May-29 10:35:28.699 [main] DEBUG nextflow.cli.Launcher - $> nextflow run phoenix/main.nf -profile test,docker -r v2.1.1 -entry PHOENIX --kraken2db /media/scratch/data_for_tools/kraken2/kraken2_standard8/ May-29 10:35:28.787 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2 May-29 10:35:28.809 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/user/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2 May-29 10:35:28.820 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-29 10:35:28.821 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-29 10:35:28.827 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode May-29 10:35:28.843 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-29 10:35:28.858 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/user/.nextflow/scm May-29 10:35:28.866 [main] DEBUG nextflow.scm.AssetManager - Listing projects in folder: /home/user/.nextflow/assets May-29 10:35:29.742 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/user/.nextflow/assets/cdcgov/phoenix/.git/config; branch: master; remote: origin; url: https://github.com/CDCgov/phoenix.git May-29 10:35:29.772 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] May-29 10:35:29.781 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/user/.nextflow/assets/cdcgov/phoenix/.git/config; branch: master; remote: origin; url: https://github.com/CDCgov/phoenix.git May-29 10:35:30.360 [main] DEBUG nextflow.config.ConfigBuilder - Found config home: /home/user/.nextflow/config May-29 10:35:30.362 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/user/.nextflow/assets/cdcgov/phoenix/nextflow.config May-29 10:35:30.365 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/user/.nextflow/config May-29 10:35:30.366 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/user/.nextflow/assets/cdcgov/phoenix/nextflow.config May-29 10:35:30.374 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/user/.nextflow/secrets/store.json May-29 10:35:30.377 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@411cd156] - activable => nextflow.secret.LocalSecretsProvider@411cd156 May-29 10:35:30.389 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` May-29 10:35:30.430 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` May-29 10:35:32.444 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, kraken, pdc_kth, googlels, hpc_custom, test_pass, daisybio, eddie, medair, biowulf, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, utd_europa, terra, genotoul, nci_gadi, cdcsge_test, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, cdcsge, seg_globe, amd_tower, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] May-29 10:35:32.490 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration May-29 10:35:32.492 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/cdcgov/phoenix` [elegant_hugle] DSL2 - revision: 5a5a7a51e1 [v2.1.1] May-29 10:35:32.493 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-29 10:35:32.493 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] May-29 10:35:32.558 [main] DEBUG nextflow.Session - Session UUID: d5210e28-1464-4738-9616-e87780ab3dc2 May-29 10:35:32.558 [main] DEBUG nextflow.Session - Run name: elegant_hugle May-29 10:35:32.558 [main] DEBUG nextflow.Session - Executor pool size: 112 May-29 10:35:32.567 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null May-29 10:35:32.572 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=336; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-29 10:35:32.591 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.2 build 5914 Created: 29-05-2024 06:19 UTC (02:19 EDT) System: Linux 5.15.0-107-generic Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.22+7-post-Ubuntu-0ubuntu222.04.1 Encoding: UTF-8 (UTF-8) Process: 949958@bioinfo1 [127.0.1.1] CPUs: 112 - Mem: 314.5 GB (306.3 GB) - Swap: 8 GB (8 GB) May-29 10:35:32.610 [main] DEBUG nextflow.Session - Work-dir: /home/user/work [ext2/ext3] May-29 10:35:32.650 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-29 10:35:32.661 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-29 10:35:32.737 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-29 10:35:32.748 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 113; maxThreads: 1000 May-29 10:35:32.813 [main] DEBUG nextflow.Session - Session start May-29 10:35:32.815 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/user/phx_output/pipeline_info/execution_trace_2024-05-29_10-35-32.txt May-29 10:35:32.823 [main] DEBUG nextflow.Session - Using default localLib path: /home/user/.nextflow/assets/cdcgov/phoenix/lib May-29 10:35:32.827 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/user/.nextflow/assets/cdcgov/phoenix/lib May-29 10:35:32.828 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/user/.nextflow/assets/cdcgov/phoenix/lib/nfcore_external_java_deps.jar May-29 10:35:33.840 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-29 10:35:33.992 [main] INFO nextflow.Nextflow - ------------------------------------------------------  ___ _____   | \ | | __ ___ |\ | | \ /   |___/ |___| / \ |___ | \ | | \/   | | | \__/ |___ | \| __|__ / \     cdcgov/phoenix v2.1.1 ------------------------------------------------------ Core Nextflow options revision : v2.1.1 runName : elegant_hugle containerEngine : docker launchDir : /home/user workDir : /home/user/work projectDir : /home/user/.nextflow/assets/cdcgov/phoenix userName : user profile : test,docker configFiles : /home/user/.nextflow/config, /home/user/.nextflow/assets/cdcgov/phoenix/nextflow.config Required Options input : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/samplesheet.csv kraken2db : /media/scratch/data_for_tools/kraken2/kraken2_standard8/ Options for -entry SCAFFOLDS and CDC_SCAFFOLDS indir : null Options for -entry SRA and CDC_SRA input_sra : null use_sra : false Optional options outdir : /home/user/phx_output coverage : 30 busco_db_path : null create_ncbi_sheet : false Institutional config options custom_config_version : master config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function Max job request options max_cpus : 6 max_memory : 14.GB max_time : 6.h !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use cdcgov/phoenix for your analysis please cite: * PHoeNIx See README.md for DOI for Citation. https://github.com/CDCgov/phoenix#readme * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/cdcgov/phoenix/blob/main/CITATIONS.md ------------------------------------------------------ May-29 10:35:46.883 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:INPUT_CHECK:SAMPLESHEET_CHECK May-29 10:35:46.885 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLESHEET_CHECK` matches process PHOENIX:PHOENIX_EXTERNAL:INPUT_CHECK:SAMPLESHEET_CHECK May-29 10:35:46.896 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:46.896 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:46.901 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-29 10:35:46.906 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=112; memory=314.5 GB; capacity=112; pollInterval=100ms; dumpInterval=5m May-29 10:35:46.908 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) May-29 10:35:47.009 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK May-29 10:35:47.010 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ASSET_CHECK` matches process PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK May-29 10:35:47.018 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.018 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.041 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:CORRUPTION_CHECK May-29 10:35:47.041 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CORRUPTION_CHECK` matches process PHOENIX:PHOENIX_EXTERNAL:CORRUPTION_CHECK May-29 10:35:47.047 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.047 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.082 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:GET_RAW_STATS May-29 10:35:47.083 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GET_RAW_STATS` matches process PHOENIX:PHOENIX_EXTERNAL:GET_RAW_STATS May-29 10:35:47.087 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.088 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.109 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:BBDUK May-29 10:35:47.110 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBDUK` matches process PHOENIX:PHOENIX_EXTERNAL:BBDUK May-29 10:35:47.115 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.115 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.133 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:FASTP_TRIMD May-29 10:35:47.133 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process PHOENIX:PHOENIX_EXTERNAL:FASTP_TRIMD May-29 10:35:47.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP_TRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:FASTP_TRIMD May-29 10:35:47.138 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.138 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.152 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:FASTP_SINGLES May-29 10:35:47.152 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP_SINGLES` matches process PHOENIX:PHOENIX_EXTERNAL:FASTP_SINGLES May-29 10:35:47.155 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.156 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.203 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:GET_TRIMD_STATS May-29 10:35:47.205 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GET_TRIMD_STATS` matches process PHOENIX:PHOENIX_EXTERNAL:GET_TRIMD_STATS May-29 10:35:47.212 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.213 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.245 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:FASTQCTRIMD May-29 10:35:47.247 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQCTRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:FASTQCTRIMD May-29 10:35:47.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.287 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_TRIMD May-29 10:35:47.288 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_KRAKEN2` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_TRIMD May-29 10:35:47.289 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_TRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_TRIMD May-29 10:35:47.291 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.291 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.301 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2MPA_TRIMD May-29 10:35:47.302 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KREPORT2MPA_TRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2MPA_TRIMD May-29 10:35:47.304 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.304 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.310 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2KRONA_TRIMD May-29 10:35:47.311 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KREPORT2KRONA_TRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2KRONA_TRIMD May-29 10:35:47.313 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.313 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.320 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRONA_KTIMPORTTEXT_TRIMD May-29 10:35:47.321 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRONA_KTIMPORTTEXT_TRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRONA_KTIMPORTTEXT_TRIMD May-29 10:35:47.323 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.323 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.337 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_BH_TRIMD May-29 10:35:47.339 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_BH_TRIMD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_BH_TRIMD May-29 10:35:47.341 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.341 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.381 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SPADES` matches process PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:SPADES May-29 10:35:47.385 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.385 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.402 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:DETERMINE_TAXA_ID_FAILURE May-29 10:35:47.402 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DETERMINE_TAXA_ID_FAILURE` matches process PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:DETERMINE_TAXA_ID_FAILURE May-29 10:35:47.405 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.405 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.437 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:GENERATE_PIPELINE_STATS_FAILURE May-29 10:35:47.438 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GENERATE_PIPELINE_STATS_FAILURE` matches process PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:GENERATE_PIPELINE_STATS_FAILURE May-29 10:35:47.441 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.441 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.461 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:CREATE_SUMMARY_LINE_FAILURE May-29 10:35:47.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_SUMMARY_LINE_FAILURE` matches process PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:CREATE_SUMMARY_LINE_FAILURE May-29 10:35:47.464 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.464 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.476 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:RENAME_FASTA_HEADERS May-29 10:35:47.476 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RENAME_FASTA_HEADERS` matches process PHOENIX:PHOENIX_EXTERNAL:RENAME_FASTA_HEADERS May-29 10:35:47.479 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.479 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.486 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:BBMAP_REFORMAT May-29 10:35:47.486 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BBMAP_REFORMAT` matches process PHOENIX:PHOENIX_EXTERNAL:BBMAP_REFORMAT May-29 10:35:47.488 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.488 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:SCAFFOLD_COUNT_CHECK May-29 10:35:47.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SCAFFOLD_COUNT_CHECK` matches process PHOENIX:PHOENIX_EXTERNAL:SCAFFOLD_COUNT_CHECK May-29 10:35:47.515 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.515 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.530 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV May-29 10:35:47.531 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GAMMA|GAMMAS` matches process PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV May-29 10:35:47.531 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GAMMA_HV` matches process PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV May-29 10:35:47.534 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.534 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.541 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR May-29 10:35:47.541 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GAMMA|GAMMAS` matches process PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR May-29 10:35:47.542 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GAMMA_AR` matches process PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR May-29 10:35:47.544 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.544 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.555 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF May-29 10:35:47.556 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GAMMA_PF` matches process PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF May-29 10:35:47.558 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.558 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.566 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:QUAST May-29 10:35:47.567 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:QUAST` matches process PHOENIX:PHOENIX_EXTERNAL:QUAST May-29 10:35:47.569 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.569 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.583 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD May-29 10:35:47.584 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_KRAKEN2` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD May-29 10:35:47.585 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_WTASMBLD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD May-29 10:35:47.588 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.588 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.600 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT May-29 10:35:47.601 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKENTOOLS_MAKEKREPORT` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT May-29 10:35:47.602 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.602 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.606 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD May-29 10:35:47.608 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KREPORT2KRONA_WTASMBLD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD May-29 10:35:47.609 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.609 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.618 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD May-29 10:35:47.619 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_BH_WTASMBLD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD May-29 10:35:47.621 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.622 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.627 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD May-29 10:35:47.628 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRONA_KTIMPORTTEXT_WTASMBLD` matches process PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD May-29 10:35:47.630 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.630 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.641 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:MASH_DIST May-29 10:35:47.641 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MASH_DIST` matches process PHOENIX:PHOENIX_EXTERNAL:MASH_DIST May-29 10:35:47.643 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.643 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.651 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS May-29 10:35:47.652 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DETERMINE_TOP_MASH_HITS` matches process PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS May-29 10:35:47.654 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.654 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.666 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:FASTANI May-29 10:35:47.667 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTANI` matches process PHOENIX:PHOENIX_EXTERNAL:FASTANI May-29 10:35:47.669 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.669 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.673 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI May-29 10:35:47.674 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FORMAT_ANI` matches process PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI May-29 10:35:47.675 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.675 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.687 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID May-29 10:35:47.687 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DETERMINE_TAXA_ID` matches process PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID May-29 10:35:47.689 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.689 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.709 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST May-29 10:35:47.710 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MLST` matches process PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST May-29 10:35:47.712 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.712 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.723 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST May-29 10:35:47.724 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CHECK_MLST` matches process PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST May-29 10:35:47.726 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.726 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name PHOENIX:PHOENIX_EXTERNAL:PROKKA May-29 10:35:47.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PROKKA` matches process PHOENIX:PHOENIX_EXTERNAL:PROKKA May-29 10:35:47.745 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.745 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER May-29 10:35:47.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GET_TAXA_FOR_AMRFINDER` matches process PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER May-29 10:35:47.759 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.759 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.775 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN May-29 10:35:47.775 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:AMRFINDERPLUS_RUN` matches process PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN May-29 10:35:47.778 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.778 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.788 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO May-29 10:35:47.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CALCULATE_ASSEMBLY_RATIO` matches process PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO May-29 10:35:47.790 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.791 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.853 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS May-29 10:35:47.854 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GENERATE_PIPELINE_STATS` matches process PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS May-29 10:35:47.856 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.856 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.893 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE May-29 10:35:47.893 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CREATE_SUMMARY_LINE` matches process PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE May-29 10:35:47.895 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.895 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.909 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES May-29 10:35:47.909 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FETCH_FAILED_SUMMARIES` matches process PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES May-29 10:35:47.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.945 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES May-29 10:35:47.946 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATHER_SUMMARY_LINES` matches process PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES May-29 10:35:47.947 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.948 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.958 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:GRIPHIN May-29 10:35:47.958 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GRIPHIN` matches process PHOENIX:PHOENIX_EXTERNAL:GRIPHIN May-29 10:35:47.960 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.960 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:47.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS May-29 10:35:47.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS May-29 10:35:47.992 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:47.992 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:48.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name PHOENIX:PHOENIX_EXTERNAL:MULTIQC May-29 10:35:48.058 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process PHOENIX:PHOENIX_EXTERNAL:MULTIQC May-29 10:35:48.059 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-29 10:35:48.059 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-29 10:35:48.075 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: CORRUPTION_CHECK, CREATE_SRA_SAMPLESHEET, RENAME_SRA_FASTA, BUSCO, GAMMA_PF, PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR, GENERATE_PIPELINE_STATS_FAILURE, KRONA_KTIMPORTTEXT, GET_RAW_STATS, PROKKA, PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES, PHOENIX:PHOENIX_EXTERNAL:FASTP_TRIMD, KRAKEN2_BH_WTASMBLD, GET_TAXA_FOR_AMRFINDER, KRAKENTOOLS_MAKEKREPORT, BBMAP_REFORMAT, QUAST, PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:DETERMINE_TAXA_ID_FAILURE, GRIPHIN, GENERATE_PIPELINE_STATS_EXQC, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_TRIMD, PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO, CREATE_SAMPLESHEET, GENERATE_PIPELINE_STATS_FAILURE_EXQC, KRONA_KTIMPORTTEXT_ASMBLD, DETERMINE_TAXA_ID_FAILURE, FORMAT_ANI, FASTQC, GAMMA_AR, SRATOOLS_PREFETCH, SRST2_AR, KRAKEN2_BH_ASMBLD, PHOENIX:PHOENIX_EXTERNAL:CORRUPTION_CHECK, KRONA_KTIMPORTTEXT_TRIMD, MULTIQC, PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES, SCAFFOLDS_SAMPLESHEET_CHECK, PHOENIX:PHOENIX_EXTERNAL:MASH_DIST, PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS, PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST, READ_COUNT_CHECK, PHOENIX:PHOENIX_EXTERNAL:FASTQCTRIMD, KRAKEN2_ASMBLD, CREATE_SUMMARY_LINE_FAILURE, BBDUK, PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK, KRAKEN2_TRIMD, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2KRONA_TRIMD, ENTREZDIRECT_ESEARCH, SAMPLESHEET_CHECK, PHOENIX:PHOENIX_EXTERNAL:QUAST, MLST, PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN, PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE, PHOENIX:PHOENIX_EXTERNAL:BBDUK, KRAKEN_BEST_HIT, PHOENIX:PHOENIX_EXTERNAL:MULTIQC, GENERATE_PIPELINE_STATS, KREPORT2MPA_ASMBLD, GAMMA_HV, CHECK_MLST_WITH_SRST2, KRAKENTOOLS_KREPORT2MPA, FASTANI, PHOENIX:PHOENIX_EXTERNAL:BBMAP_REFORMAT, DETERMINE_TAXA_ID, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD, PHOENIX:PHOENIX_EXTERNAL:FASTANI, GAMMA, FASTQCTRIMD, GET_TRIMD_STATS, ASSET_CHECK, FASTP_SINGLES, PHOENIX:PHOENIX_EXTERNAL:INPUT_CHECK:SAMPLESHEET_CHECK, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD, KREPORT2KRONA_ASMBLD, PHOENIX:PHOENIX_EXTERNAL:GRIPHIN, FASTP, PHOENIX:PHOENIX_EXTERNAL:FASTP_SINGLES, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_BH_TRIMD, CALCULATE_ASSEMBLY_RATIO, PHOENIX:PHOENIX_EXTERNAL:GET_TRIMD_STATS, PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST, CREATE_SUMMARY_LINE, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRONA_KTIMPORTTEXT_TRIMD, CREATE_NCBI_UPLOAD_SHEET, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT, KRAKEN2_KRAKEN2, KREPORT2MPA_TRIMD, MASH_DIST, GATHER_SUMMARY_LINES, FETCH_FAILED_SUMMARIES, PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER, KREPORT2KRONA_WTASMBLD, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD, RENAME_FASTA_HEADERS, KRONA_KTIMPORTTEXT_WTASMBLD, DETERMINE_TOP_MASH_HITS, PHOENIX:PHOENIX_EXTERNAL:RENAME_FASTA_HEADERS, GAMMA_S, PHOENIX:PHOENIX_EXTERNAL:PROKKA, FASTP_TRIMD, PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:SPADES, PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS, SCAFFOLD_COUNT_CHECK, SPADES, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2MPA_TRIMD, SRATOOLS_FASTERQDUMP, PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID, SRST2_MLST, PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI, PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS, GET_MLST_SRST2, PHOENIX:PHOENIX_EXTERNAL:SCAFFOLD_COUNT_CHECK, PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD, KRAKEN2_BH_TRIMD, PHOENIX:PHOENIX_EXTERNAL:GET_RAW_STATS, KREPORT2KRONA_TRIMD, PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV, AMRFINDERPLUS_RUN, CHECK_MLST, PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF, KRAKEN2_WTASMBLD, PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:GENERATE_PIPELINE_STATS_FAILURE, CUSTOM_DUMPSOFTWAREVERSIONS, KRAKEN2_KRONA, PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:CREATE_SUMMARY_LINE_FAILURE May-29 10:35:48.093 [main] DEBUG nextflow.Session - Igniting dataflow network (64) May-29 10:35:48.123 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:INPUT_CHECK:SAMPLESHEET_CHECK May-29 10:35:48.123 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK May-29 10:35:48.123 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:CORRUPTION_CHECK May-29 10:35:48.123 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GET_RAW_STATS May-29 10:35:48.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:BBDUK May-29 10:35:48.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:FASTP_TRIMD May-29 10:35:48.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:FASTP_SINGLES May-29 10:35:48.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GET_TRIMD_STATS May-29 10:35:48.124 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:FASTQCTRIMD May-29 10:35:48.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_TRIMD May-29 10:35:48.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2MPA_TRIMD May-29 10:35:48.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2KRONA_TRIMD May-29 10:35:48.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRONA_KTIMPORTTEXT_TRIMD May-29 10:35:48.125 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_BH_TRIMD May-29 10:35:48.126 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:SPADES May-29 10:35:48.135 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:DETERMINE_TAXA_ID_FAILURE May-29 10:35:48.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:GENERATE_PIPELINE_STATS_FAILURE May-29 10:35:48.138 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:CREATE_SUMMARY_LINE_FAILURE May-29 10:35:48.139 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:RENAME_FASTA_HEADERS May-29 10:35:48.140 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:BBMAP_REFORMAT May-29 10:35:48.141 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:SCAFFOLD_COUNT_CHECK May-29 10:35:48.142 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV May-29 10:35:48.143 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR May-29 10:35:48.144 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF May-29 10:35:48.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:QUAST May-29 10:35:48.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD May-29 10:35:48.145 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT May-29 10:35:48.146 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD May-29 10:35:48.146 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD May-29 10:35:48.146 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD May-29 10:35:48.146 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:MASH_DIST May-29 10:35:48.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS May-29 10:35:48.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:FASTANI May-29 10:35:48.147 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI May-29 10:35:48.148 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID May-29 10:35:48.149 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST May-29 10:35:48.149 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST May-29 10:35:48.149 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:PROKKA May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES May-29 10:35:48.150 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES May-29 10:35:48.151 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:GRIPHIN May-29 10:35:48.151 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS May-29 10:35:48.153 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PHOENIX:PHOENIX_EXTERNAL:MULTIQC May-29 10:35:48.172 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_8a6a0084ca0e15ad: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/bbduk.nf Script_6830843d3a3bbf6f: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fastani.nf Script_c83570616de6177b: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/krakentools_makekreport.nf Script_4b7048503a6b2435: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/griphin.nf Script_239e43930873791a: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/generate_pipeline_stats_exqc.nf Script_389759a61265f255: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/get_trimd_stats.nf Script_348c8bf4eb4a5adc: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/sratools/fasterq.nf Script_b74bff8e87bfb173: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/nf-core/modules/multiqc/main.nf Script_59a65a3d3b33106b: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/sra_prep.nf Script_f27eb11b2509f670: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/scaffolds_samplesheet_check.nf Script_e823903119815a87: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fastqc.nf Script_70e8f28bf1cc21b8: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/create_sra_samplesheet.nf Script_1cebaeb1a17bb72d: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/gammas.nf Script_acab324ddee4a5ce: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/do_mlst.nf Script_64f4b53ce0bf6503: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/create_ncbi_upload_sheet.nf Script_6a67f8ddfb40c106: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/create_samplesheet.nf Script_488180caa4cf13d7: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/kraken2.nf Script_34b1db44da94f2c2: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/phoenix_summary_line_failure.nf Script_555c1052becd39e6: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/krakentools_kreport2mpa.nf Script_4cec54b13e9c3f75: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/scaffolds.nf Script_f4b1f87b212a212d: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/get_taxa_for_amrfinder.nf Script_198dd1c464b00fb1: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fairy_read_count_check.nf Script_93a4d39975503698: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fairy_corruption_check.nf Script_cf2edfb31c732388: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/input_check.nf Script_a25cc29722c70add: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fairy_scaffold_count_check.nf Script_e14fdfc8f4ad7f80: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/determine_taxa_id.nf Script_022bdeaefad98499: /home/user/.nextflow/assets/cdcgov/phoenix/main.nf Script_3a1414691f8ea6bd: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fetch_failed_summaries.nf Script_7c6fcb0385c995f2: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/run_amrfinder.nf Script_2458a989afe3a64f: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/contig_less500.nf Script_b2b183eeac2b2f2a: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/confirm_dups.nf Script_d71a19023d249ee3: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/kraken_bh.nf Script_089d1a9a4ca8431d: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/asset_check.nf Script_00c4a70fd83256c7: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/kraken2krona.nf Script_3336a3be0e2c1a2e: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/mlst.nf Script_b10999d908b29fcc: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fastp_singles.nf Script_0ffa466d031be2f5: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/check_mlst.nf Script_ba83c676b86339e4: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/cdc_scaffolds.nf Script_e662451bbea34845: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/determine_top_mash_hits.nf Script_75ab3d20fdf226d5: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/prokka.nf Script_285201157c8f6705: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/rename_fasta_headers.nf Script_116d08cfa5e22ddd: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/generate_pipeline_stats.nf Script_2d191234ad240b16: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/create_input_channel.nf Script_1b4b65aef5801d4d: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/srst2_ar.nf Script_dc36800de4186e69: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/generate_pipeline_stats.nf Script_d85f9cc9db2c60da: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/spades.nf Script_03517d5cab84ff7d: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/generate_pipeline_stats_failure_exqc.nf Script_3184a9bb11b3b323: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/sratools/prefetch.nf Script_0ecadded5988133a: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/get_mlst_srst2.nf Script_b4eeae67f2829d4b: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/determine_taxa_id_failure.nf Script_69e42846f5984315: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/rename_sra.nf Script_5b3ae8bce5b8486b: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/quast.nf Script_095ff9f5dfb9a05f: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/krakentools_kreport2krona.nf Script_f905b37c99ab7543: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/srst2_mlst_local.nf Script_90c358f4987286cd: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/phoenix_summary_line.nf Script_d09b729c0a5a4d97: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/phoenix_summary.nf Script_29a0a43fedd751a7: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/check_mlst_with_srst2.nf Script_395e86162316df7b: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/assembly_ratio.nf Script_e3517491684440fc: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/gamma.nf Script_766980d4d7ea5a1f: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/ktimporttext.nf Script_a9c4f4a7b45d6f9b: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/busco.nf Script_7cd514756b308ba6: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/nf-core/modules/custom/dumpsoftwareversions/main.nf Script_87960b581acedc08: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/fastp.nf Script_23e0dc3e4ab792a6: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/spades_failure.nf Script_3ccee7bc58e215d4: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/get_sra_metadata.nf Script_be2f76b43dde59f9: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/mash_distance.nf Script_a514776dbd3c02a5: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/samplesheet_check.nf Script_eb2259e4fd1f27a1: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/get_raw_stats.nf Script_d43a81a94567de3f: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/cdc_phoenix.nf Script_6277dc68df0ddc96: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../modules/local/format_ANI_best_hit.nf Script_2b1f59aedef6c9e6: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/phoenix.nf Script_963351bc65cb44a6: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/../../modules/local/generate_pipeline_stats_failure.nf Script_d699e26b333310aa: /home/user/.nextflow/assets/cdcgov/phoenix/./workflows/../subworkflows/local/add_empty_channel.nf May-29 10:35:48.172 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination May-29 10:35:48.172 [main] DEBUG nextflow.Session - Session await May-29 10:35:48.344 [Actor Thread 99] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/user/.nextflow/assets/cdcgov/phoenix/assets/databases/REFSEQ_20240124_Bacteria_complete.msh.gz May-29 10:35:48.351 [Actor Thread 105] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.015 s; total time: 0.016 s May-29 10:35:48.357 [Actor Thread 105] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/user/work/collect-file/f4f1059f0c2fc29bd0c74b5405223ae0 May-29 10:35:48.359 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/samplesheet.csv to work dir: /home/user/work/stage-d5210e28-1464-4738-9616-e87780ab3dc2/07/e75d37258a0b21e4e89532e2731643/samplesheet.csv May-29 10:35:48.365 [Actor Thread 105] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-4901061178349209162 May-29 10:35:48.630 [Actor Thread 113] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/user/.nextflow/assets/cdcgov/phoenix/bin/check_samplesheet.py May-29 10:35:48.685 [Actor Thread 99] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/user/.nextflow/assets/cdcgov/phoenix/assets/databases/mlst_db_20240124.tar.gz May-29 10:35:48.707 [Task submitter] WARN nextflow.container.DockerBuilder - Undocumented setting `docker.userEmulation` is not supported any more - please remove it from your config May-29 10:35:48.726 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-29 10:35:48.727 [Task submitter] INFO nextflow.Session - [0b/587202] Submitted process > PHOENIX:PHOENIX_EXTERNAL:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) May-29 10:35:48.755 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-29 10:35:48.756 [Task submitter] INFO nextflow.Session - [c4/766fa5] Submitted process > PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK (1) May-29 10:35:50.220 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: PHOENIX:PHOENIX_EXTERNAL:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /home/user/work/0b/587202c09a9ee3863bb92a06af21c5] May-29 10:35:50.222 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=336; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-29 10:35:50.268 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=336; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-29 10:35:50.554 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/Test_Sample_R1.fastq.gz to work dir: /home/user/work/stage-d5210e28-1464-4738-9616-e87780ab3dc2/01/ae36afaf5634670c95b2c9dfae7ff2/Test_Sample_R1.fastq.gz May-29 10:35:50.555 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/Test_Sample_R2.fastq.gz to work dir: /home/user/work/stage-d5210e28-1464-4738-9616-e87780ab3dc2/e8/e7dbf147752a595c97b9e1096f900f/Test_Sample_R2.fastq.gz May-29 10:35:51.385 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK (1); status: COMPLETED; exit: 0; error: -; workDir: /home/user/work/c4/766fa585618b6e147af554939d596b] May-29 10:35:51.394 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK (1); work-dir=/home/user/work/c4/766fa585618b6e147af554939d596b error [java.nio.file.AccessDeniedException]: /home/user/work/c4/766fa585618b6e147af554939d596b/db May-29 10:35:51.409 [TaskFinalizer-2] ERROR nextflow.processor.TaskProcessor - Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:ASSET_CHECK (1)' Caused by: /home/user/work/c4/766fa585618b6e147af554939d596b/db java.nio.file.AccessDeniedException: /home/user/work/c4/766fa585618b6e147af554939d596b/db at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) at java.base/sun.nio.fs.UnixFileSystemProvider.newDirectoryStream(UnixFileSystemProvider.java:432) at java.base/java.nio.file.Files.newDirectoryStream(Files.java:472) at java.base/java.nio.file.FileTreeWalker.visit(FileTreeWalker.java:300) at java.base/java.nio.file.FileTreeWalker.next(FileTreeWalker.java:373) at java.base/java.nio.file.Files.walkFileTree(Files.java:2761) at nextflow.file.FileHelper.visitFiles(FileHelper.groovy:817) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.processor.TaskProcessor.fetchResultFiles(TaskProcessor.groovy:1738) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.processor.TaskProcessor.collectOutFiles(TaskProcessor.groovy:1665) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.processor.TaskProcessor.collectOutputs(TaskProcessor.groovy:1540) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.processor.TaskProcessor.collectOutputs(TaskProcessor.groovy:1521) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:2386) at nextflow.processor.TaskPollingMonitor.finalizeTask(TaskPollingMonitor.groovy:676) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82) at nextflow.processor.TaskPollingMonitor$_checkTaskStatus_lambda8.doCall(TaskPollingMonitor.groovy:666) at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) May-29 10:35:51.421 [TaskFinalizer-2] DEBUG nextflow.Session - Session aborted -- Cause: /home/user/work/c4/766fa585618b6e147af554939d596b/db May-29 10:35:51.480 [TaskFinalizer-2] DEBUG nextflow.Session - The following nodes are still active: [process] PHOENIX:PHOENIX_EXTERNAL:CORRUPTION_CHECK status=ACTIVE port 0: (queue) closed; channel: - port 1: (value) bound ; channel: busco_val port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GET_RAW_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: busco_val port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:BBDUK status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: contaminants port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:FASTP_TRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: save_trimmed_fail port 2: (value) bound ; channel: save_merged port 3: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:FASTP_SINGLES status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GET_TRIMD_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: busco_val port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:FASTQCTRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_TRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: kraken_type port 2: (value) bound ; channel: save_output_fastqs port 3: (value) bound ; channel: save_reads_assignment port 4: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2MPA_TRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KREPORT2KRONA_TRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: type port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRONA_KTIMPORTTEXT_TRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: type port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_TRIMD:KRAKEN2_BH_TRIMD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: kraken_type port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:SPADES status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: extended_qc port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:DETERMINE_TAXA_ID_FAILURE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: nodes_file port 2: (value) bound ; channel: names_file port 3: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:GENERATE_PIPELINE_STATS_FAILURE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: coverage port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:SPADES_WF:CREATE_SUMMARY_LINE_FAILURE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: extended_qc port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:RENAME_FASTA_HEADERS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:BBMAP_REFORMAT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:SCAFFOLD_COUNT_CHECK status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: extended_qc port 2: (value) bound ; channel: coverage port 3: (value) bound ; channel: nodes_file port 4: (value) bound ; channel: names_file port 5: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GAMMA_HV status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: db port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GAMMA_AR status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: db port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GAMMA_PF status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: db port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:QUAST status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_WTASMBLD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: kraken_type port 2: (value) bound ; channel: save_output_fastqs port 3: (value) bound ; channel: save_reads_assignment port 4: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKENTOOLS_MAKEKREPORT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KREPORT2KRONA_WTASMBLD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: type port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRAKEN2_BH_WTASMBLD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: kraken_type port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:KRAKEN2_WTASMBLD:KRONA_KTIMPORTTEXT_WTASMBLD status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: type port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:MASH_DIST status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TOP_MASH_HITS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:FASTANI status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:FORMAT_ANI status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:DETERMINE_TAXA_ID status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: nodes_file port 2: (value) bound ; channel: names_file port 3: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:DO_MLST:MLST status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:DO_MLST:CHECK_MLST status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:PROKKA status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: proteins port 2: (value) bound ; channel: prodigal_tf port 3: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GET_TAXA_FOR_AMRFINDER status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:AMRFINDERPLUS_RUN status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: db port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:CALCULATE_ASSEMBLY_RATIO status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: ncbi_database port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GENERATE_PIPELINE_STATS_WF:GENERATE_PIPELINE_STATS status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: coverage port 2: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:CREATE_SUMMARY_LINE status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:FETCH_FAILED_SUMMARIES status=ACTIVE port 0: (queue) OPEN ; channel: directory port 1: (value) OPEN ; channel: failed_summaries port 2: (value) OPEN ; channel: summaries port 3: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GATHER_SUMMARY_LINES status=ACTIVE port 0: (queue) OPEN ; channel: summary_line_files port 1: (queue) OPEN ; channel: outdir_path port 2: (value) bound ; channel: busco_val port 3: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:GRIPHIN status=ACTIVE port 0: (queue) OPEN ; channel: summary_line_files port 1: (value) bound ; channel: original_samplesheet port 2: (value) bound ; channel: db port 3: (queue) OPEN ; channel: outdir port 4: (value) bound ; channel: coverage port 5: (value) bound ; channel: entry port 6: (value) bound ; channel: scaffolds_entry port 7: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:CUSTOM_DUMPSOFTWAREVERSIONS status=ACTIVE port 0: (queue) OPEN ; channel: versions port 1: (cntrl) - ; channel: $ [process] PHOENIX:PHOENIX_EXTERNAL:MULTIQC status=ACTIVE port 0: (value) OPEN ; channel: multiqc_files port 1: (cntrl) - ; channel: $ May-29 10:35:51.485 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop May-29 10:35:51.506 [main] DEBUG nextflow.Session - Session await > all processes finished May-29 10:35:51.506 [main] DEBUG nextflow.Session - Session await > all barriers passed May-29 10:35:51.577 [Actor Thread 160] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.007 s; total time: 0.007 s May-29 10:35:51.584 [Actor Thread 109] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PHOENIX:PHOENIX_EXTERNAL:CORRUPTION_CHECK; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException May-29 10:35:51.584 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=PHOENIX:PHOENIX_EXTERNAL:PROKKA; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException May-29 10:35:51.591 [Actor Thread 160] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /home/user/work/collect-file/1cb4d71a1a725981dad7b34e2f7bdc87 May-29 10:35:51.599 [main] INFO nextflow.Nextflow - -[cdcgov/phoenix] Pipeline completed with errors- May-29 10:35:51.602 [Actor Thread 160] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-3561209604668665398 May-29 10:35:51.611 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=464ms; failedDuration=2.8s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=3; peakMemory=5 GB; ] May-29 10:35:51.611 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file May-29 10:35:51.614 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report May-29 10:35:52.152 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline May-29 10:35:52.555 [Actor Thread 113] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/Test_Sample_R1.fastq.gz May-29 10:35:54.556 [Actor Thread 113] INFO nextflow.file.FilePorter - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/Test_Sample_R2.fastq.gz May-29 10:35:56.161 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-29 10:35:56.220 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye