Jun-08 12:54:47.456 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/sarek -r 3.2.0 --skip_tools haplotypecaller_filter,baserecalibrator,markduplicates -profile docker --input sample-sheet.csv --outdir sarek-test-jointVC --max_time 336.h --max_cpus 64 --max_memory 256.GB --save_mapped --genome R64-1-1 --tools haplotypecaller,vep --vep_out_format tab --vep_include_fasta
Jun-08 12:54:47.558 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.04.1
Jun-08 12:54:47.587 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/ubuntu/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2
Jun-08 12:54:47.599 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-08 12:54:47.601 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-08 12:54:47.604 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jun-08 12:54:47.616 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-08 12:54:47.632 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/ubuntu/.nextflow/scm
Jun-08 12:54:49.099 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git
Jun-08 12:54:49.128 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-08 12:54:49.136 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ubuntu/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git
Jun-08 12:54:50.190 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config
Jun-08 12:54:50.192 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config
Jun-08 12:54:50.214 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker`
Jun-08 12:54:53.679 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, uge, rosalind_uge, lugh, test_full_germline, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, public_aws_ecr, tigem, tubingen_apg, google, ipop_up, googlels, use_gatk_spark, eddie, medair, alignment_to_fastq, apptainer, bi, bigpurple, sbc_sharc, adcra, cedars, tools, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, targeted, icr_davros, ceres, save_bam_mapped, munin, arm, rosalind, hasta, annotation, cfc, uzh, split_fastq, ebc, ku_sund_dangpu, ccga_dx, variantcalling_channels, crick, recalibrate_bam, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, skip_bqsr, genotoul, skip_markduplicates, abims, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, trimming, cambridge, tools_tumoronly, podman, cheaha, xanadu, test, prepare_recalibration_bam, computerome, tools_germline, seg_globe, sanger, dkfz, tools_somatic_ascat, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, psmn, umi, eva, markduplicates_bam, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, tools_somatic, cbe, markduplicates_cram, recalibrate_cram, no_intervals, prepare_recalibration_cram, pair, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac]
Jun-08 12:54:53.741 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jun-08 12:54:53.742 [main] INFO  nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [cheesy_heyrovsky] DSL2 - revision: 71fac185a9 [3.2.0]
Jun-08 12:54:53.743 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-08 12:54:53.743 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-08 12:54:53.747 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /home/ubuntu/.nextflow/secrets/store.json
Jun-08 12:54:53.751 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@c14bbab] - activable => nextflow.secret.LocalSecretsProvider@c14bbab
Jun-08 12:54:53.820 [main] DEBUG nextflow.Session - Session UUID: 63d7cba7-5fbf-4dc8-b7d8-f5c004e0af2b
Jun-08 12:54:53.820 [main] DEBUG nextflow.Session - Run name: cheesy_heyrovsky
Jun-08 12:54:53.821 [main] DEBUG nextflow.Session - Executor pool size: 64
Jun-08 12:54:53.832 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-08 12:54:53.864 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.04.1 build 5866
  Created: 15-04-2023 06:51 UTC (09:51 EEST)
  System: Linux 5.15.0-69-generic
  Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src
  Encoding: UTF-8 (UTF-8)
  Process: 3907641@bioinfosrv [10.252.254.98]
  CPUs: 64 - Mem: 251.7 GB (117.3 GB) - Swap: 0 (0)
Jun-08 12:54:53.883 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/reproducible-sarek-error/work [ext2/ext3]
Jun-08 12:54:53.883 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ubuntu/.nextflow/assets/nf-core/sarek/bin
Jun-08 12:54:53.895 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-08 12:54:53.908 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-08 12:54:54.051 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-08 12:54:54.074 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000
Jun-08 12:54:54.190 [main] DEBUG nextflow.Session - Session start
Jun-08 12:54:54.199 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/ubuntu/reproducible-sarek-error/sarek-test-jointVC/pipeline_info/execution_trace_2023-06-08_12-54-51.txt
Jun-08 12:54:54.215 [main] DEBUG nextflow.Session - Using default localLib path: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib
Jun-08 12:54:54.221 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib
Jun-08 12:54:54.223 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ubuntu/.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar
Jun-08 12:54:55.962 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-08 12:54:56.072 [main] INFO  nextflow.Nextflow - 

-[2m----------------------------------------------------[0m-
                                        [0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m        ___     __   __   __   ___     [0;32m/,-._.--~'[0m
[0;34m  |\ | |__  __ /  ` /  \ |__) |__         [0;33m}  {[0m
[0;34m  | \| |       \__, \__/ |  \ |___     [0;32m\`-._,-`-,[0m
                                        [0;32m`._,._,'[0m
[0;37m      ____[0m
[0;37m    .´ _  `.[0m
[0;37m   /  [0;32m|\[0m`-_ \[0m     [0;34m __        __   ___     [0m
[0;37m  |   [0;32m| \[0m  `-|[0m    [0;34m|__`  /\  |__) |__  |__/[0m
[0;37m   \ [0;32m|   \[0m  /[0m     [0;34m.__| /¯¯\ |  \ |___ |  \[0m
[0;37m    `[0;32m|[0m____[0;32m\[0m´[0m

[0;35m  nf-core/sarek v3.2.0-g71fac18[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
  [0;34mrevision         : [0;32m3.2.0[0m
  [0;34mrunName          : [0;32mcheesy_heyrovsky[0m
  [0;34mcontainerEngine  : [0;32mdocker[0m
  [0;34mlaunchDir        : [0;32m/home/ubuntu/reproducible-sarek-error[0m
  [0;34mworkDir          : [0;32m/home/ubuntu/reproducible-sarek-error/work[0m
  [0;34mprojectDir       : [0;32m/home/ubuntu/.nextflow/assets/nf-core/sarek[0m
  [0;34muserName         : [0;32mubuntu[0m
  [0;34mprofile          : [0;32mdocker[0m
  [0;34mconfigFiles      : [0;32m/home/ubuntu/.nextflow/assets/nf-core/sarek/nextflow.config[0m

[1mInput/output options[0m
  [0;34minput            : [0;32msample-sheet.csv[0m
  [0;34moutdir           : [0;32msarek-test-jointVC[0m

[1mMain options[0m
  [0;34mtools            : [0;32mhaplotypecaller,vep[0m
  [0;34mskip_tools       : [0;32mhaplotypecaller_filter,baserecalibrator,markduplicates[0m

[1mPreprocessing[0m
  [0;34msave_mapped      : [0;32mtrue[0m

[1mAnnotation[0m
  [0;34mvep_include_fasta: [0;32mtrue[0m
  [0;34mvep_out_format   : [0;32mtab[0m

[1mReference genome options[0m
  [0;34mgenome           : [0;32mR64-1-1[0m
  [0;34mbwa              : [0;32ms3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/[0m
  [0;34mfasta            : [0;32ms3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa[0m
  [0;34msnpeff_db        : [0;32m105[0m
  [0;34msnpeff_genome    : [0;32mR64-1-1[0m
  [0;34msnpeff_version   : [0;32m5.1[0m
  [0;34mvep_genome       : [0;32mR64-1-1[0m
  [0;34mvep_species      : [0;32msaccharomyces_cerevisiae[0m
  [0;34mvep_cache_version: [0;32m108[0m
  [0;34mvep_version      : [0;32m108.2[0m
  [0;34migenomes_base    : [0;32ms3://ngi-igenomes/igenomes[0m

[1mMax job request options[0m
  [0;34mmax_cpus         : [0;32m64[0m
  [0;34mmax_memory       : [0;32m256.GB[0m
  [0;34mmax_time         : [0;32m336.h[0m

!! Only displaying parameters that differ from the pipeline defaults !!
Displaying all reference genome parameters
-[2m----------------------------------------------------[0m-
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
-[2m----------------------------------------------------[0m-
Jun-08 12:55:00.551 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 1.16.2
Jun-08 12:55:00.642 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@1.16.2' resolved
Jun-08 12:55:00.643 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@1.16.2'
Jun-08 12:55:02.022 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@1.16.2
Jun-08 12:55:02.363 [main] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3]
Jun-08 12:55:02.363 [main] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/
Jun-08 12:55:02.416 [main] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider
Jun-08 12:55:02.430 [main] DEBUG nextflow.file.FileHelper - AWS S3 config details: {max_error_retry=5}
Jun-08 12:55:04.224 [main] DEBUG com.upplication.s3fs.AmazonS3Client - Setting S3 glacierRetrievalTier=null
Jun-08 12:55:07.723 [main] WARN  nextflow.Nextflow - If Haplotypecaller is specified, without `--dbsnp` or `--known_indels no filtering will be done. For filtering, please provide at least one of `--dbsnp` or `--known_indels`.
For more information see FilterVariantTranches (single-sample, default): https://gatk.broadinstitute.org/hc/en-us/articles/5358928898971-FilterVariantTranches
For more information see VariantRecalibration (--joint_germline): https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator
For more information on GATK Best practice germline variant calling: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-
Jun-08 12:55:31.598 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jun-08 12:55:31.604 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jun-08 12:55:31.618 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.618 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.629 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jun-08 12:55:31.636 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=251.7 GB; capacity=64; pollInterval=100ms; dumpInterval=5m
Jun-08 12:55:31.750 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jun-08 12:55:31.751 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jun-08 12:55:31.757 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.757 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.766 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jun-08 12:55:31.768 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_HASHTABLE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jun-08 12:55:31.774 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.774 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.782 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jun-08 12:55:31.783 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_CREATESEQUENCEDICTIONARY` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jun-08 12:55:31.789 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.789 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.798 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jun-08 12:55:31.799 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MSISENSORPRO_SCAN` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jun-08 12:55:31.802 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.802 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.813 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jun-08 12:55:31.814 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jun-08 12:55:31.819 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.819 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.838 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jun-08 12:55:31.839 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jun-08 12:55:31.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jun-08 12:55:31.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_DBSNP` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jun-08 12:55:31.844 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.844 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jun-08 12:55:31.860 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jun-08 12:55:31.861 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jun-08 12:55:31.862 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_GERMLINE_RESOURCE` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jun-08 12:55:31.866 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.867 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jun-08 12:55:31.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jun-08 12:55:31.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jun-08 12:55:31.883 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_SNPS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jun-08 12:55:31.886 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.886 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.897 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jun-08 12:55:31.898 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jun-08 12:55:31.899 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jun-08 12:55:31.900 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_KNOWN_INDELS` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jun-08 12:55:31.905 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.905 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:31.914 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jun-08 12:55:31.915 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jun-08 12:55:31.916 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jun-08 12:55:31.916 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_PON` matches process NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jun-08 12:55:31.921 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:31.921 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.027 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
Jun-08 12:55:32.030 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.031 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.038 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jun-08 12:55:32.038 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_INTERVALS_BED` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jun-08 12:55:32.040 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.040 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.094 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jun-08 12:55:32.095 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jun-08 12:55:32.096 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jun-08 12:55:32.096 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TABIX_BGZIPTABIX_INTERVAL_SPLIT` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jun-08 12:55:32.098 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.099 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.113 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jun-08 12:55:32.113 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jun-08 12:55:32.114 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jun-08 12:55:32.117 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.117 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.151 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jun-08 12:55:32.152 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jun-08 12:55:32.156 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.156 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.167 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jun-08 12:55:32.169 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jun-08 12:55:32.171 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.171 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.178 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jun-08 12:55:32.178 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_UNMAP_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jun-08 12:55:32.180 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.180 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.187 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jun-08 12:55:32.188 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_MAP_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jun-08 12:55:32.190 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.190 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jun-08 12:55:32.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_MERGE_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jun-08 12:55:32.215 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.215 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.223 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jun-08 12:55:32.224 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_UNMAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jun-08 12:55:32.226 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.226 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jun-08 12:55:32.233 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:COLLATE_FASTQ_MAP` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jun-08 12:55:32.235 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.235 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.245 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jun-08 12:55:32.246 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jun-08 12:55:32.247 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.247 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTQC
Jun-08 12:55:32.265 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_SAREK:SAREK:FASTQC
Jun-08 12:55:32.268 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.268 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.282 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:FASTP
Jun-08 12:55:32.283 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_SAREK:SAREK:FASTP
Jun-08 12:55:32.286 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.286 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.310 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jun-08 12:55:32.311 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jun-08 12:55:32.311 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jun-08 12:55:32.311 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jun-08 12:55:32.312 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jun-08 12:55:32.313 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.313 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.322 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jun-08 12:55:32.322 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM1_MEM|BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jun-08 12:55:32.322 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM2_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jun-08 12:55:32.323 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jun-08 12:55:32.323 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWAMEM.*_MEM` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jun-08 12:55:32.324 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.324 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.332 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jun-08 12:55:32.332 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DRAGMAP_ALIGN` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jun-08 12:55:32.333 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:(BWAMEM.*_MEM|DRAGMAP_ALIGN)` matches process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jun-08 12:55:32.334 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.334 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.357 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.360 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.360 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.372 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.372 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.382 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
Jun-08 12:55:32.383 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
Jun-08 12:55:32.384 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAM_TO_CRAM_MAPPING` matches process NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
Jun-08 12:55:32.385 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.385 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.432 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS
Jun-08 12:55:32.433 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS` matches process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS
Jun-08 12:55:32.435 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.435 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.460 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH
Jun-08 12:55:32.460 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH` matches process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH
Jun-08 12:55:32.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.484 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jun-08 12:55:32.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_CONVERT` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jun-08 12:55:32.485 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jun-08 12:55:32.486 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:CRAM_TO_BAM` matches process NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jun-08 12:55:32.487 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.487 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.538 [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_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
Jun-08 12:55:32.539 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_HAPLOTYPECALLER` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
Jun-08 12:55:32.541 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.542 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.564 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
Jun-08 12:55:32.564 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_MERGEVCFS` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
Jun-08 12:55:32.565 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_HAPLOTYPECALLER` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
Jun-08 12:55:32.566 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.567 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:32.587 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.587 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.596 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.596 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.597 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MERGE_BAM|INDEX_MERGE_BAM` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.597 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)` matches process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:32.598 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.599 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.646 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jun-08 12:55:32.646 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jun-08 12:55:32.647 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_STATS` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jun-08 12:55:32.648 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.648 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.668 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jun-08 12:55:32.668 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jun-08 12:55:32.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jun-08 12:55:32.669 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_COUNT` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jun-08 12:55:32.672 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.672 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.701 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jun-08 12:55:32.702 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jun-08 12:55:32.702 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jun-08 12:55:32.702 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_TSTV_QUAL` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jun-08 12:55:32.706 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.706 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.737 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jun-08 12:55:32.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jun-08 12:55:32.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_.*` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jun-08 12:55:32.739 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:VCFTOOLS_SUMMARY` matches process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jun-08 12:55:32.742 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.742 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.796 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP
Jun-08 12:55:32.797 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ENSEMBLVEP_VEP` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP
Jun-08 12:55:32.798 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.799 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.808 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
Jun-08 12:55:32.809 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
Jun-08 12:55:32.810 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)` matches process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
Jun-08 12:55:32.811 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.811 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.842 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jun-08 12:55:32.843 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNZIP.*|UNTAR.*|TABIX.*|BUILD_INTERVALS|CREATE_INTERVALS_BED|CUSTOM_DUMPSOFTWAREVERSIONS|VCFTOOLS|BCFTOOLS.*|SAMTOOLS_INDEX` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jun-08 12:55:32.843 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jun-08 12:55:32.845 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.845 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.925 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_SAREK:SAREK:MULTIQC
Jun-08 12:55:32.926 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_SAREK:SAREK:MULTIQC
Jun-08 12:55:32.927 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jun-08 12:55:32.927 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jun-08 12:55:32.940 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKEGRAPH, CONTROLFREEC_MAKEGRAPH, SAMTOOLS_VIEW_MAP_MAP, SVDB_MERGE, MERGE_GENOTYPEGVCFS, SAMTOOLS_MERGE, BWA_MEM, GATK4_APPLYBQSR_SPARK, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE, ADD_INFO_TO_VCF, SAMTOOLS_VIEW_UNMAP_UNMAP, FILTERVARIANTTRANCHES, BUILD_INTERVALS, CAT_FASTQ, CONTROLFREEC_FREEC2CIRCOS, SAMTOOLS_STATS, INDEX_MERGE_BAM, MUTECT2, GATK4_HAPLOTYPECALLER, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX, TABIX_EXT_VCF, VCFTOOLS, NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX, 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, NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS, TABIX_GERMLINE_RESOURCE, ASSESS_SIGNIFICANCE, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT, CALLUMICONSENSUS, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER, TABIX_KNOWN_SNPS, CAT_CAT, NFCORE_SAREK:SAREK:FASTQC, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON, GATHERPILEUPSUMMARIES_NORMAL, SAMTOOLS_FAIDX, MERGE_BAM, STRELKA_GERMLINE, TIDDIT_SV, GETPILEUPSUMMARIES_TUMOR, STRELKA_SINGLE, SAMTOOLS_BAM2FQ, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP, BWAMEM2_MEM, VCFTOOLS_SUMMARY, NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE, UNZIP_ALLELES, BCFTOOLS_STATS, GATK4_GETPILEUPSUMMARIES, LEARNREADORIENTATIONMODEL, NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM, GATK4_VARIANTRECALIBRATOR, FASTP, NFCORE_SAREK:SAREK:CRAM_TO_BAM, MERGE_FREEBAYES, MSISENSORPRO_SCAN, GATK4_MERGEVCFS, GATHERPILEUPSUMMARIES_TUMOR, UNTAR, TABIX_BGZIPTABIX_INTERVAL_SPLIT, MERGE_DEEPVARIANT_VCF, CNVKIT_REFERENCE, ENSEMBLVEP_VEP, FREEC2BED, UNZIP_LOCI, GATK4_FILTERVARIANTTRANCHES, TABIX_KNOWN_INDELS, SNPEFF_SNPEFF, CREATE_INTERVALS_BED, BAM_TO_CRAM, GROUPREADSBYUMI, NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN, BAM_TO_CRAM_MAPPING, FASTQTOBAM, CONTROLFREEC_FREEC, NFCORE_SAREK:SAREK:MULTIQC, BWAMEM1_MEM, GATK4_ESTIMATELIBRARYCOMPLEXITY, CRAM_TO_BAM, GATK4_APPLYVQSR_SNP, GATK4_APPLYBQSR, VCFTOOLS_TSTV_QUAL, GATK4_BASERECALIBRATOR, GERMLINE_VCFS_CONCAT, NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM, NFCORE_SAREK:SAREK:FASTP, TABIX_DBSNP, FILTERMUTECTCALLS, CNNSCOREVARIANTS, SNPEFF_DOWNLOAD, GATK4_LEARNREADORIENTATIONMODEL, BWA_INDEX, MANTA_GERMLINE, INDEX_MARKDUPLICATES, GERMLINE_VCFS_CONCAT_SORT, MERGE_HAPLOTYPECALLER, STRELKA_SOMATIC, FREEC_SOMATIC, GATK4_MUTECT2, VARIANTRECALIBRATOR_INDEL, CUSTOM_DUMPSOFTWAREVERSIONS, SAMTOOLS_MERGE_UNMAP, FGBIO_FASTQTOBAM, CRAM_TO_BAM_RECAL, ENSEMBLVEP_DOWNLOAD, 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, MERGE_CRAM, GATK4_CNNSCOREVARIANTS, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP, NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM, TABIX_BGZIP_TIDDIT_SV, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED, TABIX_PON, VARIANTRECALIBRATOR_SNP, TABIX_BGZIPTABIX_INTERVAL_COMBINED, UNTAR_CHR_DIR, FREEC_TUMORONLY, SAMBLASTER, FREEBAYES, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP, GATHERPILEUPSUMMARIES, INDEX_CRAM, SAMTOOLS_MPILEUP, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ, BCFTOOLS_SORT, MANTA_SOMATIC, NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP, NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS, GATK4_FILTERMUTECTCALLS, MERGE_VQSR, MUTECT2_PAIRED, BWAMEM1_INDEX, GATK4_GATHERPILEUPSUMMARIES, DRAGMAP_HASHTABLE, CNVKIT_ANTITARGET, NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN, NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX, GATK4_MARKDUPLICATES, SAMTOOLS_VIEW_UNMAP_MAP, SAMTOOLS_CONVERT, NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS, TABIX_GERMLINE_VCFS_CONCAT_SORT, TABIX_VC_DEEPVARIANT_VCF, CONTROLFREEC_FREEC2BED, MERGE_STRELKA_GENOME, TABIX_VC_DEEPVARIANT_GVCF, NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP, BAM2FASTQ, UNZIP_RT, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT, SAMTOOLS_COLLATEFASTQ, MERGEMUTECTSTATS, GATK4_APPLYVQSR, GATK4_CALCULATECONTAMINATION, NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS, DEEPVARIANT, GATK4_GENOTYPEGVCFS, MSISENSORPRO_MSI_SOMATIC, FREEC2CIRCOS, DRAGMAP_ALIGN, GATK4_INTERVALLISTTOBED, GATK4_APPLYVQSR_INDEL, FGBIO_GROUPREADSBYUMI, BCFTOOLS_MPILEUP, NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING, SAMTOOLS_VIEW, CNVKIT_BATCH, GETPILEUPSUMMARIES, FGBIO_CALLMOLECULARCONSENSUSREADS, NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS, NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP, GETPILEUPSUMMARIES_NORMAL, GATK4_GENOMICSDBIMPORT, MERGE_MUTECT2, GATK4_BASERECALIBRATOR_SPARK, ASCAT
Jun-08 12:55:33.012 [main] WARN  nextflow.Session - There's no process matching config selector: NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS
Jun-08 12:55:33.019 [main] DEBUG nextflow.Session - Igniting dataflow network (141)
Jun-08 12:55:33.033 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX
Jun-08 12:55:33.034 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX
Jun-08 12:55:33.034 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE
Jun-08 12:55:33.034 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY
Jun-08 12:55:33.034 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN
Jun-08 12:55:33.034 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX
Jun-08 12:55:33.035 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP
Jun-08 12:55:33.035 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE
Jun-08 12:55:33.035 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS
Jun-08 12:55:33.035 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS
Jun-08 12:55:33.035 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON
Jun-08 12:55:33.036 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS
Jun-08 12:55:33.036 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED
Jun-08 12:55:33.036 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT
Jun-08 12:55:33.036 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED
Jun-08 12:55:33.038 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_MAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_UNMAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_MERGE_UNMAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_UNMAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:COLLATE_FASTQ_MAP
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:CAT_FASTQ
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQC
Jun-08 12:55:33.039 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTP
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM2_MEM
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:DRAGMAP_ALIGN
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING
Jun-08 12:55:33.040 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS
Jun-08 12:55:33.041 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH
Jun-08 12:55:33.041 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CRAM_TO_BAM
Jun-08 12:55:33.042 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER
Jun-08 12:55:33.042 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:MERGE_HAPLOTYPECALLER
Jun-08 12:55:33.042 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM
Jun-08 12:55:33.042 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM
Jun-08 12:55:33.043 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
Jun-08 12:55:33.044 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT
Jun-08 12:55:33.044 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL
Jun-08 12:55:33.044 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY
Jun-08 12:55:33.044 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP
Jun-08 12:55:33.045 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:TABIX_TABIX
Jun-08 12:55:33.045 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS
Jun-08 12:55:33.046 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_SAREK:SAREK:MULTIQC
Jun-08 12:55:33.047 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jun-08 12:55:33.047 [main] DEBUG nextflow.Session - Session await
Jun-08 12:55:33.050 [Actor Thread 49] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jun-08 12:55:33.324 [Actor Thread 43] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.003 s; external sort time: 0.03 s; total time: 0.033 s
Jun-08 12:55:33.324 [Actor Thread 39] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.003 s; external sort time: 0.03 s; total time: 0.033 s
Jun-08 12:55:33.333 [Actor Thread 43] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/bc09ea248e08783e9b97a9331aa7009a
Jun-08 12:55:33.333 [Actor Thread 39] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/ff03deffaabd767a39aba7f39a28259c
Jun-08 12:55:33.352 [Actor Thread 43] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-7751954289920950126
Jun-08 12:55:33.352 [Actor Thread 39] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-1056479625279931247
Jun-08 12:55:33.564 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:33.569 [Task submitter] INFO  nextflow.Session - [4b/0b9216] Submitted process > NFCORE_SAREK:SAREK:FASTQC (SRR9041541-1)
Jun-08 12:55:33.591 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:33.592 [Task submitter] INFO  nextflow.Session - [96/2045b8] Submitted process > NFCORE_SAREK:SAREK:FASTP (SRR9041540-1)
Jun-08 12:55:33.607 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:33.608 [Task submitter] INFO  nextflow.Session - [bf/e0a263] Submitted process > NFCORE_SAREK:SAREK:FASTQC (SRR9041540-1)
Jun-08 12:55:33.622 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:33.623 [Task submitter] INFO  nextflow.Session - [fe/de913d] Submitted process > NFCORE_SAREK:SAREK:FASTP (SRR9041541-1)
Jun-08 12:55:37.521 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa to work dir: /home/ubuntu/reproducible-sarek-error/work/stage-63d7cba7-5fbf-4dc8-b7d8-f5c004e0af2b/ec/1d067926ac18bd92a735ecab66cf64/genome.fa
Jun-08 12:55:37.669 [FileTransfer-1] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download file from=s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa to=/home/ubuntu/reproducible-sarek-error/work/stage-63d7cba7-5fbf-4dc8-b7d8-f5c004e0af2b/ec/1d067926ac18bd92a735ecab66cf64/genome.fa
Jun-08 12:55:37.670 [FileTransfer-1] DEBUG com.upplication.s3fs.AmazonS3Client - Creating S3 transfer manager pool - chunk-size=104857600; max-treads=10;
Jun-08 12:55:37.670 [FileTransfer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'S3TransferManager' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-08 12:55:39.412 [Actor Thread 42] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.MemoryUnit
Jun-08 12:55:39.427 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:39.429 [Task submitter] INFO  nextflow.Session - [0b/0f9542] Submitted process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)
Jun-08 12:55:39.441 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:39.442 [Task submitter] INFO  nextflow.Session - [e3/28ca17] Submitted process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (genome.fa)
Jun-08 12:55:42.282 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/0b/0f95421b2c798e93da24186bf7b29e]
Jun-08 12:55:42.520 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 12:55:42.521 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 12:55:42.584 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:42.586 [Task submitter] INFO  nextflow.Session - [4f/14af7c] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([genome.fa])
Jun-08 12:55:45.822 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:BUILD_INTERVALS ([genome.fa]); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/4f/14af7cf3bf0662c7f96228c6cffad0]
Jun-08 12:55:45.857 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-08 12:55:45.883 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:45.885 [Task submitter] INFO  nextflow.Session - [c0/7e39ff] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED ([genome.fa])
Jun-08 12:55:45.917 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:45.918 [Task submitter] INFO  nextflow.Session - [f0/3aa115] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.fa.bed)
Jun-08 12:55:48.286 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED ([genome.fa]); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/c0/7e39ff77c6178c31d4af21e145295a]
Jun-08 12:55:48.298 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jun-08 12:55:48.971 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.fa.bed); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/f0/3aa11592ec7a2b1a6725d9c7e949d9]
Jun-08 12:55:49.024 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:55:49.026 [Task submitter] INFO  nextflow.Session - [d7/95eeea] Submitted process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (I_1-230218)
Jun-08 12:55:51.082 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (I_1-230218); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d7/95eeea10bfbc5c7606b265d9af8234]
Jun-08 12:55:51.089 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT > Skipping output binding because one or more optional files are missing: fileoutparam<1:2>
Jun-08 12:55:51.111 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/e3/28ca17f19cfb6abc751493b69d483d]
Jun-08 12:55:58.684 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_SAREK:SAREK:FASTP (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/fe/de913d372dd6865bb404e2ebd201b6]
Jun-08 12:55:58.695 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 12:55:58.695 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 12:56:05.042 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0 to work dir: /home/ubuntu/reproducible-sarek-error/work/stage-63d7cba7-5fbf-4dc8-b7d8-f5c004e0af2b/f4/1da255eac4af8e588382ef1b0e964f/version0.6.0
Jun-08 12:56:05.185 [FileTransfer-2] DEBUG c.u.s3fs.S3FileSystemProvider - S3 download directory from=s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0 to=/home/ubuntu/reproducible-sarek-error/work/stage-63d7cba7-5fbf-4dc8-b7d8-f5c004e0af2b/f4/1da255eac4af8e588382ef1b0e964f/version0.6.0
Jun-08 12:56:07.041 [Actor Thread 49] INFO  nextflow.file.FilePorter - Staging foreign file: s3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0
Jun-08 12:56:08.149 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:08.150 [Task submitter] INFO  nextflow.Session - [da/0bcf65] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:15.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_SAREK:SAREK:FASTP (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/96/2045b86536e5bc53e2da1da6d47470]
Jun-08 12:56:15.854 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:15.855 [Task submitter] INFO  nextflow.Session - [ad/2fa48b] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:15.859 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 12:56:15.859 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 12:56:20.943 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; 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/0bcf659ffcae3010178e9c7e248e9f]
Jun-08 12:56:20.952 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:20.953 [Task submitter] INFO  nextflow.Session - [22/5aa8a0] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:20.959 [Actor Thread 22] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:28.474 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; 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/ad/2fa48bd4218c559859ca21d5c9f72b]
Jun-08 12:56:28.482 [Actor Thread 23] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:28.482 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:28.483 [Task submitter] INFO  nextflow.Session - [a4/77e492] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:33.547 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/22/5aa8a0d391875aa1d36411992c6808]
Jun-08 12:56:33.553 [Actor Thread 23] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:33.557 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:33.558 [Task submitter] INFO  nextflow.Session - [f8/29253e] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:41.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/a4/77e4924cc97fbb8a9b3a7440f6e326]
Jun-08 12:56:41.165 [Actor Thread 44] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:41.173 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:41.181 [Task submitter] INFO  nextflow.Session - [63/103ae2] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:42.192 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: NFCORE_SAREK:SAREK:FASTQC (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/4b/0b9216885c9f1a57a4100c0338ebde]
Jun-08 12:56:45.795 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; 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/f8/29253e9f9f4f00e85610612b5d0549]
Jun-08 12:56:45.800 [Actor Thread 46] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:45.805 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:45.807 [Task submitter] INFO  nextflow.Session - [4c/370c13] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:53.120 [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/63/103ae2c757ed4a3b5a88c2fea542f2]
Jun-08 12:56:53.126 [Actor Thread 44] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:53.127 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:53.128 [Task submitter] INFO  nextflow.Session - [07/77f538] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:56:57.954 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; 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/4c/370c132573ad7235c8f98f34a32ddf]
Jun-08 12:56:57.962 [Actor Thread 46] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:56:57.963 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:56:57.965 [Task submitter] INFO  nextflow.Session - [41/5eb71d] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:57:05.157 [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/07/77f538c7e00f1088a23e8917fdc736]
Jun-08 12:57:05.161 [Actor Thread 23] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:57:05.162 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:05.162 [Task submitter] INFO  nextflow.Session - [6e/349c98] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:57:10.752 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; 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/41/5eb71dc63eccff1500f4728711b659]
Jun-08 12:57:10.756 [Actor Thread 23] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:57:10.760 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:10.761 [Task submitter] INFO  nextflow.Session - [63/11a350] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:57:17.925 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; 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/6e/349c9810de9e286dcdb9122465e16b]
Jun-08 12:57:17.930 [Actor Thread 60] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:57:17.932 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:17.933 [Task submitter] INFO  nextflow.Session - [29/5df4d3] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1)
Jun-08 12:57:23.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/63/11a3507ac8c98e157d9688de8e6107]
Jun-08 12:57:23.407 [Actor Thread 46] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:57:23.412 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:23.413 [Task submitter] INFO  nextflow.Session - [f7/84b872] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:57:29.984 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041541-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/29/5df4d3af003085eacc0a12a8d7275e]
Jun-08 12:57:29.990 [Actor Thread 60] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:S1, sample:SRR9041541, sex:NA, status:0, id:SRR9041541, data_type:bam] size=12
Jun-08 12:57:29.994 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:29.995 [Task submitter] INFO  nextflow.Session - [29/f7ebfa] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:57:31.008 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:31.009 [Task submitter] INFO  nextflow.Session - [0c/0de0f5] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541)
Jun-08 12:57:38.457 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_SAREK:SAREK:FASTQC (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/bf/e0a263867ab9661d0df3ff063c8ce7]
Jun-08 12:57:40.226 [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/f7/84b872633b91d0c261ead4ecbdaaff]
Jun-08 12:57:40.230 [Actor Thread 64] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:57:40.233 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:40.233 [Task submitter] INFO  nextflow.Session - [60/5fb1e4] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:57:47.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; 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/29/f7ebfa90410a34abc8842fe678cf9e]
Jun-08 12:57:47.412 [Actor Thread 64] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:57:47.412 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:47.413 [Task submitter] INFO  nextflow.Session - [49/cf8238] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:57:56.657 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; 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/60/5fb1e4e58deffc5642db39d3aeb939]
Jun-08 12:57:56.662 [Actor Thread 64] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:57:56.664 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:57:56.665 [Task submitter] INFO  nextflow.Session - [a9/50bcd8] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:04.035 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; 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/49/cf8238800e5917376c0592e0bddfb0]
Jun-08 12:58:04.041 [Actor Thread 60] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:58:04.042 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:04.046 [Task submitter] INFO  nextflow.Session - [13/0170e3] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:12.629 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/a9/50bcd81787979155a6a653ec19f435]
Jun-08 12:58:12.636 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:12.638 [Task submitter] INFO  nextflow.Session - [42/eb84a8] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:12.638 [Actor Thread 46] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:58:21.455 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; 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/13/0170e3966f371c72d69b30c45d6e70]
Jun-08 12:58:21.462 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:21.463 [Actor Thread 44] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:58:21.463 [Task submitter] INFO  nextflow.Session - [8f/34f45c] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:29.463 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; 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/42/eb84a8cd8793202a1af5581decefe5]
Jun-08 12:58:29.471 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:29.473 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:58:29.474 [Task submitter] INFO  nextflow.Session - [9c/f62876] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:38.491 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; 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/8f/34f45cf74aaa0e9e57a4efc5e67800]
Jun-08 12:58:38.497 [Actor Thread 44] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:58:38.498 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:38.499 [Task submitter] INFO  nextflow.Session - [2e/6529a0] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:46.441 [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/9c/f628765ea9756a7322ad5af06ea3d9]
Jun-08 12:58:46.446 [Actor Thread 57] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:58:46.449 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:46.450 [Task submitter] INFO  nextflow.Session - [94/3189d5] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:55.138 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; 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/2e/6529a0fe7d1a4e3cc9de5751dd9d98]
Jun-08 12:58:55.146 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:58:55.147 [Task submitter] INFO  nextflow.Session - [4d/608caf] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM (SRR9041540-1)
Jun-08 12:58:55.157 [Actor Thread 44] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:59:03.568 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; 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/94/3189d5e6d2b7440798c487ff873ff6]
Jun-08 12:59:03.576 [Actor Thread 64] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:59:12.583 [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/4d/608caf55be28ddf2f5d4cf40c497dc]
Jun-08 12:59:12.588 [Actor Thread 60] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=[patient:P1, sample:SRR9041540, sex:NA, status:0, id:SRR9041540, data_type:bam] size=12
Jun-08 12:59:12.621 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:59:12.622 [Task submitter] INFO  nextflow.Session - [55/5ff0b3] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540)
Jun-08 12:59:27.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/0c/0de0f5158801c9955a65f264a18a47]
Jun-08 12:59:27.073 [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/0c/0de0f5158801c9955a65f264a18a47/SRR9041541.sorted.cram` (pattern: `SRR9041541.sorted.cram`)
Jun-08 12:59:27.076 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 12:59:27.077 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 12:59:27.096 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:59:27.097 [Task submitter] INFO  nextflow.Session - [24/ae82e1] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041541)
Jun-08 12:59:37.991 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/24/ae82e166199b1044e25ca2cdcaaa9f]
Jun-08 12:59:37.996 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 12:59:37.996 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 12:59:38.837 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 12:59:38.839 [Task submitter] INFO  nextflow.Session - [ab/2ff5e2] Submitted process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041541)
Jun-08 13:00:09.259 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/ab/2ff5e257bec2733cf8f050199b6e13]
Jun-08 13:00:13.197 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:00:13.198 [Task submitter] INFO  nextflow.Session - [25/1de5ff] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041541)
Jun-08 13:00:13.203 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:00:13.204 [Task submitter] INFO  nextflow.Session - [d3/5fb6f9] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041541)
Jun-08 13:00:13.210 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:00:13.210 [Task submitter] INFO  nextflow.Session - [51/1a0c77] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541)
Jun-08 13:00:19.828 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/d3/5fb6f9320759b5177bff13b6971a7e]
Jun-08 13:00:19.844 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:00:19.844 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:00:19.844 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:00:19.845 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:00:19.845 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:00:19.845 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:00:19.845 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:00:31.756 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below
~> TaskHandler[id: 88; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/55/5ff0b3843015c56036e1003f1f59f1]
~> TaskHandler[id: 92; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/25/1de5ff5c5afe3b7163a2948555fa47]
~> TaskHandler[id: 93; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/51/1a0c77c0e305d3921015bb670e1c2b]
Jun-08 13:00:45.989 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/25/1de5ff5c5afe3b7163a2948555fa47]
Jun-08 13:02:11.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/55/5ff0b3843015c56036e1003f1f59f1]
Jun-08 13:02:11.656 [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/55/5ff0b3843015c56036e1003f1f59f1/SRR9041540.sorted.cram` (pattern: `SRR9041540.sorted.cram`)
Jun-08 13:02:11.660 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:02:11.660 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:02:11.677 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:02:11.678 [Task submitter] INFO  nextflow.Session - [6c/daebec] Submitted process > NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041540)
Jun-08 13:02:30.920 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/6c/daebec274c53a7fd48641c328e21a5]
Jun-08 13:02:30.926 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:02:30.926 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_MERGE_INDEX_SAMTOOLS:INDEX_MERGE_BAM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:02:31.674 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:02:31.676 [Task submitter] INFO  nextflow.Session - [7a/9911fe] Submitted process > NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041540)
Jun-08 13:03:25.772 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: NFCORE_SAREK:SAREK:BAM_TO_CRAM_MAPPING (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7a/9911fec14be1fd2ab0a7a4e36d8041]
Jun-08 13:03:25.784 [Actor Thread 23] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.002 s; external sort time: 0.001 s; total time: 0.003 s
Jun-08 13:03:25.792 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/beff384bf6af84609c197ac7b05092b2
Jun-08 13:03:25.794 [Actor Thread 23] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6744690378925350726
Jun-08 13:03:27.041 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:03:27.042 [Task submitter] INFO  nextflow.Session - [ce/874a16] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041540)
Jun-08 13:03:27.048 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:03:27.049 [Task submitter] INFO  nextflow.Session - [7d/35225d] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540)
Jun-08 13:03:27.054 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:03:27.055 [Task submitter] INFO  nextflow.Session - [18/dc1e1f] Submitted process > NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041540)
Jun-08 13:03:37.113 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/18/dc1e1f03f5212e3b6ad84ab00da8ce]
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:03:37.126 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:MOSDEPTH > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:04:18.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/ce/874a1606a0c5c94d872b86f63e24a3]
Jun-08 13:04:42.653 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/51/1a0c77c0e305d3921015bb670e1c2b]
Jun-08 13:04:42.658 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:04:42.686 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:04:42.686 [Task submitter] INFO  nextflow.Session - [a2/7fec99] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041541)
Jun-08 13:04:42.693 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:04:42.693 [Task submitter] INFO  nextflow.Session - [ec/37b23b] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041541)
Jun-08 13:04:42.700 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:04:42.701 [Task submitter] INFO  nextflow.Session - [49/773deb] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041541)
Jun-08 13:04:42.707 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:04:42.707 [Task submitter] INFO  nextflow.Session - [bd/bd8b75] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041541)
Jun-08 13:04:43.404 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:04:43.405 [Task submitter] INFO  nextflow.Session - [40/1eb14f] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (SRR9041541)
Jun-08 13:04:44.773 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/a2/7fec991b1688c3262a165ffc9df495]
Jun-08 13:04:45.768 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/bd/bd8b75a9346a7c7d7582cbe842d484]
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<7:1>
Jun-08 13:04:45.815 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<12:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<13:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<14:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<15:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<16:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<17:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<18:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<20:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<21:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<22:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<23:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<24:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<25:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<26:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<27:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<28:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<29:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<30:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<31:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<32:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<33:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<34:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<35:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<36:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<37:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<38:1>
Jun-08 13:04:45.816 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<39:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<40:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<41:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<42:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<43:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<44:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<45:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<46:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<47:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<48:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<49:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<50:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<51:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<52:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<53:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<54:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<55:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<56:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<57:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<58:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<59:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<60:1>
Jun-08 13:04:45.817 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<61:1>
Jun-08 13:04:45.841 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/49/773debc9b62135434adbc8f00f8217]
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<7:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<12:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<13:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<14:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<15:1>
Jun-08 13:04:45.881 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<16:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<18:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<19:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<20:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<21:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<22:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<23:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<24:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<25:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<26:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<27:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<28:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<29:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<30:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<31:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<32:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<33:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<34:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<35:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<36:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<37:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<38:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<39:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<40:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<41:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<42:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<43:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<44:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<45:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<46:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<47:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<48:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<49:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<50:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<51:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<52:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<53:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<54:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<55:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<56:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<57:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<58:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<59:1>
Jun-08 13:04:45.882 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<60:1>
Jun-08 13:04:45.883 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<61:1>
Jun-08 13:04:45.918 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/ec/37b23b90e1e09e3233eab80bde7cdf]
Jun-08 13:04:45.961 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<7:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<12:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<13:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<14:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<15:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<16:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<17:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<19:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<20:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<21:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<22:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<23:1>
Jun-08 13:04:45.962 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<24:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<25:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<26:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<27:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<28:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<29:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<30:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<31:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<32:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<33:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<34:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<35:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<36:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<37:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<38:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<39:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<40:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<41:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<42:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<43:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<44:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<45:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<46:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<47:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<48:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<49:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<50:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<51:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<52:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<53:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<54:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<55:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<56:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<57:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<58:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<59:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<60:1>
Jun-08 13:04:45.963 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<61:1>
Jun-08 13:05:17.356 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (SRR9041541); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/40/1eb14f0c08fef2da3d43ee793ca7a4]
Jun-08 13:05:17.362 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:05:17.362 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:05:31.779 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7d/35225d7a3ff86d475670a0917cf2bc]
Jun-08 13:10:31.782 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540); status: RUNNING; exit: -; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7d/35225d7a3ff86d475670a0917cf2bc]
Jun-08 13:11:57.866 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/7d/35225d7a3ff86d475670a0917cf2bc]
Jun-08 13:11:57.872 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:11:57.882 [Actor Thread 42] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s
Jun-08 13:11:57.888 [Actor Thread 42] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/5d18287549e90dcc0e3bd57c6e8cc8e0
Jun-08 13:11:57.890 [Actor Thread 42] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-16728545258091292898
Jun-08 13:11:57.897 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:11:57.898 [Task submitter] INFO  nextflow.Session - [bc/13ac9c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041540)
Jun-08 13:11:57.909 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:11:57.909 [Task submitter] INFO  nextflow.Session - [29/e0f11a] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041540)
Jun-08 13:11:57.915 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:11:57.916 [Task submitter] INFO  nextflow.Session - [82/024efb] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041540)
Jun-08 13:11:57.951 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:11:57.952 [Task submitter] INFO  nextflow.Session - [43/42cf32] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041540)
Jun-08 13:11:58.779 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:11:58.780 [Task submitter] INFO  nextflow.Session - [cc/585f85] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (SRR9041540)
Jun-08 13:11:59.702 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/bc/13ac9c35d27b9edab83286313b2395]
Jun-08 13:12:00.895 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/29/e0f11a4d0d4e9471b591a4484c3d78]
Jun-08 13:12:00.931 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<7:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<12:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<13:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<14:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<15:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<16:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<17:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<19:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<20:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<21:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<22:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<23:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<24:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<25:1>
Jun-08 13:12:00.932 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<26:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<27:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<28:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<29:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<30:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<31:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<32:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<33:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<34:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<35:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<36:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<37:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<38:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<39:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<40:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<41:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<42:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<43:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<44:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<45:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<46:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<47:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<48:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<49:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<50:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<51:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<52:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<53:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<54:1>
Jun-08 13:12:00.933 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<55:1>
Jun-08 13:12:00.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<56:1>
Jun-08 13:12:00.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<57:1>
Jun-08 13:12:00.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<58:1>
Jun-08 13:12:00.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<59:1>
Jun-08 13:12:00.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<60:1>
Jun-08 13:12:00.934 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL > Skipping output binding because one or more optional files are missing: fileoutparam<61:1>
Jun-08 13:12:00.937 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/82/024efbf030c8f76181b0a1fe4a7381]
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<7:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:12:00.964 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<12:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<13:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<14:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<15:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<16:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<17:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<18:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<20:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<21:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<22:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<23:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<24:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<25:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<26:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<27:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<28:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<29:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<30:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<31:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<32:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<33:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<34:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<35:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<36:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<37:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<38:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<39:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<40:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<41:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<42:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<43:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<44:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<45:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<46:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<47:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<48:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<49:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<50:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<51:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<52:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<53:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<54:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<55:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<56:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<57:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<58:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<59:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<60:1>
Jun-08 13:12:00.965 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY > Skipping output binding because one or more optional files are missing: fileoutparam<61:1>
Jun-08 13:12:00.993 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/43/42cf3218ab3af2ef7098f8052e105a]
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<4:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<7:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<8:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<9:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<10:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<11:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<12:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<13:1>
Jun-08 13:12:01.014 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<14:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<15:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<16:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<18:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<19:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<20:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<21:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<22:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<23:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<24:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<25:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<26:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<27:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<28:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<29:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<30:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<31:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<32:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<33:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<34:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<35:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<36:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<37:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<38:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<39:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<40:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<41:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<42:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<43:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<44:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<45:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<46:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<47:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<48:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<49:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<50:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<51:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<52:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<53:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<54:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<55:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<56:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<57:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<58:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<59:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<60:1>
Jun-08 13:12:01.015 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT > Skipping output binding because one or more optional files are missing: fileoutparam<61:1>
Jun-08 13:12:06.140 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP (SRR9041540); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/cc/585f85b754a5ca8e0437f4fe9cd26b]
Jun-08 13:12:06.145 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP > Skipping output binding because one or more optional files are missing: fileoutparam<0:1>
Jun-08 13:12:06.146 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jun-08 13:12:06.197 [Actor Thread 28] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 50; slices: 1; internal sort time: 0.041 s; external sort time: 0.006 s; total time: 0.047 s
Jun-08 13:12:06.222 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/ubuntu/reproducible-sarek-error/work/collect-file/606d5a8fff85a3e9f71cc1693d4b34af
Jun-08 13:12:06.224 [Actor Thread 28] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-2025953076591881431
Jun-08 13:12:06.317 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:12:06.318 [Task submitter] INFO  nextflow.Session - [90/d106b1] Submitted process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS (1)
Jun-08 13:12:07.731 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS (1); status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/90/d106b1c02ad89f7bfb76d8b3bdd41e]
Jun-08 13:12:07.758 [Actor Thread 37] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/ubuntu/.nextflow/assets/nf-core/sarek/assets/multiqc_config.yml
Jun-08 13:12:07.786 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jun-08 13:12:07.788 [Task submitter] INFO  nextflow.Session - [39/201a50] Submitted process > NFCORE_SAREK:SAREK:MULTIQC
Jun-08 13:12:51.996 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: NFCORE_SAREK:SAREK:MULTIQC; status: COMPLETED; exit: 0; error: -; workDir: /home/ubuntu/reproducible-sarek-error/work/39/201a507c3b29d2e93c618d6a691cda]
Jun-08 13:12:52.005 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-08 13:12:52.007 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-08 13:12:52.033 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Jun-08 13:12:52.037 [main] INFO  nextflow.Nextflow - -[0;35m[nf-core/sarek][0;32m Pipeline completed successfully[0m-
Jun-08 13:12:52.046 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=58; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=4h 1m 22s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=7; peakCpus=56; peakMemory=82 GB; ]
Jun-08 13:12:52.046 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jun-08 13:12:52.049 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jun-08 13:12:52.178 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
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Jun-08 13:12:52.988 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jun-08 13:12:53.306 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jun-08 13:12:53.306 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@1.16.2'
Jun-08 13:12:53.306 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon
Jun-08 13:12:53.357 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jun-08 13:12:53.362 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'S3TransferManager' shutdown completed (hard=false)
Jun-08 13:12:53.362 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye