log.txt

May-07 23:01:49.322 [main] DEBUG nextflow.cli.Launcher - $> nextflow run . -profile test,docker --fasta /Users/benjaminwehnert/GID1A_SUNi_ref_small.fasta --reading_frame 352-1383 --min_counts 2 --mutagenesis_type max_diff_to_wt --outdir ./results
May-07 23:01:49.500 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.4
May-07 23:01:49.524 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/benjaminwehnert/.nextflow/plugins; core-plugins: nf-amazon@2.5.3,nf-azure@1.6.1,nf-cloudcache@0.4.1,nf-codecommit@0.2.1,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2-patch1,nf-tower@1.9.1,nf-wave@1.4.2-patch1
May-07 23:01:49.533 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-07 23:01:49.534 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-07 23:01:49.536 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
May-07 23:01:49.549 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
May-07 23:01:50.385 [main] WARN  nextflow.config.Manifest - Invalid config manifest attribute `contributors`
May-07 23:01:50.406 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /Users/benjaminwehnert/dmscore/nextflow.config
May-07 23:01:50.408 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/benjaminwehnert/dmscore/nextflow.config
May-07 23:01:50.426 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/benjaminwehnert/.nextflow/secrets/store.json
May-07 23:01:50.428 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@169268a7] - activable => nextflow.secret.LocalSecretsProvider@169268a7
May-07 23:01:50.438 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker`
May-07 23:01:51.909 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, giga, incliva, ilifu, ki_luria, uge, icr_alma, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, ccga_med, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, ceci_nic5, humantechnopole, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, seattlechildrens, icr_davros, ceres, arm, munin, rosalind, hasta, cfc, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, alliance_canada, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, mssm, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, seadragon, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, genouest, cbe, unsw_katana, gitpod, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac, fsu_draco]
May-07 23:01:51.958 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
May-07 23:01:51.972 [main] DEBUG nextflow.cli.CmdRun - Launching `./main.nf` [modest_coulomb] DSL2 - revision: 84101fc51c
May-07 23:01:51.974 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.3.0]
May-07 23:01:51.974 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
May-07 23:01:51.974 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.3.0]
May-07 23:01:51.975 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.3.0
May-07 23:01:51.983 [main] INFO  org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.3.0' resolved
May-07 23:01:51.983 [main] INFO  org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.3.0'
May-07 23:01:51.990 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.3.0
May-07 23:01:52.045 [main] DEBUG nextflow.Session - Session UUID: 2397b75e-3882-46d7-ba2c-8549f8a2b4a6
May-07 23:01:52.045 [main] DEBUG nextflow.Session - Run name: modest_coulomb
May-07 23:01:52.046 [main] DEBUG nextflow.Session - Executor pool size: 8
May-07 23:01:52.053 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
May-07 23:01:52.057 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-07 23:01:52.077 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.4 build 5917
  Created: 01-08-2024 07:05 UTC (09:05 CEST)
  System: Mac OS X 15.0
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.13+0
  Encoding: UTF-8 (UTF-8)
  Process: 31358@MacBook-Air-von-Benjamin.local [127.0.0.1]
  CPUs: 8 - Mem: 8 GB (94.6 MB) - Swap: 8 GB (737.5 MB)
May-07 23:01:52.088 [main] DEBUG nextflow.Session - Work-dir: /Users/benjaminwehnert/dmscore/work [Mac OS X]
May-07 23:01:52.088 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/benjaminwehnert/dmscore/bin
May-07 23:01:52.104 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
May-07 23:01:52.123 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-07 23:01:52.143 [main] DEBUG nextflow.Session - Observer factory: ValidationObserverFactory
May-07 23:01:52.174 [main] WARN  nextflow.config.Manifest - Invalid config manifest attribute `contributors`
May-07 23:01:52.195 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-07 23:01:52.205 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
May-07 23:01:52.264 [main] DEBUG nextflow.Session - Session start
May-07 23:01:52.266 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/benjaminwehnert/dmscore/results/pipeline_info/execution_trace_2025-05-07_23-01-50.txt
May-07 23:01:52.411 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-07 23:01:53.516 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
May-07 23:01:53.917 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
May-07 23:01:53.918 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
May-07 23:01:53.920 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
May-07 23:01:53.921 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
May-07 23:01:54.131 [main] WARN  nextflow.script.ScriptBinding - Access to undefined parameter `custom_codon_library` -- Initialise it to a default value eg. `params.custom_codon_library = some_value`
May-07 23:01:54.356 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema
May-07 23:01:54.357 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema
May-07 23:01:54.359 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema
May-07 23:01:54.360 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema
May-07 23:01:54.574 [main] INFO  nextflow.Nextflow -
------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/dmscore 1.0.0dev
------------------------------------------------------
Input/output options
  input                     : https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/samplesheet_qc_only.csv
  outdir                    : ./results
  min_counts                : 2
  mutagenesis_type          : max_diff_to_wt

Reference genome options
  genome                    : R64-1-1
  fasta                     : /Users/benjaminwehnert/GID1A_SUNi_ref_small.fasta

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Generic options
  trace_report_suffix       : 2025-05-07_23-01-50

Core Nextflow options
  runName                   : modest_coulomb
  containerEngine           : docker
  launchDir                 : /Users/benjaminwehnert/dmscore
  workDir                   : /Users/benjaminwehnert/dmscore/work
  projectDir                : /Users/benjaminwehnert/dmscore
  userName                  : benjaminwehnert
  profile                   : test,docker
  configFiles               : /Users/benjaminwehnert/dmscore/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

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

May-07 23:01:54.576 [main] DEBUG n.validation.ValidationExtension - Starting parameters validation
May-07 23:01:54.920 [main] DEBUG nextflow.validation.SchemaEvaluator - Started validating /BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/samplesheet_qc_only.csv
May-07 23:01:55.945 [main] DEBUG nextflow.validation.SchemaEvaluator - Validation of file 'https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/samplesheet_qc_only.csv' passed!
May-07 23:01:56.095 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://ngi-igenomes/igenomes/'
May-07 23:01:56.099 [main] DEBUG n.validation.ValidationExtension - Finishing parameters validation
May-07 23:01:56.178 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DMSCORE:DMSCORE:FASTQC
May-07 23:01:56.182 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_DMSCORE:DMSCORE:FASTQC
May-07 23:01:56.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.202 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
May-07 23:01:56.206 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=8 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
May-07 23:01:56.209 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
May-07 23:01:56.359 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DMSCORE:DMSCORE:MULTIQC
May-07 23:01:56.360 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_DMSCORE:DMSCORE:MULTIQC
May-07 23:01:56.362 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.363 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DMSCORE:DMSCORE:BWA_INDEX
May-07 23:01:56.373 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWA_INDEX` matches process NFCORE_DMSCORE:DMSCORE:BWA_INDEX
May-07 23:01:56.375 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.375 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_DMSCORE:DMSCORE:BWA_MEM
May-07 23:01:56.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWA_MEM` matches process NFCORE_DMSCORE:DMSCORE:BWA_MEM
May-07 23:01:56.394 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.395 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.404 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DMSCORE:DMSCORE:BAMFILTER_DMS
May-07 23:01:56.406 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAMFILTER_DMS` matches process NFCORE_DMSCORE:DMSCORE:BAMFILTER_DMS
May-07 23:01:56.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DMSCORE:DMSCORE:PREMERGE
May-07 23:01:56.418 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PREMERGE` matches process NFCORE_DMSCORE:DMSCORE:PREMERGE
May-07 23:01:56.420 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.420 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.429 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_DMSCORE:DMSCORE:GATK_SATURATIONMUTAGENESIS
May-07 23:01:56.430 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK_SATURATIONMUTAGENESIS` matches process NFCORE_DMSCORE:DMSCORE:GATK_SATURATIONMUTAGENESIS
May-07 23:01:56.433 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.433 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.443 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ
May-07 23:01:56.443 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DMSANALYSIS_AASEQ` matches process NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ
May-07 23:01:56.446 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.446 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.458 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS
May-07 23:01:56.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DMSANALYSIS_POSSIBLE_MUTATIONS` matches process NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS
May-07 23:01:56.461 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.461 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_PROCESS_GATK
May-07 23:01:56.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DMSANALYSIS_PROCESS_GATK` matches process NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_PROCESS_GATK
May-07 23:01:56.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-07 23:01:56.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-07 23:01:56.499 [main] DEBUG nextflow.Session - Config process names validation disabled as requested
May-07 23:01:56.500 [main] DEBUG nextflow.Session - Igniting dataflow network (43)
May-07 23:01:56.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:FASTQC
May-07 23:01:56.508 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:MULTIQC
May-07 23:01:56.509 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:BWA_INDEX
May-07 23:01:56.509 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:BWA_MEM
May-07 23:01:56.511 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:BAMFILTER_DMS
May-07 23:01:56.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:PREMERGE
May-07 23:01:56.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:GATK_SATURATIONMUTAGENESIS
May-07 23:01:56.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ
May-07 23:01:56.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS
May-07 23:01:56.512 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_PROCESS_GATK
May-07 23:01:56.514 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_e5f965e09aa3641b: /Users/benjaminwehnert/dmscore/./workflows/../modules/local/bamprocessing/premerge.nf
  Script_113f045ba19c2c46: /Users/benjaminwehnert/dmscore/./workflows/../modules/nf-core/fastqc/main.nf
  Script_4f612cfd8c52e8cd: /Users/benjaminwehnert/dmscore/./subworkflows/local/utils_nfcore_dmscore_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf
  Script_215a636da7ab24a2: /Users/benjaminwehnert/dmscore/./workflows/../subworkflows/local/utils_nfcore_dmscore_pipeline/../../nf-core/utils_nfschema_plugin/main.nf
  Script_68606fccdecc54d9: /Users/benjaminwehnert/dmscore/./subworkflows/local/utils_nfcore_dmscore_pipeline/main.nf
  Script_0f3077e98f6a93f6: /Users/benjaminwehnert/dmscore/./workflows/../modules/nf-core/bwa/mem/main.nf
  Script_5c4e8d4051efa81e: /Users/benjaminwehnert/dmscore/./subworkflows/local/utils_nfcore_dmscore_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf
  Script_3bf8120d0b5bcde1: /Users/benjaminwehnert/dmscore/./workflows/../modules/local/dmsanalysis/possiblemutations.nf
  Script_d65a0ba0a319d7db: /Users/benjaminwehnert/dmscore/./workflows/../modules/local/dmsanalysis/aaseq.nf
  Script_4ff7366a79e0ef06: /Users/benjaminwehnert/dmscore/./workflows/../modules/local/bamprocessing/bamfilteringdms.nf
  Script_c568aae5b239c1c5: /Users/benjaminwehnert/dmscore/main.nf
  Script_09ccfa79b2802f41: /Users/benjaminwehnert/dmscore/./workflows/dmscore.nf
  Script_4955288afd8ca61e: /Users/benjaminwehnert/dmscore/./workflows/../modules/nf-core/multiqc/main.nf
  Script_a1878766b1a6b241: /Users/benjaminwehnert/dmscore/./workflows/../modules/local/dmsanalysis/processgatk.nf
  Script_37dcd664b2773148: /Users/benjaminwehnert/dmscore/./workflows/../modules/local/gatk/saturationmutagenesis.nf
  Script_25aa31c18d513c61: /Users/benjaminwehnert/dmscore/./workflows/../modules/nf-core/bwa/index/main.nf
May-07 23:01:56.514 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
May-07 23:01:56.514 [main] DEBUG nextflow.Session - Session await
May-07 23:01:56.605 [Actor Thread 1] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.011 s; total time: 0.012 s
May-07 23:01:56.605 [Actor Thread 2] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.011 s; total time: 0.012 s
May-07 23:01:56.611 [Actor Thread 2] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /Users/benjaminwehnert/dmscore/work/collect-file/4640128d9cfd4a45636425a4f43db374
May-07 23:01:56.611 [Actor Thread 1] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /Users/benjaminwehnert/dmscore/work/collect-file/04a58cc29ef1c76e5af4e2fb20a13ad7
May-07 23:01:56.619 [Actor Thread 1] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /var/folders/r0/ldrzd4wn1s3516hy0vsn8xzm0000gn/T/nxf-1651345332501275985
May-07 23:01:56.619 [Actor Thread 2] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /var/folders/r0/ldrzd4wn1s3516hy0vsn8xzm0000gn/T/nxf-12321695686053957190
May-07 23:01:56.623 [Actor Thread 3] DEBUG nextflow.util.HashBuilder - [WARN] Unknown hashing type: class Script_09ccfa79b2802f41$_runScript_closure1$_closure26
May-07 23:01:56.624 [Actor Thread 14] DEBUG nextflow.util.HashBuilder - Unable to get file attributes file: /NULL -- Cause: java.nio.file.NoSuchFileException: /NULL
May-07 23:01:56.697 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:01:56.698 [Task submitter] INFO  nextflow.Session - [d4/e141d7] Submitted process > NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ (amino_acid_sequence)
May-07 23:01:56.730 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/pMS190_GID1A_SUNi_S2_1_R2_50k.fastq to work dir: /Users/benjaminwehnert/dmscore/work/stage-2397b75e-3882-46d7-ba2c-8549f8a2b4a6/6a/8815724cee5e2e4e17200e98e8c0ad/pMS190_GID1A_SUNi_S2_1_R2_50k.fastq
May-07 23:01:56.730 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/pMS190_GID1A_SUNi_S2_1_R1_50k.fastq to work dir: /Users/benjaminwehnert/dmscore/work/stage-2397b75e-3882-46d7-ba2c-8549f8a2b4a6/40/dfe72a8fa5ce1b038fdf1aa1fb4749/pMS190_GID1A_SUNi_S2_1_R1_50k.fastq
May-07 23:01:58.744 [Actor Thread 15] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/pMS190_GID1A_SUNi_S2_1_R1_50k.fastq
May-07 23:02:00.581 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ (amino_acid_sequence); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/d4/e141d76a7c3b4130080bcdf8a831a3]
May-07 23:02:00.585 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-07 23:02:00.612 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:00.613 [Task submitter] INFO  nextflow.Session - [49/349fd9] Submitted process > NFCORE_DMSCORE:DMSCORE:BWA_INDEX (GID1A_SUNi_ref_small.fasta)
May-07 23:02:00.663 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
May-07 23:02:00.756 [Actor Thread 15] INFO  nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/pMS190_GID1A_SUNi_S2_1_R2_50k.fastq
May-07 23:02:00.757 [Actor Thread 4] WARN  nextflow.processor.TaskContext - Cannot serialize context map. Cause: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue -- Resume will not work on this process
May-07 23:02:00.763 [Actor Thread 4] DEBUG nextflow.processor.TaskContext - Failed to serialize delegate map items: [
  'meta':[Script_09ccfa79b2802f41$_runScript_closure1$_closure26] =
  'pos_range':[java.lang.String] = 352-1383
  '$':[java.lang.Boolean] = true
  'wt_seq':[nextflow.processor.TaskPath] = GID1A_SUNi_ref_small.fasta
  'script':[nextflow.processor.TaskPath] = aa_seq.R
  'task':[nextflow.processor.TaskConfig] = [container:community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa, withName:PREMERGE:[publishDir:[path:./results/intermediate_files/bam_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure9$_closure21@26dc7ffc]], memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure15@13f9d575, withName:FASTQC:[ext:[args:--quiet], containerOptions:], withLabel:error_retry:[errorStrategy:retry, maxRetries:2], when:nextflow.script.TaskClosure@264d7648, withLabel:process_high:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure9$_closure23@1b36f3f3, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure9$_closure24@5e504cf6, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure9$_closure25@35f6834], withLabel:error_ignore:[errorStrategy:ignore], resourceLimits:[cpus:4, memory:8.GB, time:1.h], withName:DMSANALYSIS_AASEQ:[publishDir:[path:./results/intermediate_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure13$_closure25@4eeda121]], withLabel:process_high_memory:[memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure11$_closure27@62e86a64], withName:BAMFILTER_DMS:[publishDir:[path:./results/intermediate_files/bam_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure8$_closure20@3e03bd33]], publishDir:[[path:./results/intermediate_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure13$_closure25@4eeda121]], withName:BWA_MEM:[publishDir:[path:./results/intermediate_files/bam_files/bwa/mem, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure7$_closure19@46e56c0f]], executor:local, stub:nextflow.script.TaskClosure@6522395b, conda:null/environment.yml, withName:GATK_SATURATIONMUTAGENESIS:[publishDir:[path:./results/intermediate_files/gatk, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure10$_closure22@4438d4d1]], cacheable:true, withLabel:process_low:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure7$_closure17@67f11340, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure7$_closure18@a998ea5, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure7$_closure19@7e85964c], withLabel:process_medium:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure8$_closure20@7c995b11, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure8$_closure21@131d3cd1, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure8$_closure22@55b774b1], tag:amino_acid_sequence, withName:MULTIQC:[ext:[args:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure5$_closure15@7d2bfbd], publishDir:[path:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure5$_closure16@31a52d85, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure5$_closure17@4ba464d4]], workDir:/Users/benjaminwehnert/dmscore/work/d4/e141d76a7c3b4130080bcdf8a831a3, exitStatus:0, ext:[:], withLabel:process_single:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure14@255893ed, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure15@13f9d575, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure16@37e5efac], withName:BWA_INDEX:[publishDir:[path:./results/intermediate_files/bam_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure6$_closure18@2f3435d0]], process:NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ, debug:false, cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure14@255893ed, index:1, label:[process_single], withLabel:process_long:[time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure10$_closure26@475e6626], maxRetries:1, maxErrors:-1, shell:bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
, withName:DMSANALYSIS_POSSIBLE_MUTATIONS:[publishDir:[path:./results/intermediate_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure11$_closure23@267852db]], name:NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_AASEQ (amino_acid_sequence), containerOptions:-u $(id -u):$(id -g), errorStrategy:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure5@3e785137, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure16@37e5efac, withName:DMSANALYSIS_PROCESS_GATK:[publishDir:[path:./results/intermediate_files/processed_gatk_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure14$_closure26@30ec799d]], hash:d4e141d76a7c3b4130080bcdf8a831a3]
]
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue
Serialization trace:
queue (org.codehaus.groovy.util.ReferenceManager$CallBackedManager)
manager (org.codehaus.groovy.util.ReferenceManager$1)
manager (org.codehaus.groovy.util.ReferenceBundle)
bundle (org.codehaus.groovy.reflection.CachedClass$4)
cachedSuperClass (org.codehaus.groovy.reflection.stdclasses.ObjectCachedClass)
cachedClass (org.codehaus.groovy.reflection.CachedMethod)
allMethods (groovy.lang.MetaClassImpl)
delegate (groovy.runtime.metaclass.NextflowDelegatingMetaClass)
metaClass (groovyx.gpars.dataflow.DataflowVariable)
first (groovyx.gpars.dataflow.stream.DataflowStream)
asyncHead (groovyx.gpars.dataflow.stream.DataflowStreamReadAdapter)
source (nextflow.extension.MapOp)
owner (nextflow.extension.MapOp$_apply_closure1)
code (groovyx.gpars.dataflow.operator.DataflowOperatorActor)
actor (groovyx.gpars.dataflow.operator.DataflowOperator)
allOperators (nextflow.Session)
session (nextflow.validation.ValidationExtension)
target (nextflow.script.FunctionDef)
definitions (nextflow.script.ScriptMeta)
meta (nextflow.script.ScriptBinding)
binding (Script_09ccfa79b2802f41)
delegate (Script_09ccfa79b2802f41$_runScript_closure1)
delegate (Script_09ccfa79b2802f41$_runScript_closure1$_closure26)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:82)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:22)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:82)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:22)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:95)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:21)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:95)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:21)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.util.KryoHelper.serialize(SerializationHelper.groovy:166)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskContext.serialize(TaskContext.groovy:198)
	at nextflow.cache.CacheDB.writeTaskEntry0(CacheDB.groovy:148)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
	at nextflow.cache.CacheDB$_putTaskAsync_closure1.doCall(CacheDB.groovy:157)
	at nextflow.cache.CacheDB$_putTaskAsync_closure1.call(CacheDB.groovy)
	at groovyx.gpars.agent.AgentBase.onMessage(AgentBase.java:102)
	at groovyx.gpars.agent.Agent.handleMessage(Agent.java:84)
	at groovyx.gpars.agent.AgentCore$1.handleMessage(AgentCore.java:48)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue
	at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:48)
	at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:26)
	at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:351)
	at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:344)
	at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:56)
	at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:461)
	at com.esotericsoftware.kryo.util.DefaultClassResolver.writeClass(DefaultClassResolver.java:79)
	at com.esotericsoftware.kryo.Kryo.writeClass(Kryo.java:488)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:57)
	... 106 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
	at jdk.internal.reflect.GeneratedConstructorAccessor39.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481)
	at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:35)
	... 114 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private final java.lang.ref.ReferenceQueue$Lock java.lang.ref.ReferenceQueue.lock accessible: module java.base does not "opens java.lang.ref" to unnamed module @7b02881e
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
	at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:282)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:217)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:156)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:133)
	... 119 common frames omitted
May-07 23:02:02.378 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_DMSCORE:DMSCORE:BWA_INDEX (GID1A_SUNi_ref_small.fasta); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/49/349fd93ff7dd98e92e426a30457fb9]
May-07 23:02:02.387 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:02.388 [Task submitter] INFO  nextflow.Session - [36/b138e8] Submitted process > NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS (table /w all possible variants)
May-07 23:02:02.422 [Actor Thread 8] WARN  nextflow.processor.TaskContext - Cannot serialize context map. Cause: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue -- Resume will not work on this process
May-07 23:02:13.067 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS (table /w all possible variants); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/36/b138e8e27f7423eea98b17aaf74451]
May-07 23:02:13.085 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:13.085 [Task submitter] INFO  nextflow.Session - [67/c2a06b] Submitted process > NFCORE_DMSCORE:DMSCORE:BWA_MEM (gid1a_1_quality_1_pe)
May-07 23:02:13.133 [Actor Thread 6] WARN  nextflow.processor.TaskContext - Cannot serialize context map. Cause: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue -- Resume will not work on this process
May-07 23:02:13.136 [Actor Thread 6] DEBUG nextflow.processor.TaskContext - Failed to serialize delegate map items: [
  'meta':[Script_09ccfa79b2802f41$_runScript_closure1$_closure26] =
  'pos_range':[java.lang.String] = 352-1383
  'mutagenesis_type':[java.lang.String] = max_diff_to_wt
  '$':[java.lang.Boolean] = true
  'wt_seq':[nextflow.processor.TaskPath] = GID1A_SUNi_ref_small.fasta
  'custom_codon_library':[nextflow.processor.TaskPath] = NULL
  'script':[nextflow.processor.TaskPath] = possible_mutations.R
  'task':[nextflow.processor.TaskConfig] = [container:community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa, withName:PREMERGE:[publishDir:[path:./results/intermediate_files/bam_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure9$_closure21@26dc7ffc]], memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure15@13f9d575, withName:FASTQC:[ext:[args:--quiet], containerOptions:], withLabel:error_retry:[errorStrategy:retry, maxRetries:2], when:nextflow.script.TaskClosure@5f4899a5, withLabel:process_high:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure9$_closure23@1b36f3f3, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure9$_closure24@5e504cf6, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure9$_closure25@35f6834], withLabel:error_ignore:[errorStrategy:ignore], resourceLimits:[cpus:4, memory:8.GB, time:1.h], withName:DMSANALYSIS_AASEQ:[publishDir:[path:./results/intermediate_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure13$_closure25@4eeda121]], withLabel:process_high_memory:[memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure11$_closure27@62e86a64], withName:BAMFILTER_DMS:[publishDir:[path:./results/intermediate_files/bam_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure8$_closure20@3e03bd33]], publishDir:[[path:./results/intermediate_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure11$_closure23@267852db]], withName:BWA_MEM:[publishDir:[path:./results/intermediate_files/bam_files/bwa/mem, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure7$_closure19@46e56c0f]], executor:local, stub:nextflow.script.TaskClosure@7069093e, conda:null/environment.yml, withName:GATK_SATURATIONMUTAGENESIS:[publishDir:[path:./results/intermediate_files/gatk, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure10$_closure22@4438d4d1]], cacheable:true, withLabel:process_low:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure7$_closure17@67f11340, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure7$_closure18@a998ea5, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure7$_closure19@7e85964c], withLabel:process_medium:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure8$_closure20@7c995b11, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure8$_closure21@131d3cd1, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure8$_closure22@55b774b1], tag:table /w all possible variants, withName:MULTIQC:[ext:[args:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure5$_closure15@7d2bfbd], publishDir:[path:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure5$_closure16@31a52d85, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure5$_closure17@4ba464d4]], workDir:/Users/benjaminwehnert/dmscore/work/36/b138e8e27f7423eea98b17aaf74451, exitStatus:0, ext:[:], withLabel:process_single:[cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure14@255893ed, memory:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure15@13f9d575, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure16@37e5efac], withName:BWA_INDEX:[publishDir:[path:./results/intermediate_files/bam_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure6$_closure18@2f3435d0]], process:NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS, debug:false, cpus:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure14@255893ed, index:1, label:[process_single], withLabel:process_long:[time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure10$_closure26@475e6626], maxRetries:1, maxErrors:-1, shell:bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
, withName:DMSANALYSIS_POSSIBLE_MUTATIONS:[publishDir:[path:./results/intermediate_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure11$_closure23@267852db]], name:NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_POSSIBLE_MUTATIONS (table /w all possible variants), containerOptions:-u $(id -u):$(id -g), errorStrategy:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure5@3e785137, time:Script126E8BAA3BC9692B58F2A1C965A1D472$_run_closure1$_closure6$_closure16@37e5efac, withName:DMSANALYSIS_PROCESS_GATK:[publishDir:[path:./results/intermediate_files/processed_gatk_files, mode:copy, saveAs:ScriptE8646A4B8FFA7429020F836DC9CB8146$_run_closure1$_closure14$_closure26@30ec799d]], hash:36b138e8e27f7423eea98b17aaf74451]
]
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue
Serialization trace:
queue (org.codehaus.groovy.util.ReferenceManager$CallBackedManager)
manager (org.codehaus.groovy.util.ReferenceManager$1)
manager (org.codehaus.groovy.util.ReferenceBundle)
bundle (org.codehaus.groovy.reflection.CachedClass$4)
cachedSuperClass (org.codehaus.groovy.reflection.stdclasses.ObjectCachedClass)
cachedClass (org.codehaus.groovy.reflection.CachedMethod)
allMethods (groovy.lang.MetaClassImpl)
delegate (groovy.runtime.metaclass.NextflowDelegatingMetaClass)
metaClass (groovyx.gpars.dataflow.DataflowVariable)
first (groovyx.gpars.dataflow.stream.DataflowStream)
asyncHead (groovyx.gpars.dataflow.stream.DataflowStreamReadAdapter)
source (nextflow.extension.MapOp)
owner (nextflow.extension.MapOp$_apply_closure1)
code (groovyx.gpars.dataflow.operator.DataflowOperatorActor)
actor (groovyx.gpars.dataflow.operator.DataflowOperator)
allOperators (nextflow.Session)
session (nextflow.validation.ValidationExtension)
target (nextflow.script.FunctionDef)
definitions (nextflow.script.ScriptMeta)
meta (nextflow.script.ScriptBinding)
binding (Script_09ccfa79b2802f41)
delegate (Script_09ccfa79b2802f41$_runScript_closure1)
delegate (Script_09ccfa79b2802f41$_runScript_closure1$_closure26)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:82)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:22)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:82)
	at com.esotericsoftware.kryo.serializers.CollectionSerializer.write(CollectionSerializer.java:22)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:95)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:21)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:523)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:61)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:495)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:95)
	at com.esotericsoftware.kryo.serializers.MapSerializer.write(MapSerializer.java:21)
	at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:599)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.util.KryoHelper.serialize(SerializationHelper.groovy:166)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.processor.TaskContext.serialize(TaskContext.groovy:198)
	at nextflow.cache.CacheDB.writeTaskEntry0(CacheDB.groovy:148)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
	at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
	at nextflow.cache.CacheDB$_putTaskAsync_closure1.doCall(CacheDB.groovy:157)
	at nextflow.cache.CacheDB$_putTaskAsync_closure1.call(CacheDB.groovy)
	at groovyx.gpars.agent.AgentBase.onMessage(AgentBase.java:102)
	at groovyx.gpars.agent.Agent.handleMessage(Agent.java:84)
	at groovyx.gpars.agent.AgentCore$1.handleMessage(AgentCore.java:48)
	at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue
	at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:48)
	at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:26)
	at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:351)
	at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:344)
	at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:56)
	at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:461)
	at com.esotericsoftware.kryo.util.DefaultClassResolver.writeClass(DefaultClassResolver.java:79)
	at com.esotericsoftware.kryo.Kryo.writeClass(Kryo.java:488)
	at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:57)
	... 106 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
	at jdk.internal.reflect.GeneratedConstructorAccessor39.newInstance(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481)
	at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:35)
	... 114 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private final java.lang.ref.ReferenceQueue$Lock java.lang.ref.ReferenceQueue.lock accessible: module java.base does not "opens java.lang.ref" to unnamed module @7b02881e
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
	at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:282)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:217)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:156)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:133)
	... 119 common frames omitted
May-07 23:02:17.570 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_DMSCORE:DMSCORE:BWA_MEM (gid1a_1_quality_1_pe); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/67/c2a06b1c7b4781da339f3e7aacd574]
May-07 23:02:17.585 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:17.586 [Task submitter] INFO  nextflow.Session - [48/c69654] Submitted process > NFCORE_DMSCORE:DMSCORE:FASTQC (gid1a_1_quality_1_pe)
May-07 23:02:17.748 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DMSCORE:DMSCORE:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<1:1>
May-07 23:02:17.749 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DMSCORE:DMSCORE:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
May-07 23:02:17.749 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DMSCORE:DMSCORE:BWA_MEM > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
May-07 23:02:17.828 [Actor Thread 14] WARN  nextflow.processor.TaskContext - Cannot serialize context map. Cause: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.lang.ref.ReferenceQueue -- Resume will not work on this process
May-07 23:02:28.533 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_DMSCORE:DMSCORE:FASTQC (gid1a_1_quality_1_pe); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/48/c69654e9b29a194ea81b7c28f63819]
May-07 23:02:28.582 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:28.583 [Task submitter] INFO  nextflow.Session - [4e/7ee9bd] Submitted process > NFCORE_DMSCORE:DMSCORE:BAMFILTER_DMS (gid1a_1_quality_1_pe)
May-07 23:02:28.752 [Actor Thread 12] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.013 s; external sort time: 0.008 s; total time: 0.021 s
May-07 23:02:28.776 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /Users/benjaminwehnert/dmscore/work/collect-file/c1149f4a215bbe0651400d7f32cdafdc
May-07 23:02:28.784 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /var/folders/r0/ldrzd4wn1s3516hy0vsn8xzm0000gn/T/nxf-15345989576056151242
May-07 23:02:32.866 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_DMSCORE:DMSCORE:BAMFILTER_DMS (gid1a_1_quality_1_pe); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/4e/7ee9bd66291d03ed6f3c2bbdfefe0d]
May-07 23:02:32.872 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:32.873 [Task submitter] INFO  nextflow.Session - [55/5dd043] Submitted process > NFCORE_DMSCORE:DMSCORE:MULTIQC
May-07 23:02:43.262 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_DMSCORE:DMSCORE:MULTIQC; status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/55/5dd0430083da5c332e7950544ac6e0]
May-07 23:02:43.292 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:43.294 [Task submitter] INFO  nextflow.Session - [aa/6e83ae] Submitted process > NFCORE_DMSCORE:DMSCORE:PREMERGE (gid1a_1_quality_1_pe)
May-07 23:02:43.298 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DMSCORE:DMSCORE:MULTIQC > Skipping output binding because one or more optional files are missing: fileoutparam<2>
May-07 23:02:46.384 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_DMSCORE:DMSCORE:PREMERGE (gid1a_1_quality_1_pe); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/aa/6e83aebc1b031afabb4d8df09e97f3]
May-07 23:02:46.488 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-07 23:02:46.489 [Task submitter] INFO  nextflow.Session - [f2/f878d3] Submitted process > NFCORE_DMSCORE:DMSCORE:GATK_SATURATIONMUTAGENESIS (gid1a_1_quality_1_pe)
May-07 23:03:05.753 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_DMSCORE:DMSCORE:GATK_SATURATIONMUTAGENESIS (gid1a_1_quality_1_pe); status: COMPLETED; exit: 0; error: -; workDir: /Users/benjaminwehnert/dmscore/work/f2/f878d301d101b20d245c27be19bbf3]
May-07 23:03:05.837 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_PROCESS_GATK (1); work-dir=null
  error [nextflow.exception.ProcessUnrecoverableException]: Path value cannot be null
May-07 23:03:05.858 [Actor Thread 2] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_PROCESS_GATK (1)'

Caused by:
  Path value cannot be null



Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
May-07 23:03:05.860 [Actor Thread 2] INFO  nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
May-07 23:03:05.865 [Actor Thread 2] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
May-07 23:03:05.866 [main] DEBUG nextflow.Session - Session await > all processes finished
May-07 23:03:05.867 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
May-07 23:03:05.867 [main] DEBUG nextflow.Session - Session await > all barriers passed
May-07 23:03:05.868 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_DMSCORE:DMSCORE:DMSANALYSIS_PROCESS_GATK; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
May-07 23:03:05.872 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
May-07 23:03:05.872 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
May-07 23:03:05.880 [main] INFO  nextflow.Nextflow - -[nf-core/dmscore] Pipeline completed with errors-
May-07 23:03:05.897 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=9; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=2m 24s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=8; peakMemory=16 GB; ]
May-07 23:03:05.898 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
May-07 23:03:05.900 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
May-07 23:03:07.314 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
May-07 23:03:07.511 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
May-07 23:03:07.545 [main] INFO  org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.3.0'
May-07 23:03:07.545 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema
May-07 23:03:07.546 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
May-07 23:03:07.547 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye