May-16 12:40:30.693 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -r dev -latest --input sample-sheet.csv --outdir sarek-test-jointVC -profile docker --max_time 336.h --max_cpus 64 --max_memory 256.GB --fasta /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa --fasta_fai /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa.fai --dict /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.dict --save_mapped --save_output_as_bam --vep_cache /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae --bwa /home/ubuntu/reproducible-sarek-error/bwa-index --igenomes_ignore --genome null --joint_germline --tools haplotypecaller,vep --dbsnp /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz --dbsnp_tbi /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz.tbi --dbsnp_vqsr '--resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz' --known_indels /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz --known_indels_tbi /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz.tbi --known_indels_vqsr '--resource:ensemblsnps,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_indels.vcf.gz' --known_snps /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz --known_snps_tbi /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz.tbi --known_snps_vqsr '--resource:ensemblindels,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_snps.vcf.gz' --vep_out_format tab --vep_include_fasta --email alex.mizeranschi@gmail.com
May-16 12:40:30.804 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.1
May-16 12:40:30.836 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ubuntu/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2
May-16 12:40:30.850 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-16 12:40:30.852 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-16 12:40:30.856 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
May-16 12:40:30.870 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
May-16 12:40:30.894 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ubuntu/.nextflow/scm
May-16 12:40:32.834 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git
May-16 12:40:32.872 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
May-16 12:40:32.887 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git
May-16 12:40:32.888 [main] INFO  nextflow.cli.CmdRun - Pulling nf-core/sarek ...
May-16 12:40:32.888 [main] DEBUG nextflow.scm.AssetManager - Pull pipeline nf-core/sarek  -- Using local path: /home/ubuntu/.nextflow/assets/nf-core/sarek
May-16 12:40:35.211 [main] INFO  nextflow.cli.CmdRun -  Fast-forward
May-16 12:40:35.233 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config
May-16 12:40:35.235 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config
May-16 12:40:35.259 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
May-16 12:40:39.098 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, uge, rosalind_uge, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, use_gatk_spark, eddie, medair, alignment_to_fastq, apptainer, bi, bigpurple, sbc_sharc, adcra, cedars, tools, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, targeted, icr_davros, ceres, save_bam_mapped, munin, arm, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, cheaha, xanadu, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, dkfz, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, psmn, umi, eva, markduplicates_bam, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac]
May-16 12:40:39.158 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
May-16 12:40:39.159 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [prickly_leavitt] DSL2 - revision: 31170119e3 [dev]
May-16 12:40:39.160 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
May-16 12:40:39.160 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
May-16 12:40:39.163 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/ubuntu/.nextflow/secrets/store.json
May-16 12:40:39.166 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@21084a6d] - activable => nextflow.secret.LocalSecretsProvider@21084a6d
May-16 12:40:39.241 [main] DEBUG nextflow.Session - Session UUID: e771778c-b2f4-4b96-a82a-686726f0ee52
May-16 12:40:39.241 [main] DEBUG nextflow.Session - Run name: prickly_leavitt
May-16 12:40:39.242 [main] DEBUG nextflow.Session - Executor pool size: 64
May-16 12:40:39.255 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-16 12:40:39.281 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.1 build 5866
  Created: 15-04-2023 06:51 UTC (09:51 EEST)
  System: Linux 5.15.0-69-generic
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS
  Encoding: UTF-8 (UTF-8)
  Process: 1592677@bioinfosrv [10.252.254.98]
  CPUs: 64 - Mem: 251.7 GB (100.4 GB) - Swap: 0 (0)
May-16 12:40:39.301 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/reproducible-sarek-error/work [ext2/ext3]
May-16 12:40:39.302 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ubuntu/.nextflow/assets/nf-core/sarek/bin
May-16 12:40:39.315 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
May-16 12:40:39.328 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-16 12:40:39.434 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-16 12:40:39.447 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000
May-16 12:40:39.527 [main] DEBUG nextflow.Session - Session start
May-16 12:40:39.539 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ubuntu/reproducible-sarek-error/sarek-test-jointVC/pipeline_info/execution_trace_2023-05-16_12-40-36.txt
May-16 12:40:39.561 [main] DEBUG nextflow.Session - Using default localLib path: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib
May-16 12:40:39.567 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib
May-16 12:40:39.568 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar
May-16 12:40:41.312 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-16 12:40:41.429 [main] INFO  nextflow.Nextflow - 

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek v3.2dev-g3117011
------------------------------------------------------
Core Nextflow options
  revision          : dev
  runName           : prickly_leavitt
  containerEngine   : docker
  launchDir         : /home/ubuntu/reproducible-sarek-error
  workDir           : /home/ubuntu/reproducible-sarek-error/work
  projectDir        : /home/ubuntu/.nextflow/assets/nf-core/sarek
  userName          : ubuntu
  profile           : docker
  configFiles       : /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config

Input/output options
  input             : sample-sheet.csv
  outdir            : sarek-test-jointVC

Main options
  tools             : haplotypecaller,vep

Preprocessing
  save_mapped       : true
  save_output_as_bam: true

Variant Calling
  joint_germline    : true

Annotation
  vep_include_fasta : true
  vep_cache         : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae
  vep_out_format    : tab

Reference genome options
  genome            : null
  bwa               : /home/ubuntu/reproducible-sarek-error/bwa-index
  dbsnp             : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz
  dbsnp_tbi         : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.vcf.gz.tbi
  dbsnp_vqsr        : --resource:ensemblvcf,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae.vcf.gz
  dict              : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.dict
  fasta             : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa
  fasta_fai         : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae.R64-1-1-chr.fa.fai
  known_indels      : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz
  known_indels_tbi  : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_indels.vcf.gz.tbi
  known_indels_vqsr : --resource:ensemblsnps,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_indels.vcf.gz
  known_snps        : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz
  known_snps_tbi    : /home/ubuntu/reproducible-sarek-error/Saccharomyces_cerevisiae_snps.vcf.gz.tbi
  known_snps_vqsr   : --resource:ensemblindels,known=false,training=true,truth=true,prior=10.0 Saccharomyces_cerevisiae_snps.vcf.gz
  igenomes_base     : s3://ngi-igenomes/igenomes
  igenomes_ignore   : true

Max job request options
  max_cpus          : 64
  max_memory        : 256.GB
  max_time          : 336.h

Generic options
  email             : alex.mizeranschi@gmail.com

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/sarek for your analysis please cite:

* The pipeline
  https://doi.org/10.12688/f1000research.16665.2
  https://doi.org/10.5281/zenodo.4468605

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

* Software dependencies
  https://github.com/nf-core/sarek/blob/master/CITATIONS.md
------------------------------------------------------
May-16 12:41:09.540 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
May-16 12:41:09.544 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
May-16 12:41:09.557 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.557 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.564 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
May-16 12:41:09.570 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=251.7 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
May-16 12:41:09.652 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
May-16 12:41:09.653 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
May-16 12:41:09.671 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.671 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.680 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
May-16 12:41:09.681 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
May-16 12:41:09.685 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.685 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.709 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
May-16 12:41:09.710 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
May-16 12:41:09.714 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.714 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.719 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
May-16 12:41:09.720 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
May-16 12:41:09.722 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.722 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.733 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
May-16 12:41:09.734 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
May-16 12:41:09.739 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.740 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.765 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
May-16 12:41:09.765 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
May-16 12:41:09.766 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
May-16 12:41:09.766 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
May-16 12:41:09.770 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.770 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
May-16 12:41:09.787 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
May-16 12:41:09.787 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
May-16 12:41:09.788 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
May-16 12:41:09.791 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.791 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.801 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
May-16 12:41:09.801 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
May-16 12:41:09.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
May-16 12:41:09.802 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
May-16 12:41:09.804 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.804 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.812 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
May-16 12:41:09.812 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
May-16 12:41:09.813 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
May-16 12:41:09.813 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
May-16 12:41:09.815 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.815 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
May-16 12:41:09.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
May-16 12:41:09.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
May-16 12:41:09.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
May-16 12:41:09.826 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.826 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.954 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
May-16 12:41:09.957 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.957 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
May-16 12:41:09.963 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
May-16 12:41:09.965 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.965 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:09.996 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
May-16 12:41:09.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
May-16 12:41:09.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
May-16 12:41:09.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
May-16 12:41:09.999 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:09.999 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
May-16 12:41:10.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
May-16 12:41:10.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
May-16 12:41:10.009 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.009 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.028 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
May-16 12:41:10.029 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
May-16 12:41:10.032 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.032 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.040 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
May-16 12:41:10.041 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
May-16 12:41:10.042 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.043 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.047 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
May-16 12:41:10.048 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
May-16 12:41:10.050 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.050 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
May-16 12:41:10.054 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
May-16 12:41:10.055 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.055 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
May-16 12:41:10.073 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
May-16 12:41:10.074 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.074 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.079 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
May-16 12:41:10.080 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
May-16 12:41:10.081 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.081 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
May-16 12:41:10.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
May-16 12:41:10.085 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.085 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.092 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
May-16 12:41:10.092 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
May-16 12:41:10.093 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.093 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.108 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC
May-16 12:41:10.108 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC
May-16 12:41:10.111 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.111 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.118 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP
May-16 12:41:10.118 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP
May-16 12:41:10.120 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.120 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
May-16 12:41:10.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
May-16 12:41:10.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
May-16 12:41:10.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
May-16 12:41:10.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
May-16 12:41:10.136 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.136 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.141 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
May-16 12:41:10.141 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
May-16 12:41:10.142 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
May-16 12:41:10.142 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
May-16 12:41:10.142 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
May-16 12:41:10.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.143 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.148 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
May-16 12:41:10.148 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
May-16 12:41:10.148 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
May-16 12:41:10.150 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.150 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.167 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.168 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.168 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.169 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.169 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.175 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.176 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.177 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.177 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
May-16 12:41:10.185 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
May-16 12:41:10.185 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAM_TO_CRAM_MAPPING` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
May-16 12:41:10.186 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.186 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
May-16 12:41:10.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
May-16 12:41:10.218 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
May-16 12:41:10.219 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.219 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.229 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES
May-16 12:41:10.229 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES
May-16 12:41:10.229 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:INDEX_MARKDUPLICATES` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES
May-16 12:41:10.231 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.231 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.239 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
May-16 12:41:10.239 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
May-16 12:41:10.240 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.240 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.254 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
May-16 12:41:10.255 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
May-16 12:41:10.256 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.256 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.271 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM
May-16 12:41:10.272 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
May-16 12:41:10.272 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
May-16 12:41:10.272 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
May-16 12:41:10.273 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.273 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.286 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
May-16 12:41:10.286 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
May-16 12:41:10.287 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
May-16 12:41:10.287 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.287 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
May-16 12:41:10.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
May-16 12:41:10.296 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
May-16 12:41:10.296 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.297 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.314 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
May-16 12:41:10.314 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
May-16 12:41:10.315 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
May-16 12:41:10.316 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.316 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
May-16 12:41:10.325 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
May-16 12:41:10.326 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.326 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.331 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
May-16 12:41:10.332 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
May-16 12:41:10.332 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM` matches process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
May-16 12:41:10.333 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.333 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.345 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
May-16 12:41:10.345 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
May-16 12:41:10.346 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.346 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
May-16 12:41:10.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
May-16 12:41:10.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
May-16 12:41:10.356 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.356 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
May-16 12:41:10.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
May-16 12:41:10.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM_RECAL` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
May-16 12:41:10.371 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.371 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
May-16 12:41:10.399 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_HAPLOTYPECALLER` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
May-16 12:41:10.400 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.400 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
May-16 12:41:10.415 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
May-16 12:41:10.415 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_HAPLOTYPECALLER` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
May-16 12:41:10.416 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.416 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.428 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.429 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.429 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.435 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.436 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.436 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.456 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
May-16 12:41:10.457 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CNNSCOREVARIANTS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
May-16 12:41:10.458 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.458 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.465 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
May-16 12:41:10.465 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FILTERVARIANTTRANCHES` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
May-16 12:41:10.466 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.466 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT
May-16 12:41:10.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GENOMICSDBIMPORT` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT
May-16 12:41:10.482 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.482 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS
May-16 12:41:10.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_GENOTYPEGVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS
May-16 12:41:10.489 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.489 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT
May-16 12:41:10.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT
May-16 12:41:10.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_SORT` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT
May-16 12:41:10.493 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT
May-16 12:41:10.494 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.494 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS
May-16 12:41:10.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS
May-16 12:41:10.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_GENOTYPEGVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS
May-16 12:41:10.501 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.501 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.509 [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_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_INDEL
May-16 12:41:10.509 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VARIANTRECALIBRATOR_INDEL` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_INDEL
May-16 12:41:10.510 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.510 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.514 [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_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_SNP
May-16 12:41:10.514 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VARIANTRECALIBRATOR_SNP` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_SNP
May-16 12:41:10.515 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.515 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.528 [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_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_SNP
May-16 12:41:10.528 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYVQSR_SNP` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_SNP
May-16 12:41:10.529 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.529 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.532 [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_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_INDEL
May-16 12:41:10.533 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_APPLYVQSR_INDEL` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_INDEL
May-16 12:41:10.533 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.534 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.538 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_VQSR
May-16 12:41:10.538 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_VQSR
May-16 12:41:10.539 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_VQSR` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_VQSR
May-16 12:41:10.539 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.539 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.573 [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
May-16 12:41:10.574 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
May-16 12:41:10.574 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_STATS` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
May-16 12:41:10.575 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.575 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.585 [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
May-16 12:41:10.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
May-16 12:41:10.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
May-16 12:41:10.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_COUNT` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
May-16 12:41:10.587 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.608 [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
May-16 12:41:10.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
May-16 12:41:10.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
May-16 12:41:10.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_QUAL` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
May-16 12:41:10.610 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.610 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.631 [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
May-16 12:41:10.631 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
May-16 12:41:10.631 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
May-16 12:41:10.632 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_SUMMARY` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
May-16 12:41:10.633 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.633 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.676 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP
May-16 12:41:10.677 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ENSEMBLVEP_VEP` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP
May-16 12:41:10.677 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.678 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.683 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
May-16 12:41:10.684 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
May-16 12:41:10.684 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
May-16 12:41:10.684 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.684 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.703 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
May-16 12:41:10.703 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
May-16 12:41:10.703 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
May-16 12:41:10.704 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.704 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC
May-16 12:41:10.758 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC
May-16 12:41:10.759 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-16 12:41:10.759 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-16 12:41:10.768 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKEGRAPH, CONTROLFREEC_MAKEGRAPH, SAMTOOLS_VIEW_MAP_MAP, SVDB_MERGE, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS, MERGE_GENOTYPEGVCFS, SAMTOOLS_MERGE, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_VQSR, BWA_MEM, GATK4_APPLYBQSR_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE, BUILD_INTERVALS, ADD_INFO_TO_VCF, SAMTOOLS_VIEW_UNMAP_UNMAP, FILTERVARIANTTRANCHES, CAT_FASTQ, CONTROLFREEC_FREEC2CIRCOS, SAMTOOLS_STATS, INDEX_MERGE_BAM, MUTECT2, GATK4_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX, NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR, TABIX_EXT_VCF, VCFTOOLS, NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX, FASTQC, TABIX_TABIX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM, MULTIQC, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY, TABIX_GERMLINE_RESOURCE, ASSESS_SIGNIFICANCE, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT, CALLUMICONSENSUS, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER, TABIX_KNOWN_SNPS, CAT_CAT, NFCORE_SAREK:SAREK:FASTQC, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON, GATHERPILEUPSUMMARIES_NORMAL, SAMTOOLS_FAIDX, MERGE_BAM, STRELKA_GERMLINE, TIDDIT_SV, GETPILEUPSUMMARIES_TUMOR, STRELKA_SINGLE, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES, SAMTOOLS_BAM2FQ, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP, BWAMEM2_MEM, VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE, UNZIP_ALLELES, BCFTOOLS_STATS, GATK4_GETPILEUPSUMMARIES, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES, LEARNREADORIENTATIONMODEL, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM, GATK4_VARIANTRECALIBRATOR, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS, FASTP, NFCORE_SAREK:SAREK:CRAM_TO_BAM, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT, MERGE_FREEBAYES, MSISENSORPRO_SCAN, GATK4_MERGEVCFS, GATHERPILEUPSUMMARIES_TUMOR, TABIX_BGZIPTABIX_INTERVAL_SPLIT, UNTAR, MERGE_DEEPVARIANT_VCF, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_INDEL, CNVKIT_REFERENCE, ENSEMBLVEP_VEP, FREEC2BED, UNZIP_LOCI, GATK4_FILTERVARIANTTRANCHES, TABIX_KNOWN_INDELS, SNPEFF_SNPEFF, CREATE_INTERVALS_BED, BAM_TO_CRAM, GROUPREADSBYUMI, NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN, BAM_TO_CRAM_MAPPING, FASTQTOBAM, CONTROLFREEC_FREEC, NFCORE_SAREK:SAREK:MULTIQC, BWAMEM1_MEM, CRAM_TO_BAM, GATK4_ESTIMATELIBRARYCOMPLEXITY, GATK4_APPLYVQSR_SNP, GATK4_APPLYBQSR, GATK4_BASERECALIBRATOR, VCFTOOLS_TSTV_QUAL, GERMLINE_VCFS_CONCAT, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM, NFCORE_SAREK:SAREK:FASTP, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS, TABIX_DBSNP, FILTERMUTECTCALLS, CNNSCOREVARIANTS, SNPEFF_DOWNLOAD, MANTA_GERMLINE, GATK4_LEARNREADORIENTATIONMODEL, BWA_INDEX, INDEX_MARKDUPLICATES, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_SNP, GERMLINE_VCFS_CONCAT_SORT, MERGE_HAPLOTYPECALLER, STRELKA_SOMATIC, FREEC_SOMATIC, GATK4_MUTECT2, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR, VARIANTRECALIBRATOR_INDEL, CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM, FGBIO_FASTQTOBAM, ENSEMBLVEP_DOWNLOAD, CRAM_TO_BAM_RECAL, GATK4_GATHERBQSRREPORTS, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL, TABIX_BGZIPTABIX, GATK4_MARKDUPLICATES_SPARK, GATK4_CREATESEQUENCEDICTIONARY, CALCULATECONTAMINATION, MERGE_DEEPVARIANT_GVCF, COLLATE_FASTQ_MAP, TABIX_VC_FREEBAYES, MOSDEPTH, MERGE_STRELKA_INDELS, COLLATE_FASTQ_UNMAP, UNZIP, UNZIP_GC, VCFTOOLS_TSTV_COUNT, GATK4_MERGEMUTECTSTATS, CAT_MPILEUP, CONTROLFREEC_ASSESSSIGNIFICANCE, BWAMEM2_INDEX, MANTA_TUMORONLY, MERGE_STRELKA_SNVS, SAMTOOLS_VIEW_MAP_UNMAP, MERGE_STRELKA, NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM, BCFTOOLS_CONCAT, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM, SAMTOOLS_INDEX, GATK4_CNNSCOREVARIANTS, MERGE_CRAM, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP, NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM, TABIX_BGZIP_TIDDIT_SV, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED, TABIX_PON, VARIANTRECALIBRATOR_SNP, TABIX_BGZIPTABIX_INTERVAL_COMBINED, NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS, UNTAR_CHR_DIR, FREEC_TUMORONLY, SAMBLASTER, NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH, FREEBAYES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP, GATHERPILEUPSUMMARIES, NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT, SAMTOOLS_MPILEUP, INDEX_CRAM, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ, BCFTOOLS_SORT, MANTA_SOMATIC, NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP, NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS, GATK4_FILTERMUTECTCALLS, MERGE_VQSR, MUTECT2_PAIRED, BWAMEM1_INDEX, GATK4_GATHERPILEUPSUMMARIES, DRAGMAP_HASHTABLE, CNVKIT_ANTITARGET, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN, NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX, GATK4_MARKDUPLICATES, SAMTOOLS_VIEW_UNMAP_MAP, SAMTOOLS_CONVERT, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS, TABIX_GERMLINE_VCFS_CONCAT_SORT, TABIX_VC_DEEPVARIANT_VCF, MERGE_STRELKA_GENOME, CONTROLFREEC_FREEC2BED, TABIX_VC_DEEPVARIANT_GVCF, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP, BAM2FASTQ, UNZIP_RT, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT, MERGEMUTECTSTATS, SAMTOOLS_COLLATEFASTQ, GATK4_APPLYVQSR, NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM, GATK4_CALCULATECONTAMINATION, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS, DEEPVARIANT, GATK4_GENOTYPEGVCFS, MSISENSORPRO_MSI_SOMATIC, FREEC2CIRCOS, DRAGMAP_ALIGN, GATK4_INTERVALLISTTOBED, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_SNP, GATK4_APPLYVQSR_INDEL, FGBIO_GROUPREADSBYUMI, BCFTOOLS_MPILEUP, NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING, SAMTOOLS_VIEW, CNVKIT_BATCH, GETPILEUPSUMMARIES, FGBIO_CALLMOLECULARCONSENSUSREADS, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP, GETPILEUPSUMMARIES_NORMAL, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS, GATK4_GENOMICSDBIMPORT, MERGE_MUTECT2, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_INDEL, GATK4_BASERECALIBRATOR_SPARK, ASCAT
May-16 12:41:10.820 [main] WARN  nextflow.Session - There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS?
May-16 12:41:10.825 [main] DEBUG nextflow.Session - Igniting dataflow network (183)
May-16 12:41:10.844 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
May-16 12:41:10.851 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
May-16 12:41:10.851 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
May-16 12:41:10.854 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
May-16 12:41:10.857 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
May-16 12:41:10.861 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
May-16 12:41:10.861 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
May-16 12:41:10.862 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
May-16 12:41:10.862 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
May-16 12:41:10.862 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
May-16 12:41:10.862 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
May-16 12:41:10.864 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
May-16 12:41:10.864 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
May-16 12:41:10.864 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
May-16 12:41:10.864 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
May-16 12:41:10.879 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
May-16 12:41:10.881 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC
May-16 12:41:10.882 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES
May-16 12:41:10.883 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM
May-16 12:41:10.884 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM
May-16 12:41:10.885 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS
May-16 12:41:10.885 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH
May-16 12:41:10.885 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL
May-16 12:41:10.891 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
May-16 12:41:10.891 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
May-16 12:41:10.891 [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
May-16 12:41:10.892 [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
May-16 12:41:10.892 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS
May-16 12:41:10.892 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES
May-16 12:41:10.892 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT
May-16 12:41:10.892 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOTYPEGVCFS
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_INDEL
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:VARIANTRECALIBRATOR_SNP
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_SNP
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_APPLYVQSR_INDEL
May-16 12:41:10.893 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_VQSR
May-16 12:41:10.895 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
May-16 12:41:10.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
May-16 12:41:10.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
May-16 12:41:10.897 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
May-16 12:41:10.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP
May-16 12:41:10.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
May-16 12:41:10.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
May-16 12:41:10.898 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC
May-16 12:41:10.898 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
May-16 12:41:10.898 [main] DEBUG nextflow.Session - Session await
May-16 12:41:11.307 [Actor Thread 53] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.011 s; external sort time: 0.036 s; total time: 0.047 s
May-16 12:41:11.307 [Actor Thread 3] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.011 s; external sort time: 0.036 s; total time: 0.047 s
May-16 12:41:11.320 [Actor Thread 53] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/786d4092a855ec7a8861bd05e086dfd7
May-16 12:41:11.320 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/bb565d820b11d69840c0a1aa718407cc
May-16 12:41:11.343 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13777919048058079682
May-16 12:41:11.343 [Actor Thread 53] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-1808806582173007661
May-16 12:41:11.430 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:11.433 [Task submitter] INFO  nextflow.Session - [d4/5eb3ac] Submitted process > NFCORE_SAREK:SAREK:FASTQC (SRR9041541-1)
May-16 12:41:11.451 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:11.452 [Task submitter] INFO  nextflow.Session - [c0/4688ad] Submitted process > NFCORE_SAREK:SAREK:FASTP (SRR9041540-1)
May-16 12:41:11.461 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:11.462 [Task submitter] INFO  nextflow.Session - [c5/23249d] Submitted process > NFCORE_SAREK:SAREK:FASTQC (SRR9041540-1)
May-16 12:41:11.470 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:11.471 [Task submitter] INFO  nextflow.Session - [99/b3a540] Submitted process > NFCORE_SAREK:SAREK:FASTP (SRR9041541-1)
May-16 12:41:11.477 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:11.478 [Task submitter] INFO  nextflow.Session - [9a/a9fa41] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])
May-16 12:41:14.628 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa]); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/9a/a9fa4169656ea9a121f55dd0f03427]
May-16 12:41:14.731 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-16 12:41:14.732 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:14.733 [Task submitter] INFO  nextflow.Session - [cd/783e76] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])
May-16 12:41:14.742 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:14.742 [Task submitter] INFO  nextflow.Session - [ae/c910ea] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (Saccharomyces_cerevisiae.R64-1-1-chr.fa.bed)
May-16 12:41:16.361 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED ([Saccharomyces_cerevisiae.R64-1-1-chr.fa]); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/cd/783e76390899e58b8cbeef150e5ae9]
May-16 12:41:17.440 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (Saccharomyces_cerevisiae.R64-1-1-chr.fa.bed); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/ae/c910eaf2e66c1bb251330290abccbe]
May-16 12:41:17.506 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:17.507 [Task submitter] INFO  nextflow.Session - [6b/c3811f] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (I_1-230218)
May-16 12:41:18.936 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (I_1-230218); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/6b/c3811f08c5f3fbd5913c5d9ce78f55]
May-16 12:41:37.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_SAREK:SAREK:FASTP (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/99/b3a54038ff80d5f4986b30bed09493]
May-16 12:41:37.492 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
May-16 12:41:37.493 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
May-16 12:41:37.575 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:37.576 [Task submitter] INFO  nextflow.Session - [9c/aae17f] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:41:49.364 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_SAREK:SAREK:FASTP (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c0/4688ad89bcd08075c3bf3c3aea411d]
May-16 12:41:49.374 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:49.375 [Task submitter] INFO  nextflow.Session - [2f/5c8c8d] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:41:49.381 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
May-16 12:41:49.381 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
May-16 12:41:49.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/9c/aae17fe4e72d44f1f91e8db96afa8b]
May-16 12:41:49.632 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:41:49.633 [Task submitter] INFO  nextflow.Session - [da/63b2c1] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:41:49.648 [Actor Thread 10] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:00.789 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/2f/5c8c8d0f13724535443f06b5fac92f]
May-16 12:42:00.800 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:00.805 [Task submitter] INFO  nextflow.Session - [d8/9c1604] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:00.806 [Actor Thread 10] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:01.286 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/da/63b2c14ea253be44e4d5d5a48d6897]
May-16 12:42:01.293 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:01.298 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:01.299 [Task submitter] INFO  nextflow.Session - [53/eb2e82] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:12.505 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d8/9c1604dc68f288a85eee0baceeb016]
May-16 12:42:12.510 [Actor Thread 28] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:12.512 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:12.513 [Task submitter] INFO  nextflow.Session - [26/161dc5] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:12.930 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/53/eb2e825131833a6eff219710cdf9e8]
May-16 12:42:12.936 [Actor Thread 26] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:12.939 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:12.940 [Task submitter] INFO  nextflow.Session - [eb/cadfc0] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:15.259 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: NFCORE_SAREK:SAREK:FASTQC (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d4/5eb3ac622661ffc8654c4a384805e4]
May-16 12:42:24.540 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/26/161dc573c95d03ecedd8d810c0202d]
May-16 12:42:24.547 [Actor Thread 24] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:24.552 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:24.553 [Task submitter] INFO  nextflow.Session - [2d/c8f7a6] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:25.210 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/eb/cadfc073e8aff3e0df4ca96f6c575c]
May-16 12:42:25.215 [Actor Thread 24] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:25.218 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:25.220 [Task submitter] INFO  nextflow.Session - [76/e5c4a4] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:36.904 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/76/e5c4a405421904c440147066350d16]
May-16 12:42:36.911 [Actor Thread 26] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:36.912 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:36.913 [Task submitter] INFO  nextflow.Session - [90/873ee2] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:36.953 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/2d/c8f7a602b75bb4d3ef4bf385584c0c]
May-16 12:42:36.958 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:36.958 [Task submitter] INFO  nextflow.Session - [a3/211579] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:36.960 [Actor Thread 2] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:48.950 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/a3/21157976eb83eaf037ad4a426e5f83]
May-16 12:42:48.956 [Actor Thread 2] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:48.958 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:48.963 [Task submitter] INFO  nextflow.Session - [20/3ff654] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
May-16 12:42:48.974 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/90/873ee258d40df083091f1a3e9b6726]
May-16 12:42:48.978 [Actor Thread 2] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:42:48.979 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:42:48.982 [Task submitter] INFO  nextflow.Session - [1b/9b07d5] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:01.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/20/3ff654ca9cecb37a4ecaf5b092a30a]
May-16 12:43:01.222 [Actor Thread 20] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, data_type:bam, id:SRR9041541] size=12
May-16 12:43:01.223 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:01.224 [Task submitter] INFO  nextflow.Session - [7e/c3aac2] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:01.247 [Actor Thread 65] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.MemoryUnit
May-16 12:43:02.239 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:02.240 [Task submitter] INFO  nextflow.Session - [c4/9be102] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541)
May-16 12:43:02.246 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:02.246 [Task submitter] INFO  nextflow.Session - [21/0e3806] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041541)
May-16 12:43:05.461 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1b/9b07d5b410cd5fcb8ebcaf7f4b784f]
May-16 12:43:05.470 [Actor Thread 11] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:05.472 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:05.473 [Task submitter] INFO  nextflow.Session - [cc/9d6302] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:13.367 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NFCORE_SAREK:SAREK:FASTQC (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c5/23249de116b6a2ae2e51da902122a6]
May-16 12:43:18.170 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7e/c3aac2828d9a74341dca957e33d621]
May-16 12:43:18.176 [Actor Thread 21] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:18.180 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:18.182 [Task submitter] INFO  nextflow.Session - [fa/20a7bb] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:21.698 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/cc/9d63026fc29e6036259ac26511a254]
May-16 12:43:21.704 [Actor Thread 29] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:21.705 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:21.710 [Task submitter] INFO  nextflow.Session - [fa/b778ee] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:34.658 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fa/20a7bb6f3ddd2392f47cb439ecf356]
May-16 12:43:34.664 [Actor Thread 10] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:34.665 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:34.666 [Task submitter] INFO  nextflow.Session - [1d/bac3fd] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:37.928 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fa/b778ee4107500301cd15950bcfd4a5]
May-16 12:43:37.934 [Actor Thread 43] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:37.936 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:37.937 [Task submitter] INFO  nextflow.Session - [9b/26a0fc] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:51.192 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1d/bac3fd9c4f730e9247941748905837]
May-16 12:43:51.198 [Actor Thread 43] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:51.199 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:51.204 [Task submitter] INFO  nextflow.Session - [89/da078c] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:43:54.998 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/9b/26a0fce884cf5ddcb2e08d319497fc]
May-16 12:43:55.007 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:43:55.007 [Actor Thread 11] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:43:55.014 [Task submitter] INFO  nextflow.Session - [2b/a6e40f] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:44:07.600 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/89/da078ced56b08272c8d9826e54b170]
May-16 12:44:07.606 [Actor Thread 11] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:44:07.608 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:44:07.610 [Task submitter] INFO  nextflow.Session - [8c/81c590] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:44:11.233 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/2b/a6e40f0b317e91095f061d5c570bc2]
May-16 12:44:11.237 [Actor Thread 29] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:44:11.239 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:44:11.241 [Task submitter] INFO  nextflow.Session - [c3/1ade33] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:44:23.957 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/8c/81c5904d1af3bb92467e5961ee8e65]
May-16 12:44:23.963 [Actor Thread 29] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:44:23.970 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:44:23.972 [Task submitter] INFO  nextflow.Session - [af/b697da] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
May-16 12:44:27.418 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c3/1ade33108e5bd0c33e605bbd5620e9]
May-16 12:44:27.423 [Actor Thread 43] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:44:41.401 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/af/b697da19de2e888873add6308f2189]
May-16 12:44:41.407 [Actor Thread 11] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, data_type:bam, id:SRR9041540] size=12
May-16 12:44:41.442 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:44:41.444 [Task submitter] INFO  nextflow.Session - [8e/102426] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041540)
May-16 12:44:41.454 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:44:41.456 [Task submitter] INFO  nextflow.Session - [44/c49035] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540)
May-16 12:44:51.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c4/9be10220d8b1fb83ce4086bddd4f41]
May-16 12:44:51.288 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541)` is unable to find [UnixPath]: `/home/ubuntu/reproducible-sarek-error/work/c4/9be10220d8b1fb83ce4086bddd4f41/SRR9041541.sorted.cram` (pattern: `SRR9041541.sorted.cram`)
May-16 12:44:51.292 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 12:44:51.292 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 12:44:51.314 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:44:51.315 [Task submitter] INFO  nextflow.Session - [66/66180e] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041541)
May-16 12:45:02.722 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/66/66180ef0e6bd47782ab0fca74cc75f]
May-16 12:45:02.728 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 12:45:02.728 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 12:46:09.754 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 90; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/21/0e3806877af7f1ca906bf5c225be44]
~> TaskHandler[id: 92; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/8e/10242606be279b587a072870416cb7]
~> TaskHandler[id: 93; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/44/c49035da0d6ae4d45d6e5182d71dbf]
May-16 12:47:39.144 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/44/c49035da0d6ae4d45d6e5182d71dbf]
May-16 12:47:39.146 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540)` is unable to find [UnixPath]: `/home/ubuntu/reproducible-sarek-error/work/44/c49035da0d6ae4d45d6e5182d71dbf/SRR9041540.sorted.cram` (pattern: `SRR9041540.sorted.cram`)
May-16 12:47:39.150 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 12:47:39.150 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 12:47:39.175 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:47:39.176 [Task submitter] INFO  nextflow.Session - [47/d68336] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041540)
May-16 12:47:57.597 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/47/d6833650e6ffa26a97ec5ab5e3888b]
May-16 12:47:57.602 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 12:47:57.602 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 12:47:57.621 [Actor Thread 31] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s
May-16 12:47:57.631 [Actor Thread 31] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/a88d3688d20d25470a2b0d8ee348ca8f
May-16 12:47:57.642 [Actor Thread 31] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7476684566384959847
May-16 12:49:12.924 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/21/0e3806877af7f1ca906bf5c225be44]
May-16 12:49:12.935 [Task monitor] 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>
May-16 12:49:12.935 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 12:49:12.935 [Task monitor] 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>
May-16 12:49:12.960 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:49:12.961 [Task submitter] INFO  nextflow.Session - [d2/9ac1c4] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES (SRR9041541)
May-16 12:49:14.484 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d2/9ac1c4dd28d8debb0438900ff242b7]
May-16 12:49:14.491 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
May-16 12:49:14.491 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 12:49:14.518 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:49:14.519 [Task submitter] INFO  nextflow.Session - [0a/690102] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (SRR9041541)
May-16 12:49:14.526 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:49:14.527 [Task submitter] INFO  nextflow.Session - [25/c5c15d] Submitted process > NFCORE_SAREK:SAREK:CRAM_TO_BAM (SRR9041541)
May-16 12:49:14.531 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:49:14.532 [Task submitter] INFO  nextflow.Session - [8a/121567] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (SRR9041541)
May-16 12:49:14.538 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:49:14.538 [Task submitter] INFO  nextflow.Session - [eb/a5fa32] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041541)
May-16 12:49:21.544 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/8a/1215674ba2fb6f4f0f369aa1a0e13b]
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:21.560 [Task monitor] 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>
May-16 12:49:46.210 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/0a/690102df3341056eb644c97c219ea3]
May-16 12:50:14.809 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: NFCORE_SAREK:SAREK:CRAM_TO_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/25/c5c15d8766788e42baec49cb8e7b32]
May-16 12:51:09.804 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 92; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/8e/10242606be279b587a072870416cb7]
~> TaskHandler[id: 102; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/eb/a5fa326bd0e023a5d3b958166f1164]
May-16 12:54:48.220 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/eb/a5fa326bd0e023a5d3b958166f1164]
May-16 12:54:48.229 [Actor Thread 65] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:cram, num_intervals:1] size=1
May-16 12:54:48.282 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:54:48.283 [Task submitter] INFO  nextflow.Session - [19/05cd37] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041541)
May-16 12:55:56.693 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/8e/10242606be279b587a072870416cb7]
May-16 12:55:56.703 [Task monitor] 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>
May-16 12:55:56.703 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 12:55:56.703 [Task monitor] 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>
May-16 12:55:56.719 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:55:56.720 [Task submitter] INFO  nextflow.Session - [f0/4787bb] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES (SRR9041540)
May-16 12:55:58.448 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/f0/4787bb22a52c7ae05aaca8bc4a45a8]
May-16 12:55:58.453 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
May-16 12:55:58.453 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:INDEX_MARKDUPLICATES > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 12:55:58.474 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:55:58.475 [Task submitter] INFO  nextflow.Session - [bc/537b96] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (SRR9041540)
May-16 12:55:58.481 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:55:58.481 [Task submitter] INFO  nextflow.Session - [fe/fef5ab] Submitted process > NFCORE_SAREK:SAREK:CRAM_TO_BAM (SRR9041540)
May-16 12:55:58.486 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:55:58.488 [Task submitter] INFO  nextflow.Session - [52/9ed7bd] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (SRR9041540)
May-16 12:55:58.497 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 12:55:58.498 [Task submitter] INFO  nextflow.Session - [b6/3370ba] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041540)
May-16 12:56:09.005 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/52/9ed7bd8e8f6fa257d1fbce37290ab8]
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.019 [Task monitor] 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>
May-16 12:56:09.805 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- submitted tasks are shown below
~> TaskHandler[id: 103; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/19/05cd37b37e7f9647de0cd176498d37]
~> TaskHandler[id: 105; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/bc/537b965cc8f4c88ab9b9146661a3e6]
~> TaskHandler[id: 106; name: NFCORE_SAREK:SAREK:CRAM_TO_BAM (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fe/fef5ab84298364e49f2896343983dd]
~> TaskHandler[id: 108; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/b6/3370bac25a5db291522779f0e199cf]
May-16 12:56:56.159 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/bc/537b965cc8f4c88ab9b9146661a3e6]
May-16 12:57:47.219 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: NFCORE_SAREK:SAREK:CRAM_TO_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fe/fef5ab84298364e49f2896343983dd]
May-16 12:57:47.238 [Actor Thread 57] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.007 s; external sort time: 0.001 s; total time: 0.008 s
May-16 12:57:47.245 [Actor Thread 57] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/580811364dca2a699479cc7e144a685e
May-16 12:57:47.260 [Actor Thread 57] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-9640597188593103519
May-16 13:01:09.877 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 103; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/19/05cd37b37e7f9647de0cd176498d37]
~> TaskHandler[id: 108; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/b6/3370bac25a5db291522779f0e199cf]
May-16 13:03:56.132 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/19/05cd37b37e7f9647de0cd176498d37]
May-16 13:03:56.137 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
May-16 13:03:56.139 [Actor Thread 54] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:cram, num_intervals:1] size=1
May-16 13:03:56.177 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:03:56.178 [Task submitter] INFO  nextflow.Session - [a7/fd1b20] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (SRR9041541)
May-16 13:03:57.707 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/a7/fd1b20fc1148e0afcc43fbf9e81b45]
May-16 13:03:57.712 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
May-16 13:03:57.712 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-16 13:03:57.750 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:03:57.751 [Task submitter] INFO  nextflow.Session - [aa/0c56de] Submitted process > NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL (SRR9041541)
May-16 13:03:57.762 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:03:57.763 [Task submitter] INFO  nextflow.Session - [5c/400d7a] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS (SRR9041541)
May-16 13:03:57.769 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:03:57.770 [Task submitter] INFO  nextflow.Session - [4a/554657] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH (SRR9041541)
May-16 13:03:57.776 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:03:57.776 [Task submitter] INFO  nextflow.Session - [23/5878ba] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541)
May-16 13:04:04.230 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/4a/5546572bbc9709eda2e266b6c314b2]
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
May-16 13:04:04.242 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
May-16 13:04:25.978 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 111; name: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/5c/400d7ad92a95df2276a3fd4ef3e7ad]
May-16 13:04:59.373 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 112; name: NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/aa/0c56dec79658f8bdb34eee2e618305]
May-16 13:06:02.125 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/b6/3370bac25a5db291522779f0e199cf]
May-16 13:06:02.132 [Actor Thread 54] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:cram, num_intervals:1] size=1
May-16 13:06:02.146 [Actor Thread 54] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.003 s; external sort time: 0.0 s; total time: 0.003 s
May-16 13:06:02.153 [Actor Thread 54] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/57f9314e1f3bb2e794e1de85154237ad
May-16 13:06:02.164 [Actor Thread 54] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7132219393408872921
May-16 13:06:02.173 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:06:02.174 [Task submitter] INFO  nextflow.Session - [1a/03f828] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041540)
May-16 13:06:09.940 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/23/5878ba44c182fad8cdfac35c631fb1]
~> TaskHandler[id: 114; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1a/03f8280808499bb64e93159726af8f]
May-16 13:11:09.986 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/23/5878ba44c182fad8cdfac35c631fb1]
~> TaskHandler[id: 114; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1a/03f8280808499bb64e93159726af8f]
May-16 13:12:37.417 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 113; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/23/5878ba44c182fad8cdfac35c631fb1]
May-16 13:12:37.424 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-16 13:12:37.455 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:12:37.456 [Task submitter] INFO  nextflow.Session - [76/cc7f2a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS (SRR9041541)
May-16 13:13:48.760 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 115; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANTS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/76/cc7f2aa5d86c4a4c9141aa840b4174]
May-16 13:13:48.822 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-16 13:13:48.823 [Task submitter] INFO  nextflow.Session - [51/cb47c1] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (SRR9041541)
May-16 13:13:56.511 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 116; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (SRR9041541); status: COMPLETED; exit: 2; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/51/cb47c19fed5cb2f9928219e574abb9]
May-16 13:13:56.517 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (SRR9041541); work-dir=/home/ubuntu/reproducible-sarek-error/work/51/cb47c19fed5cb2f9928219e574abb9
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (SRR9041541)` terminated with an error exit status (2)
May-16 13:13:56.552 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (SRR9041541)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (SRR9041541)` terminated with an error exit status (2)

Command executed:

  gatk --java-options "-Xmx9830M" FilterVariantTranches \
      --variant SRR9041541.cnn.vcf.gz \
      --resource Saccharomyces_cerevisiae.vcf.gz --resource Saccharomyces_cerevisiae_indels.vcf.gz --resource Saccharomyces_cerevisiae_snps.vcf.gz \
      --output SRR9041541.haplotypecaller.filtered.vcf.gz \
      --tmp-dir . \
      --info-key CNN_1D
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-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 -Xmx9830M -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar FilterVariantTranches --variant SRR9041541.cnn.vcf.gz --resource Saccharomyces_cerevisiae.vcf.gz --resource Saccharomyces_cerevisiae_indels.vcf.gz --resource Saccharomyces_cerevisiae_snps.vcf.gz --output SRR9041541.haplotypecaller.filtered.vcf.gz --tmp-dir . --info-key CNN_1D
  10:13:52.825 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  10:13:52.878 INFO  FilterVariantTranches - ------------------------------------------------------------
  10:13:52.883 INFO  FilterVariantTranches - The Genome Analysis Toolkit (GATK) v4.4.0.0
  10:13:52.884 INFO  FilterVariantTranches - For support and documentation go to https://software.broadinstitute.org/gatk/
  10:13:52.884 INFO  FilterVariantTranches - Executing as ubuntu@7cde9010cfe2 on Linux v5.15.0-69-generic amd64
  10:13:52.884 INFO  FilterVariantTranches - Java runtime: OpenJDK 64-Bit Server VM v17.0.3-internal+0-adhoc..src
  10:13:52.885 INFO  FilterVariantTranches - Start Date/Time: May 16, 2023 at 10:13:52 AM GMT
  10:13:52.885 INFO  FilterVariantTranches - ------------------------------------------------------------
  10:13:52.885 INFO  FilterVariantTranches - ------------------------------------------------------------
  10:13:52.887 INFO  FilterVariantTranches - HTSJDK Version: 3.0.5
  10:13:52.887 INFO  FilterVariantTranches - Picard Version: 3.0.0
  10:13:52.887 INFO  FilterVariantTranches - Built for Spark Version: 3.3.1
  10:13:52.888 INFO  FilterVariantTranches - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  10:13:52.889 INFO  FilterVariantTranches - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  10:13:52.889 INFO  FilterVariantTranches - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  10:13:52.890 INFO  FilterVariantTranches - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  10:13:52.890 INFO  FilterVariantTranches - Deflater: IntelDeflater
  10:13:52.890 INFO  FilterVariantTranches - Inflater: IntelInflater
  10:13:52.891 INFO  FilterVariantTranches - GCS max retries/reopens: 20
  10:13:52.891 INFO  FilterVariantTranches - Requester pays: disabled
  10:13:52.892 INFO  FilterVariantTranches - Initializing engine
  10:13:53.087 INFO  FeatureManager - Using codec VCFCodec to read file file://Saccharomyces_cerevisiae.vcf.gz
  10:13:53.113 INFO  FeatureManager - Using codec VCFCodec to read file file://Saccharomyces_cerevisiae_indels.vcf.gz
  10:13:53.115 WARN  IntelInflater - Zero Bytes Written : 0
  10:13:53.122 INFO  FeatureManager - Using codec VCFCodec to read file file://Saccharomyces_cerevisiae_snps.vcf.gz
  10:13:53.133 INFO  FeatureManager - Using codec VCFCodec to read file file://SRR9041541.cnn.vcf.gz
  10:13:53.153 WARN  IndexUtils - Feature file "file://Saccharomyces_cerevisiae.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
  10:13:53.159 WARN  IntelInflater - Zero Bytes Written : 0
  10:13:53.207 INFO  FilterVariantTranches - Done initializing engine
  10:13:53.269 INFO  ProgressMeter - Starting traversal
  10:13:53.270 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
  10:13:53.271 INFO  FilterVariantTranches - Starting pass 0 through the variants
  10:13:55.710 WARN  IntelInflater - Zero Bytes Written : 0
  10:13:55.833 INFO  FilterVariantTranches - Finished pass 0 through the variants
  10:13:55.833 INFO  FilterVariantTranches - Found 0 SNPs and 0 indels with INFO score key:CNN_1D.
  10:13:55.833 INFO  FilterVariantTranches - Found 0 SNPs and 138 indels in the resources.
  10:13:55.834 INFO  FilterVariantTranches - Filtered 0 SNPs out of 0 and filtered 0 indels out of 0 with INFO score: CNN_1D.
  10:13:55.836 INFO  FilterVariantTranches - Shutting down engine
  [May 16, 2023 at 10:13:55 AM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches done. Elapsed time: 0.05 minutes.
  Runtime.totalMemory()=763363328
  ***********************************************************************
  
  A USER ERROR has occurred: Bad input: VCF contains no variants or no variants with INFO score key "CNN_1D"
  
  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Work dir:
  /home/ubuntu/reproducible-sarek-error/work/51/cb47c19fed5cb2f9928219e574abb9

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`
May-16 13:13:56.559 [Task monitor] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
May-16 13:13:56.598 [main] DEBUG nextflow.Session - Session await > all processes finished
May-16 13:13:56.624 [Actor Thread 7] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.002 s; total time: 0.002 s
May-16 13:13:56.631 [Actor Thread 7] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/e865cb7eff9b5d039e236293c8cdaaa2
May-16 13:13:56.654 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:CRAM_TO_BAM_RECAL; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
May-16 13:13:56.671 [Actor Thread 7] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-4713805675227504586
May-16 13:13:56.683 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:MERGE_GENOTYPEGVCFS; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
May-16 13:13:56.683 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
May-16 13:13:56.689 [Actor Thread 18] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
May-16 13:13:56.689 [Actor Thread 54] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
May-16 13:13:56.692 [Actor Thread 27] 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
May-16 13:13:56.700 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below
~> TaskHandler[id: 117; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT (joint_variant_calling); status: NEW; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/2a/bde6a7c598adfa0cf3377ee5d441e1]
May-16 13:13:56.754 [Actor Thread 27] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 53; slices: 1; internal sort time: 0.051 s; external sort time: 0.009 s; total time: 0.06 s
May-16 13:13:56.771 [Actor Thread 27] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/a4e1db8da49beea445ec68e78393f2ba
May-16 13:13:56.781 [Actor Thread 27] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-16609789312352353222
May-16 13:16:10.022 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 114; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1a/03f8280808499bb64e93159726af8f]
May-16 13:18:56.792 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below
~> TaskHandler[id: 117; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:GATK4_GENOMICSDBIMPORT (joint_variant_calling); status: NEW; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/2a/bde6a7c598adfa0cf3377ee5d441e1]
May-16 13:21:10.081 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 114; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1a/03f8280808499bb64e93159726af8f]
May-16 13:23:03.048 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 114; name: NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/1a/03f8280808499bb64e93159726af8f]
May-16 13:23:03.058 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
May-16 13:23:03.067 [main] DEBUG nextflow.Session - Session await > all barriers passed
May-16 13:23:03.084 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
May-16 13:23:03.310 [main] ERROR nextflow.script.WorkflowMetadata - Failed to invoke `workflow.onComplete` event handler
java.lang.NullPointerException: Cannot invoke method size() on null object
	at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91)
	at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:44)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
	at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:34)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
	at NfcoreTemplate.email(NfcoreTemplate.groovy:148)
	at NfcoreTemplate$email$5.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at Script_c0ec06da$_runScript_closure9.doCall(Script_c0ec06da:1087)
	at Script_c0ec06da$_runScript_closure9.doCall(Script_c0ec06da)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
	at groovy.lang.Closure.call(Closure.java:412)
	at groovy.lang.Closure.call(Closure.java:406)
	at nextflow.script.WorkflowMetadata$_invokeOnComplete_closure4.doCall(WorkflowMetadata.groovy:388)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
	at groovy.lang.Closure.call(Closure.java:412)
	at groovy.lang.Closure.call(Closure.java:428)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2357)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2342)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2383)
	at nextflow.script.WorkflowMetadata.invokeOnComplete(WorkflowMetadata.groovy:386)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1258)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1036)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1019)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
	at nextflow.script.WorkflowMetadata$_closure3.doCall(WorkflowMetadata.groovy:251)
	at nextflow.script.WorkflowMetadata$_closure3.call(WorkflowMetadata.groovy)
	at groovy.lang.Closure.run(Closure.java:493)
	at nextflow.Session.shutdown0(Session.groovy:694)
	at nextflow.Session.destroy(Session.groovy:644)
	at nextflow.script.ScriptRunner.shutdown(ScriptRunner.groovy:239)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:134)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
	at nextflow.cli.Launcher.run(Launcher.groovy:494)
	at nextflow.cli.Launcher.main(Launcher.groovy:653)
May-16 13:23:03.326 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=56; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=1; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=6h 40m 57s; failedDuration=15.3s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=6; peakCpus=60; peakMemory=106 GB; ]
May-16 13:23:03.326 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
May-16 13:23:03.329 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
May-16 13:23:03.699 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
  [{"cpuUsage":{"mean":133.3,"min":133.3,"q1":133.3,"q2":133.3,"q3":133.3,"max":133.3,"minLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","maxLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","q1Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","q2Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","q3Label":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])"},"process":"BUILD_INTERVALS","mem":null,"memUsage":null,"timeUsage":{"mean":0.01,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.01,"max":0.01,"minLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([Saccharomyces_cerevisiae.R64-1-1-chr.fa])","maxLabel":"NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS 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May-16 13:23:04.655 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
May-16 13:23:04.981 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
May-16 13:23:05.049 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
May-16 13:23:05.055 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye