405 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.411 [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
Jan-30 13:16:28.412 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jan-30 13:16:28.415 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.415 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.424 [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
Jan-30 13:16:28.424 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jan-30 13:16:28.426 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.426 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.444 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC
Jan-30 13:16:28.444 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC
Jan-30 13:16:28.447 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.447 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP
Jan-30 13:16:28.460 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP
Jan-30 13:16:28.462 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.462 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.487 [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_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:28.487 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:28.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:28.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:28.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:28.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:28.490 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.490 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.498 [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_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:28.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:28.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:28.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:28.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:28.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:28.502 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.502 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.511 [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_SENTIEON:DRAGMAP_ALIGN
Jan-30 13:16:28.512 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN
Jan-30 13:16:28.512 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN
Jan-30 13:16:28.512 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN
Jan-30 13:16:28.515 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.515 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high,sentieon` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM
Jan-30 13:16:28.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM
Jan-30 13:16:28.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM
Jan-30 13:16:28.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM|SENTIEON_BWAMEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM
Jan-30 13:16:28.526 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.527 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.568 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jan-30 13:16:28.569 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES|GATK4SPARK_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jan-30 13:16:28.569 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jan-30 13:16:28.572 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.572 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jan-30 13:16:28.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jan-30 13:16:28.588 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.588 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.603 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
Jan-30 13:16:28.604 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
Jan-30 13:16:28.606 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.606 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jan-30 13:16:28.641 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jan-30 13:16:28.641 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jan-30 13:16:28.642 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jan-30 13:16:28.643 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.644 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.678 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jan-30 13:16:28.679 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jan-30 13:16:28.679 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jan-30 13:16:28.681 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.681 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jan-30 13:16:28.691 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jan-30 13:16:28.692 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jan-30 13:16:28.693 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.693 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jan-30 13:16:28.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jan-30 13:16:28.732 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jan-30 13:16:28.734 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.734 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.754 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
Jan-30 13:16:28.755 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
Jan-30 13:16:28.757 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.757 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.768 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jan-30 13:16:28.768 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jan-30 13:16:28.769 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jan-30 13:16:28.772 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.772 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jan-30 13:16:28.795 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jan-30 13:16:28.796 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM_RECAL` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jan-30 13:16:28.798 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.798 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.816 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS
Jan-30 13:16:28.817 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS
Jan-30 13:16:28.818 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.818 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.831 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH
Jan-30 13:16:28.831 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH
Jan-30 13:16:28.832 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH
Jan-30 13:16:28.834 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.834 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
Jan-30 13:16:28.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
Jan-30 13:16:28.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_MPILEUP` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
Jan-30 13:16:28.871 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
Jan-30 13:16:28.873 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.873 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.894 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
Jan-30 13:16:28.895 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*BAM_NGSCHECKMATE:NGSCHECKMATE_NCM` matches process NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
Jan-30 13:16:28.897 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.897 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.948 [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
Jan-30 13:16:28.948 [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
Jan-30 13:16:28.951 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.951 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:28.973 [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
Jan-30 13:16:28.974 [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
Jan-30 13:16:28.974 [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
Jan-30 13:16:28.976 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:28.976 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.001 [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
Jan-30 13:16:29.002 [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
Jan-30 13:16:29.002 [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
Jan-30 13:16:29.002 [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
Jan-30 13:16:29.004 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.004 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.014 [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
Jan-30 13:16:29.015 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|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
Jan-30 13:16:29.016 [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
Jan-30 13:16:29.016 [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
Jan-30 13:16:29.017 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.018 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.061 [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:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
Jan-30 13:16:29.062 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CNNSCOREVARIANTS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
Jan-30 13:16:29.064 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.064 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.077 [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:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
Jan-30 13:16:29.078 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
Jan-30 13:16:29.079 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.079 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.157 [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
Jan-30 13:16:29.158 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jan-30 13:16:29.158 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_STATS` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jan-30 13:16:29.160 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.160 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.185 [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
Jan-30 13:16:29.186 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jan-30 13:16:29.186 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jan-30 13:16:29.187 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_COUNT` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jan-30 13:16:29.192 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.192 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.227 [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
Jan-30 13:16:29.228 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jan-30 13:16:29.228 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jan-30 13:16:29.228 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_QUAL` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jan-30 13:16:29.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.234 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.266 [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
Jan-30 13:16:29.267 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jan-30 13:16:29.267 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jan-30 13:16:29.267 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_SUMMARY` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jan-30 13:16:29.272 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.272 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.358 [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_SNPEFF:SNPEFF_SNPEFF
Jan-30 13:16:29.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SNPEFF_SNPEFF` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
Jan-30 13:16:29.360 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.360 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.370 [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_SNPEFF:TABIX_BGZIPTABIX
Jan-30 13:16:29.371 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
Jan-30 13:16:29.372 [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_SNPEFF:TABIX_BGZIPTABIX
Jan-30 13:16:29.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
Jan-30 13:16:29.375 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.375 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC
Jan-30 13:16:29.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC
Jan-30 13:16:29.475 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-30 13:16:29.475 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-30 13:16:29.488 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
Jan-30 13:16:29.490 [main] DEBUG nextflow.Session - Igniting dataflow network (188)
Jan-30 13:16:29.498 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jan-30 13:16:29.503 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jan-30 13:16:29.503 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jan-30 13:16:29.505 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jan-30 13:16:29.506 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jan-30 13:16:29.506 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jan-30 13:16:29.507 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS
Jan-30 13:16:29.507 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_GENOME:TABIX_PON
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jan-30 13:16:29.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jan-30 13:16:29.510 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_FQ_PAIR
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R1_FQ
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R2_FQ
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jan-30 13:16:29.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM2_MEM
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:DRAGMAP_ALIGN
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:SENTIEON_BWAMEM
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jan-30 13:16:29.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP
Jan-30 13:16:29.513 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM
Jan-30 13:16:29.514 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
Jan-30 13:16:29.514 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
Jan-30 13:16:29.514 [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
Jan-30 13:16:29.514 [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
Jan-30 13:16:29.514 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
Jan-30 13:16:29.514 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
Jan-30 13:16:29.517 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jan-30 13:16:29.517 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jan-30 13:16:29.517 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jan-30 13:16:29.517 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jan-30 13:16:29.518 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF
Jan-30 13:16:29.520 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX
Jan-30 13:16:29.521 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC
Jan-30 13:16:29.533 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_f289bdfe26d7f1cf: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../modules/nf-core/fastqc/main.nf
  Script_2b401a04ae31574b: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/main.nf
  Script_7abe1c051b661ed0: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/fastq_create_umi_consensus_fgbio/../../../modules/nf-core/fgbio/fastqtobam/main.nf
  Script_9a1f744b4af07447: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/annotation_cache_initialisation/main.nf
  Script_e6f540ffb2c944ec: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_mutect2/../../../modules/nf-core/gatk4/calculatecontamination/main.nf
  Script_028a088a254cd6dd: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_freebayes/main.nf
  Script_2719fbd471342244: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/nf-core/bam_ngscheckmate/main.nf
  Script_76c3210580c9fe21: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/main.nf
  Script_2b733a645bfb6d5a: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/main.nf
  Script_223ca400878df5b0: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/untar/main.nf
  Script_8ff83fc63a22c8fb: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_indexcov/../../../modules/local/samtools/reindex_bam/main.nf
  Script_c80bb66b9dac5c97: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_snpeff/../../../modules/nf-core/snpeff/snpeff/main.nf
  Script_a2aa0d1ede76c3e4: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_mpileup/../../../modules/nf-core/cat/cat/main.nf
  Script_0470df1d00c50fae: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_joint_calling_germline_gatk/../../../modules/nf-core/gatk4/applyvqsr/main.nf
  Script_b8b71093ffc116f1: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/post_variantcalling/../vcf_concatenate_germline/main.nf
  Script_1a83631ea747ef88: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/main.nf
  Script_f34da7b33c26ef52: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_cnvkit/../../../modules/nf-core/cnvkit/export/main.nf
  Script_9f122e32eac0f4c1: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_freebayes/../../../modules/nf-core/freebayes/main.nf
  Script_824368743d45b72e: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/main.nf
  Script_b3af914e27a1ce02: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_sentieon_dedup/../../../modules/nf-core/sentieon/dedup/main.nf
  Script_668d1f0d214380c6: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/samtools/faidx/main.nf
  Script_02b13fce0ed21a2e: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_manta/../../../modules/nf-core/manta/somatic/main.nf
  Script_129045cbcec43290: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_indexcov/../../../modules/nf-core/goleft/indexcov/main.nf
  Script_a40ac2ab631fac5b: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates_spark/../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
  Script_1f0a1eb4bf79a7fd: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_sentieon_dedup/main.nf
  Script_b8abeeceaabc9922: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_deepvariant/main.nf
  Script_0ce72e734ad77725: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/utils_nfcore_sarek_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf
  Script_64e8d3d443f4d86f: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_joint_calling_germline_sentieon/main.nf
  Script_bf84ae935173146f: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates/../cram_qc_mosdepth_samtools/main.nf
  Script_5e3dda2ff6021e1a: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_mutect2/../../../modules/nf-core/gatk4/filtermutectcalls/main.nf
  Script_ee34bf515398c533: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/utils_nfcore_sarek_pipeline/../samplesheet_to_channel/main.nf
  Script_819aadb1392fd995: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_ensemblvep/../../../modules/nf-core/ensemblvep/vep/main.nf
  Script_7a66424f9cfe9c28: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_convert_samtools/../../../modules/nf-core/cat/fastq/main.nf
  Script_2b1c6a73b143b9f1: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_strelka/main.nf
  Script_b6f6b85e4ee95525: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_baserecalibrator_spark/../../../modules/nf-core/gatk4/gatherbqsrreports/main.nf
  Script_057d3de35ec771e9: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates_spark/main.nf
  Script_d6715a92b793b124: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/bwamem2/index/main.nf
  Script_ca1602e337ab4f2a: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_cnvkit/../../../modules/nf-core/cnvkit/genemetrics/main.nf
  Script_e5fccee2ba9a7b56: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr_spark/../cram_merge_index_samtools/../../../modules/nf-core/samtools/merge/main.nf
  Script_b51e866816de7307: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/fastq_create_umi_consensus_fgbio/../../../modules/nf-core/samtools/bam2fq/main.nf
  Script_e6188ba138d07431: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_baserecalibrator/main.nf
  Script_5a1ee4df50ceb976: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/channel_markduplicates_create_csv/main.nf
  Script_af1e34c37a4660bf: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
  Script_d11b5c79ea543e09: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_tumor_only_controlfreec/main.nf
  Script_12f1b0cba653bc40: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_ascat/main.nf
  Script_319b72dc6ac6baa4: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/msisensorpro/scan/main.nf
  Script_eda4c1615e5caaae: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr/../cram_merge_index_samtools/main.nf
  Script_1690db9662109ef7: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_sentieon_haplotyper/main.nf
  Script_57ee94b0d1ea8856: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/channel_variant_calling_create_csv/main.nf
  Script_3ff1656b1d66c1f2: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_markduplicates_spark/../../../modules/nf-core/samtools/index/main.nf
  Script_1dca684e20afa7cb: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr/main.nf
  Script_1d72d5d488f8c5ea: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/fastq_create_umi_consensus_fgbio/../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf
  Script_4cb94d2c5ce6310a: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_joint_calling_germline_sentieon/../../../modules/nf-core/sentieon/gvcftyper/main.nf
  Script_b586a2201c19b6cb: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/fastq_create_umi_consensus_fgbio/../../../modules/nf-core/samblaster/main.nf
  Script_a9e4dae695eeedc0: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr/../../../modules/nf-core/gatk4/applybqsr/main.nf
  Script_ee2021533d309cc4: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_baserecalibrator_spark/main.nf
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  Script_6df0dcc77a212b33: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_controlfreec/../../../modules/nf-core/controlfreec/makegraph2/main.nf
  Script_81ec1f07ab213590: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_convert_samtools/../../../modules/nf-core/samtools/collatefastq/main.nf
  Script_1bd098db325044b1: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/channel_baserecalibrator_create_csv/main.nf
  Script_e2fb30b813036521: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_germline_manta/../../../modules/nf-core/manta/germline/main.nf
  Script_d5cab7da0897d72e: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_somatic_all/../bam_variant_calling_somatic_tiddit/main.nf
  Script_1c7d7a4569b86317: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/main.nf
  Script_ce094188ad6cffa2: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_haplotypecaller/../../../modules/nf-core/gatk4/haplotypecaller/main.nf
  Script_e7e4058441ead3e3: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_single_strelka/../../../modules/nf-core/strelka/germline/main.nf
  Script_bf5fea05e615580c: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/dragmap/hashtable/main.nf
  Script_6630dd73aedd8b51: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/download_cache_snpeff_vep/../../../modules/nf-core/ensemblvep/download/main.nf
  Script_187f79be3eba8ea9: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../vcf_annotate_bcftools/main.nf
  Script_477105648dabdd41: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/vcf_qc_bcftools_vcftools/../../../modules/nf-core/bcftools/stats/main.nf
  Script_185f79e4a174cc18: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/nf-core/bam_ngscheckmate/../../../modules/nf-core/ngscheckmate/ncm/main.nf
  Script_ba3a5724e6a02fb3: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_reference_cnvkit/../../../modules/nf-core/cnvkit/antitarget/main.nf
  Script_968436927447c3df: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_mpileup/../../../modules/nf-core/gatk4/mergevcfs/main.nf
  Script_6e58dab2f6472f41: /home/ec2-user/.nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_applybqsr_spark/../../../modules/nf-core/gatk4spark/applybqsr/main.nf
  Script_8b560cf26a0f6f39: /home/ec2-user/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/unzip/main.nf
Jan-30 13:16:29.534 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jan-30 13:16:29.534 [main] DEBUG nextflow.Session - Session await
Jan-30 13:16:29.633 [Actor Thread 8] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.014 s; total time: 0.015 s
Jan-30 13:16:29.633 [Actor Thread 35] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.014 s; total time: 0.015 s
Jan-30 13:16:29.639 [Actor Thread 8] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ec2-user/SageMaker/Nextflow/work/collect-file/43b1ef862074695b54c923f121f48e25
Jan-30 13:16:29.639 [Actor Thread 35] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ec2-user/SageMaker/Nextflow/work/collect-file/53eef030ce0fc68b0e96ca6459cd8c86
Jan-30 13:16:29.646 [Actor Thread 35] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-11710701539213889390
Jan-30 13:16:29.646 [Actor Thread 8] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-11274926855993112171
Jan-30 13:16:29.673 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:29.674 [Task submitter] INFO  nextflow.Session - [de/16304d] Submitted process > NFCORE_SAREK:SAREK:FASTP (ERR4383821-L001)
Jan-30 13:16:29.682 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:29.683 [Task submitter] INFO  nextflow.Session - [d4/82f6bd] Submitted process > NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX (Homo_sapiens_assembly38.fasta)
Jan-30 13:16:29.688 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:29.688 [Task submitter] INFO  nextflow.Session - [49/9c1daa] Submitted process > NFCORE_SAREK:SAREK:FASTQC (ERR4383817-L001)
Jan-30 13:16:29.693 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:29.693 [Task submitter] INFO  nextflow.Session - [e4/ce5c5d] Submitted process > NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (Homo_sapiens_assembly38.fasta)
Jan-30 13:16:29.700 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:29.700 [Task submitter] INFO  nextflow.Session - [39/dec557] Submitted process > NFCORE_SAREK:SAREK:FASTQC (ERR4383812-L001)
Jan-30 13:16:29.707 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:29.707 [Task submitter] INFO  nextflow.Session - [a0/399316] Submitted process > NFCORE_SAREK:SAREK:FASTQC (ERR4383821-L001)
Jan-30 13:16:32.416 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_SAREK:SAREK:FASTP (ERR4383821-L001); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/de/16304d1b8ebde8e159230b052413c1]
Jan-30 13:16:32.417 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-30 13:16:32.422 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:32.422 [Task submitter] INFO  nextflow.Session - [a8/0b3cc4] Submitted process > NFCORE_SAREK:SAREK:FASTP (ERR4383817-L001)
Jan-30 13:16:32.518 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jan-30 13:16:32.518 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jan-30 13:16:32.576 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-30 13:16:34.021 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_SAREK:SAREK:FASTP (ERR4383817-L001); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/a8/0b3cc490e30a76784db22f502cf987]
Jan-30 13:16:34.028 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:34.028 [Task submitter] INFO  nextflow.Session - [68/d3bb3f] Submitted process > NFCORE_SAREK:SAREK:FASTP (ERR4383812-L001)
Jan-30 13:16:34.031 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jan-30 13:16:34.031 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jan-30 13:16:34.874 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: NFCORE_SAREK:SAREK:FASTQC (ERR4383821-L001); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/a0/3993165bb9f5c1147a05629ae46264]
Jan-30 13:16:35.051 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_SAREK:SAREK:FASTQC (ERR4383817-L001); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/49/9c1daa9b4ebafaa6841ab4bd51dedd]
Jan-30 13:16:35.548 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_SAREK:SAREK:FASTQC (ERR4383812-L001); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/39/dec557d18cc59804c9f23eff925c1f]
Jan-30 13:16:35.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NFCORE_SAREK:SAREK:FASTP (ERR4383812-L001); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/68/d3bb3fe8458c75805c179a086851f4]
Jan-30 13:16:35.659 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:35.659 [Task submitter] INFO  nextflow.Session - [8c/0d7a16] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:16:35.660 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jan-30 13:16:35.660 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jan-30 13:16:39.110 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/8c/0d7a16d21586658b636de8aab320b8]
Jan-30 13:16:39.115 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:39.115 [Task submitter] INFO  nextflow.Session - [20/be8e2f] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:16:39.117 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:16:39.117 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:16:39.117 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:16:39.123 [Actor Thread 6] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:16:39.367 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX (Homo_sapiens_assembly38.fasta); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/d4/82f6bdafa2aea830db986297c4b30b]
Jan-30 13:16:39.371 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jan-30 13:16:39.371 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:16:40.374 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:40.374 [Task submitter] INFO  nextflow.Session - [c9/788673] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:BUILD_INTERVALS (Homo_sapiens_assembly38)
Jan-30 13:16:41.753 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 123; name: NFCORE_SAREK:PREPARE_INTERVALS:BUILD_INTERVALS (Homo_sapiens_assembly38); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/c9/7886733cc0262cf093127b4aa5f9dd]
Jan-30 13:16:42.559 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/20/be8e2f8bd8e6c6c1d37163c5ef562f]
Jan-30 13:16:42.563 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:16:42.564 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:16:42.564 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:16:42.564 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:42.564 [Task submitter] INFO  nextflow.Session - [02/69a69f] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:16:42.565 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:16:42.569 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:42.570 [Task submitter] INFO  nextflow.Session - [4e/dac1d8] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (Homo_sapiens_assembly38.bed)
Jan-30 13:16:42.573 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:42.573 [Task submitter] INFO  nextflow.Session - [3b/907842] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (Homo_sapiens_assembly38)
Jan-30 13:16:45.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 159; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (Homo_sapiens_assembly38); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/3b/9078420efb2d4e8dd5c2bd91ccf09f]
Jan-30 13:16:45.035 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:45.321 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 160; name: NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (Homo_sapiens_assembly38.bed); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/4e/dac1d8b52d47cb184b63a959a0e95c]
Jan-30 13:16:46.077 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/02/69a69f05faa3bff86f4fca4ba784f9]
Jan-30 13:16:46.082 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:16:46.082 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:16:46.082 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:16:46.082 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:46.083 [Task submitter] INFO  nextflow.Session - [8f/3ce0bf] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:16:46.083 [Actor Thread 26] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:16:46.088 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:46.089 [Task submitter] INFO  nextflow.Session - [59/164a8e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr8_1-145138636)
Jan-30 13:16:46.092 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:46.093 [Task submitter] INFO  nextflow.Session - [b7/fa557e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr10_1-133797422)
Jan-30 13:16:47.572 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 172; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr8_1-145138636); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/59/164a8ee8dbac233888f6b40bc479b2]
Jan-30 13:16:47.577 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:47.577 [Task submitter] INFO  nextflow.Session - [c3/93f8c1] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr11_1-135086622)
Jan-30 13:16:47.577 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:48.147 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 175; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr10_1-133797422); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/b7/fa557ef3cfe240714af32ebd2186cf]
Jan-30 13:16:48.151 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:48.151 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:48.152 [Task submitter] INFO  nextflow.Session - [2e/bffa04] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr3_1-198295559)
Jan-30 13:16:49.385 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (Homo_sapiens_assembly38.fasta); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/e4/ce5c5d689a749ec4942827c9158a4a]
Jan-30 13:16:49.389 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.389 [Task submitter] INFO  nextflow.Session - [4a/8553c6] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr5_1-181538259)
Jan-30 13:16:49.394 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.394 [Task submitter] INFO  nextflow.Session - [b9/b68103] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_1-248956422)
Jan-30 13:16:49.398 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.398 [Task submitter] INFO  nextflow.Session - [46/4fe644] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr15_1-101991189)
Jan-30 13:16:49.401 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.401 [Task submitter] INFO  nextflow.Session - [cd/584311] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr9_1-138394717)
Jan-30 13:16:49.404 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.404 [Task submitter] INFO  nextflow.Session - [23/343b7a] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr13_1-114364328)
Jan-30 13:16:49.409 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.410 [Task submitter] INFO  nextflow.Session - [13/0580a3] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_1-46709983)
Jan-30 13:16:49.638 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 174; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr11_1-135086622); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/c3/93f8c1dc34d4c1dfe13fc879777b1a]
Jan-30 13:16:49.642 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:49.642 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.643 [Task submitter] INFO  nextflow.Session - [3d/0df43b] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr7_1-159345973)
Jan-30 13:16:49.732 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 165; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr3_1-198295559); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/2e/bffa04dbe77d9447f52eec6949737e]
Jan-30 13:16:49.736 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:49.736 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.737 [Task submitter] INFO  nextflow.Session - [06/1b7387] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr17_1-83257441)
Jan-30 13:16:49.850 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/8f/3ce0bff38ba6b495d47a6f0adda295]
Jan-30 13:16:49.854 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:49.854 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:16:49.854 [Task submitter] INFO  nextflow.Session - [8f/137b32] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:16:49.854 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:16:49.854 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:16:49.855 [Actor Thread 22] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:16:50.690 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 168; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr5_1-181538259); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/4a/8553c650db2a1ea5cecbd1b5de46b9]
Jan-30 13:16:50.693 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:50.693 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:50.694 [Task submitter] INFO  nextflow.Session - [2a/811e45] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr6_1-170805979)
Jan-30 13:16:50.907 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 162; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr1_1-248956422); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/b9/b68103e689925d493f8e036ed73e39]
Jan-30 13:16:50.910 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:50.911 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:50.911 [Task submitter] INFO  nextflow.Session - [89/2f1b73] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_1-190214555)
Jan-30 13:16:51.620 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 164; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr13_1-114364328); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/23/343b7a3a089c402d8279ce8ae4014a]
Jan-30 13:16:51.624 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:51.624 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:51.625 [Task submitter] INFO  nextflow.Session - [95/6c742e] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_1-242193529)
Jan-30 13:16:51.775 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 166; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr15_1-101991189); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/46/4fe6445d2b5a161d6691fb54c5b363]
Jan-30 13:16:51.779 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:51.779 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:51.780 [Task submitter] INFO  nextflow.Session - [67/516a18] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrY_1-57227415)
Jan-30 13:16:52.038 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 173; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr9_1-138394717); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/cd/584311c48181069a9c2bdf13d3a233]
Jan-30 13:16:52.042 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:52.044 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:52.044 [Task submitter] INFO  nextflow.Session - [be/82cdc4] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr12_1-133275309)
Jan-30 13:16:52.494 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 161; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr21_1-46709983); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/13/0580a37b40d6eff09a2af99e3e7492]
Jan-30 13:16:52.498 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:52.499 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:52.499 [Task submitter] INFO  nextflow.Session - [06/e552c6] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr19_1-58617616)
Jan-30 13:16:53.217 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 171; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr7_1-159345973); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/3d/0df43b569ec3532f9b8422c40318ca]
Jan-30 13:16:53.221 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:53.221 [Task submitter] INFO  nextflow.Session - [cd/d75842] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr20_KI270871v1_alt_1-58661)
Jan-30 13:16:53.222 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:53.450 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 170; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr17_1-83257441); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/06/1b7387fff4adf15dc53efcefdbb4e9]
Jan-30 13:16:53.456 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:54.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 169; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr6_1-170805979); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/2a/811e45a44d5f0eb41ad5f0bba78c90]
Jan-30 13:16:54.178 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:54.774 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 167; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr4_1-190214555); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/89/2f1b73259777e78299823e517db20a]
Jan-30 13:16:54.783 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:55.685 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 163; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr2_1-242193529); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/95/6c742ef0bd0cd6e72cd4a5db392838]
Jan-30 13:16:55.689 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:55.941 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/8f/137b323df4cdf87604c56ec227757c]
Jan-30 13:16:55.945 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:16:55.945 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:16:55.945 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:16:55.945 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:16:55.945 [Task submitter] INFO  nextflow.Session - [24/b9b54c] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:16:55.946 [Actor Thread 15] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:16:56.208 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 178; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chrY_1-57227415); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/67/516a1819377247180e7265d41e9d32]
Jan-30 13:16:56.213 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:56.579 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 177; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr19_1-58617616); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/06/e552c6314b53e122283b56f39d53c5]
Jan-30 13:16:56.582 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:56.681 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 176; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr12_1-133275309); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/be/82cdc438c9ebc643020230aa077134]
Jan-30 13:16:56.685 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:16:57.131 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 179; name: NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr20_KI270871v1_alt_1-58661); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/cd/d758428554e1160fc0d308c79a0780]
Jan-30 13:16:57.135 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jan-30 13:17:00.112 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/24/b9b54c60d8ef7726d54795202af0ae]
Jan-30 13:17:00.115 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:00.116 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:00.116 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:00.119 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:00.119 [Task submitter] INFO  nextflow.Session - [1b/a569f7] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:17:00.119 [Actor Thread 6] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:03.471 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/1b/a569f7d358730019781abd025ef513]
Jan-30 13:17:03.475 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:03.475 [Task submitter] INFO  nextflow.Session - [92/9352d3] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:17:03.478 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:03.478 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:03.478 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:03.479 [Actor Thread 22] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:06.851 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/92/9352d34ab1bb81cd5136d02d9ca6b0]
Jan-30 13:17:06.855 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:06.855 [Task submitter] INFO  nextflow.Session - [ae/dcac86] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:17:06.855 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:06.855 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:06.855 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:06.856 [Actor Thread 15] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:10.191 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/ae/dcac869a6b2cc8ef76cb989e76a1ca]
Jan-30 13:17:10.195 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:10.195 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:10.195 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:10.195 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:10.195 [Task submitter] INFO  nextflow.Session - [ac/16d2a8] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:17:10.196 [Actor Thread 22] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:13.525 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/ac/16d2a8765491939341686ec7d88a09]
Jan-30 13:17:13.529 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:13.529 [Task submitter] INFO  nextflow.Session - [34/4e3ab1] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:17:13.529 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:13.530 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:13.530 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:13.531 [Actor Thread 15] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:16.904 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/34/4e3ab18b7962f2c330a8a4315e2c92]
Jan-30 13:17:16.907 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:16.907 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:16.907 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:16.908 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:16.908 [Task submitter] INFO  nextflow.Session - [62/dfb0ef] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821)
Jan-30 13:17:16.908 [Actor Thread 6] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:20.268 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/62/dfb0ef7d25fcac5a98ba75e38f38ba]
Jan-30 13:17:20.272 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:20.272 [Task submitter] INFO  nextflow.Session - [68/8a5e76] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:20.273 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:20.273 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:20.273 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:20.274 [Actor Thread 15] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383821] size=12
Jan-30 13:17:21.278 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:21.278 [Task submitter] INFO  nextflow.Session - [5c/c44eae] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (ERR4383821)
Jan-30 13:17:23.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/68/8a5e76da322fe009ce8525fb677101]
Jan-30 13:17:23.629 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:23.630 [Task submitter] INFO  nextflow.Session - [8e/5ce062] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:23.630 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:23.630 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:23.630 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:23.631 [Actor Thread 22] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:26.867 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/8e/5ce062a3c255a1fd6606775c78bf1e]
Jan-30 13:17:26.874 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:26.874 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:26.874 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:26.874 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:26.874 [Task submitter] INFO  nextflow.Session - [71/e148a6] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:26.875 [Actor Thread 39] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:30.285 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/71/e148a6089c4c0c3536ffe3d11a8f51]
Jan-30 13:17:30.289 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:30.289 [Task submitter] INFO  nextflow.Session - [48/f3b413] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:30.290 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:30.291 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:30.291 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:30.291 [Actor Thread 37] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:33.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/48/f3b4135f42626125611cbdfee917af]
Jan-30 13:17:33.604 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:33.605 [Task submitter] INFO  nextflow.Session - [6a/781b16] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:33.605 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:33.605 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:33.605 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:33.607 [Actor Thread 1] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:36.940 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/6a/781b168b8fd341414e6df044e4c81d]
Jan-30 13:17:36.943 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:36.944 [Task submitter] INFO  nextflow.Session - [6d/a4d94b] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:36.945 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:36.945 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:36.945 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:36.946 [Actor Thread 16] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:40.211 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 180; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/5c/c44eae54a43c273888ace51f36783f]
Jan-30 13:17:40.216 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:40.217 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:40.302 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/6d/a4d94bf472e7a122d2510854704bae]
Jan-30 13:17:40.305 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:40.306 [Task submitter] INFO  nextflow.Session - [65/aec7c7] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:40.306 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:40.306 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:40.306 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:40.307 [Actor Thread 23] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:40.309 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:40.310 [Task submitter] INFO  nextflow.Session - [f7/5bfdc7] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (ERR4383821)
Jan-30 13:17:40.315 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:40.315 [Task submitter] INFO  nextflow.Session - [85/485674] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (ERR4383821)
Jan-30 13:17:40.319 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:40.319 [Task submitter] INFO  nextflow.Session - [60/da18ef] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:17:43.649 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/65/aec7c71bf7d2f5ec448b2e40ebd20d]
Jan-30 13:17:43.653 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:43.653 [Task submitter] INFO  nextflow.Session - [f2/a652f8] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:43.654 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:43.654 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:43.654 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:43.655 [Actor Thread 38] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:46.273 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 188; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/60/da18ef495e51a4552cc2a439693cc5]
Jan-30 13:17:46.280 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:46.280 [Task submitter] INFO  nextflow.Session - [66/1947a0] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:17:46.284 [Actor Thread 31] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:17:46.950 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/f2/a652f85d233386aa6c646ae499680e]
Jan-30 13:17:46.954 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:46.954 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:46.954 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:46.955 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:46.955 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:46.955 [Task submitter] INFO  nextflow.Session - [3a/c0e3be] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:50.213 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/3a/c0e3beba50727a5d86e057ea82f7d1]
Jan-30 13:17:50.217 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:50.217 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:50.217 [Task submitter] INFO  nextflow.Session - [89/321f90] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:50.217 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:50.217 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:50.218 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:50.560 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 197; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/66/1947a09b59ade3e6bc38273cbf84f0]
Jan-30 13:17:50.563 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:17:50.567 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:50.567 [Task submitter] INFO  nextflow.Session - [08/ae9cbd] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:17:52.022 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 181; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/f7/5bfdc7790cd7607580f8249b350912]
Jan-30 13:17:52.027 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:52.027 [Task submitter] INFO  nextflow.Session - [5b/bf34c1] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:17:53.668 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/89/321f902907257471b943c89b415391]
Jan-30 13:17:53.672 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:53.672 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:53.672 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:53.672 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:53.672 [Task submitter] INFO  nextflow.Session - [b3/e5e77c] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:53.673 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:55.436 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 195; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/08/ae9cbdfd963e98310b4737fd3cdeb7]
Jan-30 13:17:55.439 [Actor Thread 31] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:17:55.440 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:55.441 [Task submitter] INFO  nextflow.Session - [08/7f8d94] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:17:56.887 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 190; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/5b/bf34c18540b8bba68b23120af16ae8]
Jan-30 13:17:56.889 [Actor Thread 31] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:17:56.891 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:56.891 [Task submitter] INFO  nextflow.Session - [5e/822f34] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:17:56.963 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/b3/e5e77c86b2f79cc9931059b73c1dd1]
Jan-30 13:17:56.966 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:17:56.967 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:17:56.967 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:17:56.967 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:56.967 [Task submitter] INFO  nextflow.Session - [ec/fd0871] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817)
Jan-30 13:17:56.967 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:17:59.870 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 193; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/08/7f8d94817949d8ab15b73e7656e8ec]
Jan-30 13:17:59.874 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:17:59.874 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:17:59.874 [Task submitter] INFO  nextflow.Session - [2a/1ce657] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:00.424 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/ec/fd0871d6509ea9575e0d062565eaf6]
Jan-30 13:18:00.428 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:00.428 [Task submitter] INFO  nextflow.Session - [05/e4a5f4] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:00.428 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:00.429 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:00.429 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:00.429 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383817, sample:ERR4383817, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383817] size=12
Jan-30 13:18:01.022 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 194; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/5e/822f34b68696c50eddfd7673f60405]
Jan-30 13:18:01.025 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:01.026 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:01.027 [Task submitter] INFO  nextflow.Session - [fe/f789d4] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:03.017 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 182; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/85/4856744f882d0254b1158a433fc48b]
Jan-30 13:18:03.021 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:03.021 [Task submitter] INFO  nextflow.Session - [43/daddc5] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:03.025 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:03.025 [Task submitter] INFO  nextflow.Session - [e7/113aab] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jan-30 13:18:03.026 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jan-30 13:18:04.126 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 186; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/2a/1ce657874395c13c2a91b6eb9aa3d5]
Jan-30 13:18:04.129 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:04.130 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:04.130 [Task submitter] INFO  nextflow.Session - [5b/b015c1] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:04.291 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/05/e4a5f40f057cc1b6d59024ec8a227a]
Jan-30 13:18:04.294 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:04.295 [Task submitter] INFO  nextflow.Session - [5d/6a97ac] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:04.297 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:04.297 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:04.297 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:04.298 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:06.432 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 201; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/fe/f789d4a67f16cbe19b7fdcdeca9bf6]
Jan-30 13:18:06.435 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:06.438 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:06.438 [Task submitter] INFO  nextflow.Session - [ef/5aa379] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:07.783 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/5d/6a97aca4d3aae509f09461286f9a8d]
Jan-30 13:18:07.787 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:07.787 [Task submitter] INFO  nextflow.Session - [d1/dd1d93] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:07.788 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:07.788 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:07.788 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:07.789 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:08.424 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 202; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/43/daddc53d4ac0a91f74120046218b82]
Jan-30 13:18:08.427 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:08.428 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:08.428 [Task submitter] INFO  nextflow.Session - [51/bcf992] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:08.524 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 187; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/e7/113aab5593dfb3d12360d7424956e4]
Jan-30 13:18:08.527 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:08.529 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:08.529 [Task submitter] INFO  nextflow.Session - [f3/f5f311] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:08.629 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 191; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/5b/b015c1619ab2eac232c591c22d4fe3]
Jan-30 13:18:08.632 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:08.633 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:08.633 [Task submitter] INFO  nextflow.Session - [38/5d7d69] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:11.197 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 200; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/ef/5aa379ee98a27b4287fafaf9f0f081]
Jan-30 13:18:11.201 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:11.202 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:11.203 [Task submitter] INFO  nextflow.Session - [63/9cd6d3] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:11.993 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/d1/dd1d93fe7d07f6ffceac3999e057fd]
Jan-30 13:18:11.997 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:11.997 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:11.997 [Task submitter] INFO  nextflow.Session - [e6/9d9a7a] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:11.997 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:11.997 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:11.998 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:13.773 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 198; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/51/bcf9925254b4cd5eb0fe4e53f0d18f]
Jan-30 13:18:13.777 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:13.777 [Task submitter] INFO  nextflow.Session - [36/bb1bd1] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:13.778 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:14.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 192; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/38/5d7d693aee5b7f78a5acc26575dad3]
Jan-30 13:18:14.816 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:14.816 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:14.817 [Task submitter] INFO  nextflow.Session - [73/e53dc6] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:15.117 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 199; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/f3/f5f311ac23c9c698315e18239ee855]
Jan-30 13:18:15.120 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:15.121 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:15.121 [Task submitter] INFO  nextflow.Session - [b6/139e1d] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821)
Jan-30 13:18:15.671 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/e6/9d9a7a466d27d8f4a2026cd0da1bf7]
Jan-30 13:18:15.674 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:15.674 [Task submitter] INFO  nextflow.Session - [8b/253258] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:15.675 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:15.675 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:15.675 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:15.676 [Actor Thread 4] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:15.780 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 189; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/63/9cd6d38b99910a33c8c92221afa53c]
Jan-30 13:18:15.784 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:19.444 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 120; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/8b/253258e366160de7ab4b1a51bb4eb6]
Jan-30 13:18:19.447 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:19.447 [Task submitter] INFO  nextflow.Session - [28/5bb2cb] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:19.448 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:19.448 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:19.448 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:19.450 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:19.672 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 185; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/36/bb1bd1fd31355f704987487065bc00]
Jan-30 13:18:19.676 [Actor Thread 41] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:19.808 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 184; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/73/e53dc6d124b0fedf2ce107e6275850]
Jan-30 13:18:19.811 [Actor Thread 30] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:19.812 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:19.812 [Task submitter] INFO  nextflow.Session - [22/f46713] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (ERR4383817)
Jan-30 13:18:19.945 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 196; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383821); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/b6/139e1dd20b67d9ffbfa8c847335a32]
Jan-30 13:18:19.948 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821, num_intervals:19] size=19
Jan-30 13:18:20.950 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:20.951 [Task submitter] INFO  nextflow.Session - [a7/90ffec] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383821)
Jan-30 13:18:23.429 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 115; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812); status: COMPLETED; exit: 0; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/28/5bb2cb63db273b7c03e5fd5f312ecc]
Jan-30 13:18:23.433 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-30 13:18:23.433 [Task submitter] INFO  nextflow.Session - [01/7f7b29] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383812)
Jan-30 13:18:23.434 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jan-30 13:18:23.434 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-30 13:18:23.434 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jan-30 13:18:23.434 [Actor Thread 31] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:23.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 204; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383821); status: COMPLETED; exit: 3; error: -; workDir: /home/ec2-user/SageMaker/Nextflow/work/a7/90ffec26869807b4a16efc256b6e03]
Jan-30 13:18:23.634 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383821); work-dir=/home/ec2-user/SageMaker/Nextflow/work/a7/90ffec26869807b4a16efc256b6e03
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383821)` terminated with an error exit status (3)
Jan-30 13:18:23.648 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383821)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383821)` terminated with an error exit status (3)


Command executed:

  gatk --java-options "-Xmx3276M -XX:-UsePerfData" \
      GatherBQSRReports \
      --input ERR4383821_chr3_1-198295559.recal.table --input ERR4383821_chr11_1-135086622.recal.table --input ERR4383821_chr8_1-145138636.recal.table --input ERR4383821_chr4_1-190214555.recal.table --input ERR4383821_chr17_1-83257441.recal.table --input ERR4383821_chr7_1-159345973.recal.table --input ERR4383821_chr2_1-242193529.recal.table --input ERR4383821_chrY_1-57227415.recal.table --input ERR4383821_chr20_KI270871v1_alt_1-58661.recal.table --input ERR4383821_chr13_1-114364328.recal.table --input ERR4383821_chr5_1-181538259.recal.table --input ERR4383821_chr19_1-58617616.recal.table --input ERR4383821_chr10_1-133797422.recal.table --input ERR4383821_chr6_1-170805979.recal.table --input ERR4383821_chr12_1-133275309.recal.table --input ERR4383821_chr15_1-101991189.recal.table --input ERR4383821_chr1_1-248956422.recal.table --input ERR4383821_chr21_1-46709983.recal.table --input ERR4383821_chr9_1-138394717.recal.table \
      --output ERR4383821.recal.table \
      --tmp-dir . \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  3

Command output:
  (empty)

Command error:
  Using GATK jar /usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar
  Running:
      java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx3276M -XX:-UsePerfData -jar /usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar GatherBQSRReports --input ERR4383821_chr3_1-198295559.recal.table --input ERR4383821_chr11_1-135086622.recal.table --input ERR4383821_chr8_1-145138636.recal.table --input ERR4383821_chr4_1-190214555.recal.table --input ERR4383821_chr17_1-83257441.recal.table --input ERR4383821_chr7_1-159345973.recal.table --input ERR4383821_chr2_1-242193529.recal.table --input ERR4383821_chrY_1-57227415.recal.table --input ERR4383821_chr20_KI270871v1_alt_1-58661.recal.table --input ERR4383821_chr13_1-114364328.recal.table --input ERR4383821_chr5_1-181538259.recal.table --input ERR4383821_chr19_1-58617616.recal.table --input ERR4383821_chr10_1-133797422.recal.table --input ERR4383821_chr6_1-170805979.recal.table --input ERR4383821_chr12_1-133275309.recal.table --input ERR4383821_chr15_1-101991189.recal.table --input ERR4383821_chr1_1-248956422.recal.table --input ERR4383821_chr21_1-46709983.recal.table --input ERR4383821_chr9_1-138394717.recal.table --output ERR4383821.recal.table --tmp-dir .
  13:18:23.019 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  13:18:23.121 INFO  GatherBQSRReports - ------------------------------------------------------------
  13:18:23.123 INFO  GatherBQSRReports - The Genome Analysis Toolkit (GATK) v4.5.0.0
  13:18:23.124 INFO  GatherBQSRReports - For support and documentation go to https://software.broadinstitute.org/gatk/
  13:18:23.124 INFO  GatherBQSRReports - Executing as root@ded6b0abc527 on Linux v5.10.230-223.885.amzn2.x86_64 amd64
  13:18:23.124 INFO  GatherBQSRReports - Java runtime: OpenJDK 64-Bit Server VM v17.0.10-internal+0-adhoc..src
  13:18:23.124 INFO  GatherBQSRReports - Start Date/Time: January 30, 2025 at 1:18:22 PM GMT
  13:18:23.124 INFO  GatherBQSRReports - ------------------------------------------------------------
  13:18:23.124 INFO  GatherBQSRReports - ------------------------------------------------------------
  13:18:23.125 INFO  GatherBQSRReports - HTSJDK Version: 4.1.0
  13:18:23.125 INFO  GatherBQSRReports - Picard Version: 3.1.1
  13:18:23.125 INFO  GatherBQSRReports - Built for Spark Version: 3.5.0
  13:18:23.125 INFO  GatherBQSRReports - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  13:18:23.125 INFO  GatherBQSRReports - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  13:18:23.126 INFO  GatherBQSRReports - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  13:18:23.126 INFO  GatherBQSRReports - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  13:18:23.126 INFO  GatherBQSRReports - Deflater: IntelDeflater
  13:18:23.126 INFO  GatherBQSRReports - Inflater: IntelInflater
  13:18:23.126 INFO  GatherBQSRReports - GCS max retries/reopens: 20
  13:18:23.126 INFO  GatherBQSRReports - Requester pays: disabled
  13:18:23.127 INFO  GatherBQSRReports - Initializing engine
  13:18:23.127 INFO  GatherBQSRReports - Done initializing engine
  13:18:23.179 INFO  GatherBQSRReports - Shutting down engine
  [January 30, 2025 at 1:18:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports done. Elapsed time: 0.00 minutes.
  Runtime.totalMemory()=104857600
  org.broadinstitute.hellbender.exceptions.GATKException: there is no usable data in any input file
  	at org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.lambda$gatherReports$2(RecalibrationReport.java:119)
  	at java.base/java.util.Optional.orElseThrow(Optional.java:403)
  	at org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.gatherReports(RecalibrationReport.java:119)
  	at org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.gatherReportsIntoOneFile(RecalibrationReport.java:85)
  	at org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports.doWork(GatherBQSRReports.java:37)
  	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
  	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
  	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
  	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
  	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
  	at org.broadinstitute.hellbender.Main.main(Main.java:306)

Work dir:
  /home/ec2-user/SageMaker/Nextflow/work/a7/90ffec26869807b4a16efc256b6e03

Container:
  quay.io/biocontainers/gatk4:4.5.0.0--py36hdfd78af_0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Jan-30 13:18:23.651 [TaskFinalizer-3] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Jan-30 13:18:23.653 [TaskFinalizer-3] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
Jan-30 13:18:23.653 [main] DEBUG nextflow.Session - Session await > all processes finished
Jan-30 13:18:23.661 [Actor Thread 33] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:bam, id:ERR4383812] size=12
Jan-30 13:18:23.665 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jan-30 13:18:23.665 [Actor Thread 29] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jan-30 13:18:23.667 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-30 13:18:23.668 [Actor Thread 15] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.006 s; total time: 0.006 s
Jan-30 13:18:23.668 [Actor Thread 39] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jan-30 13:18:23.669 [Actor Thread 1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-30 13:18:23.669 [Actor Thread 45] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-30 13:18:23.676 [Actor Thread 15] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ec2-user/SageMaker/Nextflow/work/collect-file/b42afdbb03a989967cf2803833b8f24d
Jan-30 13:18:23.676 [Actor Thread 38] ERROR nextflow.extension.OperatorImpl - @unknown
nextflow.exception.AbortOperationException: Join mismatch for the following entries: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821] values=
	at nextflow.extension.JoinOp.checkForMismatch(JoinOp.groovy:290)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
	at nextflow.extension.JoinOp$_handler_closure2.doCall(JoinOp.groovy:135)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:257)
	at groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324)
	at groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59)
	at jdk.internal.reflect.GeneratedMethodAccessor133.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:633)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:624)
	at groovyx.gpars.actor.Actor.callDynamic(Actor.java:369)
	at groovyx.gpars.actor.Actor.handleTermination(Actor.java:320)
	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:86)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:834)
Jan-30 13:18:23.679 [Actor Thread 15] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-15187094239777064714
Jan-30 13:18:23.681 [Actor Thread 1] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 8; slices: 1; internal sort time: 0.006 s; external sort time: 0.001 s; total time: 0.007 s
Jan-30 13:18:23.681 [Actor Thread 38] DEBUG nextflow.Session - Session aborted -- Cause: Join mismatch for the following entries: key=[patient:ERR4383821, sample:ERR4383821, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383821] values=
Jan-30 13:18:23.684 [Actor Thread 1] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ec2-user/SageMaker/Nextflow/work/collect-file/19000d7b49053881f2d7cbb39a541863
Jan-30 13:18:23.686 [Actor Thread 1] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-1539771990168126203
Jan-30 13:18:23.725 [Actor Thread 38] DEBUG nextflow.Session - The following nodes are still active:
  [operator] join

Jan-30 13:18:23.732 [Actor Thread 38] DEBUG nextflow.Session - 
Thread[pool-2-thread-32,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-2,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 51,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 31,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-1,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 50,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 5,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-5,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 6,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-7,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-18,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-21,5,main]
  java.base@11.0.9.1-internal/java.lang.Object.wait(Native Method)
  java.base@11.0.9.1-internal/java.lang.Object.wait(Object.java:328)
  java.base@11.0.9.1-internal/java.lang.ProcessImpl.waitFor(ProcessImpl.java:495)
  app//nextflow.executor.local.LocalTaskHandler$_submit_closure1.doCall(LocalTaskHandler.groovy:109)
  app//nextflow.executor.local.LocalTaskHandler$_submit_closure1.call(LocalTaskHandler.groovy)
  app//groovy.lang.Closure.run(Closure.java:505)
  java.base@11.0.9.1-internal/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
  java.base@11.0.9.1-internal/java.util.concurrent.FutureTask.run(FutureTask.java:264)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-10,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Task submitter,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2211)
  app//nextflow.processor.TaskPollingMonitor.awaitSlots(TaskPollingMonitor.groovy:399)
  app//nextflow.processor.TaskPollingMonitor.submitLoop(TaskPollingMonitor.groovy:420)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  java.base@11.0.9.1-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@11.0.9.1-internal/java.lang.reflect.Method.invoke(Method.java:566)
  app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
  app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
  app//groovy.lang.Closure.call(Closure.java:433)
  app//groovy.lang.Closure.call(Closure.java:412)
  app//groovy.lang.Closure.run(Closure.java:505)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 47,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-8,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-7,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[process reaper,10,system]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-3,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-4,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[main,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  app//nextflow.util.Barrier$_awaitCompletion_closure3.doCall(Barrier.groovy:92)
  app//nextflow.util.Barrier$_awaitCompletion_closure3.call(Barrier.groovy)
  app//nextflow.extension.Bolts.withLock(Bolts.groovy:337)
  app//nextflow.extension.Bolts.withLock(Bolts.groovy)
  app//nextflow.util.Barrier.awaitCompletion(Barrier.groovy:89)
  app//nextflow.Session.await(Session.groovy:679)
  app//nextflow.script.ScriptRunner.await(ScriptRunner.groovy:256)
  app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:144)
  app//nextflow.cli.CmdRun.run(CmdRun.groovy:376)
  app//nextflow.cli.Launcher.run(Launcher.groovy:503)
  app//nextflow.cli.Launcher.main(Launcher.groovy:658)

Thread[process reaper,10,system]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-9,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-6,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-26,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-28,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[process reaper,10,system]
  java.base@11.0.9.1-internal/java.lang.ProcessHandleImpl.waitForProcessExit0(Native Method)
  java.base@11.0.9.1-internal/java.lang.ProcessHandleImpl$1.run(ProcessHandleImpl.java:138)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-9,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 8,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 10,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Thread-4,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:513)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:675)
  app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  java.base@11.0.9.1-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@11.0.9.1-internal/java.lang.reflect.Method.invoke(Method.java:566)
  app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
  app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
  app//groovy.lang.Closure.call(Closure.java:433)
  app//groovy.lang.Closure.call(Closure.java:412)
  app//groovy.lang.Closure.run(Closure.java:505)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 33,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 25,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-12,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-7,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-5,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 46,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-1,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Finalizer,8,system]
  java.base@11.0.9.1-internal/java.lang.Object.wait(Native Method)
  java.base@11.0.9.1-internal/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
  java.base@11.0.9.1-internal/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
  java.base@11.0.9.1-internal/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:170)

Thread[Signal Dispatcher,9,system]

Thread[AnsiLogObserver,5,main]
  java.base@11.0.9.1-internal/java.lang.Object.wait(Native Method)
  app//nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:185)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  java.base@11.0.9.1-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@11.0.9.1-internal/java.lang.reflect.Method.invoke(Method.java:566)
  app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
  app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
  app//groovy.lang.Closure.call(Closure.java:433)
  app//groovy.lang.Closure.call(Closure.java:412)
  app//groovy.lang.Closure.run(Closure.java:505)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 26,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 15,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 38,5,main]
  java.base@11.0.9.1-internal/java.lang.Thread.dumpThreads(Native Method)
  java.base@11.0.9.1-internal/java.lang.Thread.getAllStackTraces(Thread.java:1658)
  app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188)
  app//nextflow.Session.abort(Session.groovy:800)
  java.base@11.0.9.1-internal/java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(DirectMethodHandle$Holder)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x0000000800504c40.invoke(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001ad840.guardWithCatch(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001ad040.reinvoke(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001ad440.guard(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001ad040.reinvoke(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001ad440.guard(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001ad040.reinvoke(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x0000000800245840.invoke(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x0000000800196040.invokeExact_MT(LambdaForm$MH)
  app//org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$DMH/0x0000000800175840.invokeStatic(LambdaForm$DMH)
  java.base@11.0.9.1-internal/java.lang.invoke.LambdaForm$MH/0x00000008001aec40.invoke(LambdaForm$MH)
  java.base@11.0.9.1-internal/java.lang.invoke.Invokers$Holder.linkToCallSite(Invokers$Holder)
  app//nextflow.extension.DataflowHelper$3.afterStop(DataflowHelper.groovy:261)
  app//groovyx.gpars.dataflow.operator.DataflowProcessor.fireAfterStop(DataflowProcessor.java:324)
  app//groovyx.gpars.dataflow.operator.DataflowProcessorActor.afterStop(DataflowProcessorActor.java:59)
  jdk.internal.reflect.GeneratedMethodAccessor133.invoke(Unknown Source)
  java.base@11.0.9.1-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@11.0.9.1-internal/java.lang.reflect.Method.invoke(Method.java:566)
  app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
  app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
  app//org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:633)
  app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:624)
  app//groovyx.gpars.actor.Actor.callDynamic(Actor.java:369)
  app//groovyx.gpars.actor.Actor.handleTermination(Actor.java:320)
  app//groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:86)
  app//groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 28,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[process reaper,10,system]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-9,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 23,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 20,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 42,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 49,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[process reaper,10,system]
  java.base@11.0.9.1-internal/java.lang.ProcessHandleImpl.waitForProcessExit0(Native Method)
  java.base@11.0.9.1-internal/java.lang.ProcessHandleImpl$1.run(ProcessHandleImpl.java:138)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-8,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-20,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-8,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 11,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-4,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-10,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-15,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[process reaper,10,system]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 16,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Common-Cleaner,8,InnocuousThreadGroup]
  java.base@11.0.9.1-internal/java.lang.Object.wait(Native Method)
  java.base@11.0.9.1-internal/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
  java.base@11.0.9.1-internal/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:148)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)
  java.base@11.0.9.1-internal/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:134)

Thread[Actor Thread 12,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-11,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-6,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-2,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 44,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-10,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Reference Handler,10,system]
  java.base@11.0.9.1-internal/java.lang.ref.Reference.waitForReferencePendingList(Native Method)
  java.base@11.0.9.1-internal/java.lang.ref.Reference.processPendingReferences(Reference.java:241)
  java.base@11.0.9.1-internal/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:213)

Thread[PublishDir-2,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-1,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 39,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-3,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 41,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 29,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-19,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-4,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 34,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-27,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 43,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 22,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 27,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-6,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 4,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 45,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-30,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 13,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-24,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 48,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 17,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-23,5,main]
  java.base@11.0.9.1-internal/java.lang.Object.wait(Native Method)
  java.base@11.0.9.1-internal/java.lang.Object.wait(Object.java:328)
  java.base@11.0.9.1-internal/java.lang.ProcessImpl.waitFor(ProcessImpl.java:495)
  app//nextflow.executor.local.LocalTaskHandler$_submit_closure1.doCall(LocalTaskHandler.groovy:109)
  app//nextflow.executor.local.LocalTaskHandler$_submit_closure1.call(LocalTaskHandler.groovy)
  app//groovy.lang.Closure.run(Closure.java:505)
  java.base@11.0.9.1-internal/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
  java.base@11.0.9.1-internal/java.util.concurrent.FutureTask.run(FutureTask.java:264)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 1,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Task monitor,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2211)
  app//nextflow.processor.TaskPollingMonitor$_await_closure5.doCall(TaskPollingMonitor.groovy:529)
  app//nextflow.processor.TaskPollingMonitor$_await_closure5.call(TaskPollingMonitor.groovy)
  app//nextflow.extension.Bolts.withLock(Bolts.groovy:337)
  app//nextflow.extension.Bolts.withLock(Bolts.groovy)
  app//nextflow.processor.TaskPollingMonitor.await(TaskPollingMonitor.groovy:528)
  app//nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:453)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  java.base@11.0.9.1-internal/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  java.base@11.0.9.1-internal/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.base@11.0.9.1-internal/java.lang.reflect.Method.invoke(Method.java:566)
  app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
  app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
  app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
  app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
  app//org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
  app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
  app//org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
  app//nextflow.processor.TaskPollingMonitor$_start_closure2.doCall(TaskPollingMonitor.groovy:318)
  app//nextflow.processor.TaskPollingMonitor$_start_closure2.call(TaskPollingMonitor.groovy)
  app//groovy.lang.Closure.run(Closure.java:505)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 52,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-16,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-22,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 30,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Attach Listener,9,system]

Thread[pool-2-thread-31,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 7,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-25,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 24,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 37,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[PublishDir-5,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-13,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 19,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-29,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[TaskFinalizer-3,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 2,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-14,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[JGit-FileStoreAttributeReader-1,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[pool-2-thread-17,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.park(LockSupport.java:194)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2081)
  java.base@11.0.9.1-internal/java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:433)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Thread[Actor Thread 3,5,main]
  java.base@11.0.9.1-internal/jdk.internal.misc.Unsafe.park(Native Method)
  java.base@11.0.9.1-internal/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361)
  java.base@11.0.9.1-internal/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
  java.base@11.0.9.1-internal/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  java.base@11.0.9.1-internal/java.lang.Thread.run(Thread.java:834)

Jan-30 13:18:23.732 [Actor Thread 38] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
Jan-30 13:18:23.732 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-30 13:18:23.733 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jan-30 13:18:23.737 [Actor Thread 38] ERROR nextflow.extension.DataflowHelper - @unknown
java.lang.IllegalStateException: A DataflowVariable can only be assigned once. Use bind() to allow for equal values to be passed into already-bound variables.
	at groovyx.gpars.dataflow.expression.DataflowExpression.bindUnique(DataflowExpression.java:383)
	at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:88)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:834)
Jan-30 13:18:23.742 [main] INFO  nextflow.Nextflow - -[nf-core/sarek] Pipeline completed with errors-
Jan-30 13:18:23.745 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (2)
Jan-30 13:18:23.755 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=82; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=5; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=2; succeedDuration=42m 39s; failedDuration=5.2s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=9; peakCpus=43; peakMemory=72 GB; ]
Jan-30 13:18:23.755 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jan-30 13:18:23.756 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jan-30 13:18:24.254 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jan-30 13:18:24.417 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jan-30 13:18:24.446 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-prov@1.2.2'
Jan-30 13:18:24.446 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-prov
Jan-30 13:18:24.446 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.1.1'
Jan-30 13:18:24.446 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema
Jan-30 13:18:24.448 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye