Oct-20 10:35:42.070 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/viralrecon -r 2.6.0 --input /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/LCMV_ABQ_Sample_sheet_run2.csv --outdir /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/ABQ/S --platform illumina --protocol metagenomic -profile singularity --skip_nextclade --fasta /xena/scratch/fmtwohig/LCMV_Stock_Seq_ABQ/LCMVABQS.fasta --kraken2_db /xena/scratch/fmtwohig/k2_pluspf_20240605.tar.gz --kraken2_db_name pluspf --skip_assembly --min_mapped_reads 10 Oct-20 10:35:42.272 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.04.7 Oct-20 10:35:42.317 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/users/fmtwohig/.nextflow/plugins; core-plugins: nf-amazon@2.15.0-patch1,nf-azure@1.16.0-patch1,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.1,nf-k8s@1.0.0,nf-tower@1.11.4-patch1,nf-wave@1.12.1 Oct-20 10:35:42.370 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-20 10:35:42.371 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-20 10:35:42.377 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Oct-20 10:35:42.398 [main] INFO org.pf4j.AbstractPluginManager - No plugins Oct-20 10:35:42.437 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /users/fmtwohig/.nextflow/scm Oct-20 10:35:43.970 [main] DEBUG nextflow.scm.AssetManager - Git config: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/viralrecon.git Oct-20 10:35:44.041 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Oct-20 10:35:44.060 [main] DEBUG nextflow.scm.AssetManager - Git config: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/.git/config; branch: null; remote: origin; url: https://github.com/nf-core/viralrecon.git Oct-20 10:35:45.276 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/nextflow.config Oct-20 10:35:45.280 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/nextflow.config Oct-20 10:35:45.294 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /users/fmtwohig/.nextflow/secrets/store.json Oct-20 10:35:45.298 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@7ed49a7f] - activable => nextflow.secret.LocalSecretsProvider@7ed49a7f Oct-20 10:35:45.319 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Oct-20 10:35:47.950 [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, tes, scw, unc_longleaf, tigem, tubingen_apg, apollo, ipop_up, vsc_calcua, pdc_kth, ceci_nic5, ccga_cau, humantechnopole, stjude, daisybio, eddie, medair, biowulf, bi, bigpurple, adcra, cedars, test_full_nanopore, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, fred_hutch, seattlechildrens, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, eva_grace, 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, test_sispa, ucl_cscluster, tuos_stanage, azurebatch, hki, seadragon, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, unity, test_nanopore, cropdiversityhpc, nygc, fgcz, conda, crg, test_full_sispa, singularity, mpcdf_viper, pe2, dirac, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, genouest, cbe, unsw_katana, utd_juno, phoenix, gitpod, test_full_illumina, seawulf, uod_hpc, fub_curta, lovelace, uct_hpc, aws_tower, binac, fsu_draco] Oct-20 10:35:48.039 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Oct-20 10:35:48.041 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/viralrecon` [distracted_lagrange] DSL2 - revision: 3731dd3a32 [2.6.0] Oct-20 10:35:48.043 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Oct-20 10:35:48.044 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Oct-20 10:35:48.133 [main] DEBUG nextflow.Session - Session UUID: 24698ec1-5385-48fc-b830-c5fd299be667 Oct-20 10:35:48.134 [main] DEBUG nextflow.Session - Run name: distracted_lagrange Oct-20 10:35:48.135 [main] DEBUG nextflow.Session - Executor pool size: 64 Oct-20 10:35:48.147 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Oct-20 10:35:48.154 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Oct-20 10:35:48.188 [main] DEBUG nextflow.cli.CmdRun - Version: 25.04.7 build 5955 Created: 08-09-2025 13:29 UTC (07:29 MDT) System: Linux 3.10.0-1160.108.1.el7.x86_64 Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 23.0.2-internal-adhoc.conda.src Encoding: UTF-8 (UTF-8) Process: 13952@xena-bigmem04.xena.alliance.unm.edu [172.16.1.28] CPUs: 64 - Mem: 1 TB (1023.5 GB) - Swap: 0 (0) Oct-20 10:35:48.366 [main] DEBUG nextflow.Session - Work-dir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work [nfs] Oct-20 10:35:48.423 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Oct-20 10:35:48.438 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-20 10:35:48.472 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory Oct-20 10:35:48.532 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Oct-20 10:35:48.546 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 65; maxThreads: 1000 Oct-20 10:35:48.672 [main] DEBUG nextflow.Session - Session start Oct-20 10:35:48.679 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/ABQ/S/pipeline_info/execution_trace_2025-10-20_10-35-46.txt Oct-20 10:35:48.692 [main] DEBUG nextflow.Session - Using default localLib path: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/lib Oct-20 10:35:48.701 [main] DEBUG nextflow.Session - Adding to the classpath library: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/lib Oct-20 10:35:48.701 [main] DEBUG nextflow.Session - Adding to the classpath library: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/lib/nfcore_external_java_deps.jar Oct-20 10:35:50.157 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-20 10:35:50.271 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/viralrecon v2.6.0-g3731dd3 ------------------------------------------------------ Core Nextflow options revision : 2.6.0 runName : distracted_lagrange containerEngine : singularity launchDir : /xena/scratch/fmtwohig/LCMV_Stock_Seq_2 workDir : /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work projectDir : /users/fmtwohig/.nextflow/assets/nf-core/viralrecon userName : fmtwohig profile : singularity configFiles : /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/nextflow.config Input/output options input : /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/LCMV_ABQ_Sample_sheet_run2.csv platform : illumina protocol : metagenomic outdir : /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/ABQ/S Reference genome options fasta : /xena/scratch/fmtwohig/LCMV_Stock_Seq_ABQ/LCMVABQS.fasta Nanopore/Illumina options skip_nextclade : true Illumina QC, read trimming and filtering options kraken2_db : /xena/scratch/fmtwohig/k2_pluspf_20240605.tar.gz kraken2_db_name : pluspf Illumina variant calling options min_mapped_reads: 10 Illumina de novo assembly options skip_assembly : true !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/viralrecon for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.3901628 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/viralrecon/blob/master/CITATIONS.md ------------------------------------------------------ Oct-20 10:36:03.039 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Oct-20 10:36:03.044 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Oct-20 10:36:03.067 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.068 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.080 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Oct-20 10:36:03.092 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=64; memory=1 TB; capacity=64; pollInterval=100ms; dumpInterval=5m Oct-20 10:36:03.096 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Oct-20 10:36:03.134 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES': maxForks=0; fair=false; array=0 Oct-20 10:36:03.202 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB Oct-20 10:36:03.209 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:PREPARE_GENOME:UNTAR_.*` matches process NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB Oct-20 10:36:03.215 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.215 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.216 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB': maxForks=0; fair=false; array=0 Oct-20 10:36:03.239 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD Oct-20 10:36:03.240 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BOWTIE2_BUILD` matches process NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD Oct-20 10:36:03.247 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.247 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.248 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD': maxForks=0; fair=false; array=0 Oct-20 10:36:03.263 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:SNPEFF_BUILD Oct-20 10:36:03.265 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SNPEFF_BUILD` matches process NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:SNPEFF_BUILD Oct-20 10:36:03.270 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.270 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.271 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:SNPEFF_BUILD': maxForks=0; fair=false; array=0 Oct-20 10:36:03.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK Oct-20 10:36:03.294 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLESHEET_CHECK` matches process NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK Oct-20 10:36:03.299 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.299 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.300 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK': maxForks=0; fair=false; array=0 Oct-20 10:36:03.366 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:CAT_FASTQ Oct-20 10:36:03.368 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_VIRALRECON:ILLUMINA:CAT_FASTQ Oct-20 10:36:03.374 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.374 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.375 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CAT_FASTQ': maxForks=0; fair=false; array=0 Oct-20 10:36:03.408 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-20 10:36:03.411 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-20 10:36:03.415 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.416 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.417 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW': maxForks=0; fair=false; array=0 Oct-20 10:36:03.442 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP Oct-20 10:36:03.443 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP Oct-20 10:36:03.450 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.450 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.451 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP': maxForks=0; fair=false; array=0 Oct-20 10:36:03.480 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-20 10:36:03.483 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-20 10:36:03.486 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.486 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.487 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM': maxForks=0; fair=false; array=0 Oct-20 10:36:03.542 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 Oct-20 10:36:03.543 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:KRAKEN2_KRAKEN2` matches process NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 Oct-20 10:36:03.549 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.549 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.550 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2': maxForks=0; fair=false; array=0 Oct-20 10:36:03.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN Oct-20 10:36:03.587 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BOWTIE2_ALIGN` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN Oct-20 10:36:03.592 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.592 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.593 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN': maxForks=0; fair=false; array=0 Oct-20 10:36:03.614 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Oct-20 10:36:03.616 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_ALIGN_BOWTIE2:.*:SAMTOOLS_SORT` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Oct-20 10:36:03.620 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.620 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.621 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT': maxForks=0; fair=false; array=0 Oct-20 10:36:03.638 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Oct-20 10:36:03.640 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_ALIGN_BOWTIE2:.*:SAMTOOLS_INDEX` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Oct-20 10:36:03.644 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.644 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.645 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX': maxForks=0; fair=false; array=0 Oct-20 10:36:03.674 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Oct-20 10:36:03.677 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_ALIGN_BOWTIE2:.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Oct-20 10:36:03.680 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.680 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.681 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS': maxForks=0; fair=false; array=0 Oct-20 10:36:03.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Oct-20 10:36:03.697 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_ALIGN_BOWTIE2:.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Oct-20 10:36:03.700 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.700 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.701 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT': maxForks=0; fair=false; array=0 Oct-20 10:36:03.711 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Oct-20 10:36:03.716 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:FASTQ_ALIGN_BOWTIE2:.*:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Oct-20 10:36:03.719 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.720 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.721 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS': maxForks=0; fair=false; array=0 Oct-20 10:36:03.777 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS Oct-20 10:36:03.778 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PICARD_COLLECTMULTIPLEMETRICS` matches process NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS Oct-20 10:36:03.783 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.783 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.784 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS': maxForks=0; fair=false; array=0 Oct-20 10:36:03.820 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME Oct-20 10:36:03.823 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MOSDEPTH_GENOME` matches process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME Oct-20 10:36:03.832 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.832 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.833 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME': maxForks=0; fair=false; array=0 Oct-20 10:36:03.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME Oct-20 10:36:03.861 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLOT_MOSDEPTH_REGIONS_GENOME` matches process NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME Oct-20 10:36:03.865 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.865 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.865 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME': maxForks=0; fair=false; array=0 Oct-20 10:36:03.900 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP Oct-20 10:36:03.902 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_MPILEUP` matches process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP Oct-20 10:36:03.907 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.907 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.908 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP': maxForks=0; fair=false; array=0 Oct-20 10:36:03.949 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_NORM Oct-20 10:36:03.951 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_NORM` matches process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_NORM Oct-20 10:36:03.956 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.956 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.958 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_NORM': maxForks=0; fair=false; array=0 Oct-20 10:36:03.978 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:TABIX_TABIX Oct-20 10:36:03.980 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:VARIANTS_BCFTOOLS:.*:TABIX_TABIX` matches process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:TABIX_TABIX Oct-20 10:36:03.984 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:03.984 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:03.985 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:TABIX_TABIX': maxForks=0; fair=false; array=0 Oct-20 10:36:04.005 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:BCFTOOLS_STATS Oct-20 10:36:04.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:VARIANTS_BCFTOOLS:.*:BCFTOOLS_STATS` matches process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:BCFTOOLS_STATS Oct-20 10:36:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.012 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.013 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:BCFTOOLS_STATS': maxForks=0; fair=false; array=0 Oct-20 10:36:04.063 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VARIANTS_QC:ASCIIGENOME Oct-20 10:36:04.065 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ASCIIGENOME` matches process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VARIANTS_QC:ASCIIGENOME Oct-20 10:36:04.070 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.071 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VARIANTS_QC:ASCIIGENOME': maxForks=0; fair=false; array=0 Oct-20 10:36:04.110 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_FILTER Oct-20 10:36:04.112 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_FILTER` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_FILTER Oct-20 10:36:04.116 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.116 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.117 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_FILTER': maxForks=0; fair=false; array=0 Oct-20 10:36:04.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:TABIX_TABIX Oct-20 10:36:04.137 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:CONSENSUS_BCFTOOLS:TABIX_TABIX` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:TABIX_TABIX Oct-20 10:36:04.140 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.140 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.141 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:TABIX_TABIX': maxForks=0; fair=false; array=0 Oct-20 10:36:04.162 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MAKE_BED_MASK` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:MAKE_BED_MASK Oct-20 10:36:04.167 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.167 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.168 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:MAKE_BED_MASK': maxForks=0; fair=false; array=0 Oct-20 10:36:04.185 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MERGE Oct-20 10:36:04.189 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_MERGE` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MERGE Oct-20 10:36:04.192 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.192 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.193 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MERGE': maxForks=0; fair=false; array=0 Oct-20 10:36:04.209 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MASKFASTA Oct-20 10:36:04.211 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_MASKFASTA` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MASKFASTA Oct-20 10:36:04.215 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.215 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.216 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MASKFASTA': maxForks=0; fair=false; array=0 Oct-20 10:36:04.238 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_CONSENSUS Oct-20 10:36:04.240 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BCFTOOLS_CONSENSUS` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_CONSENSUS Oct-20 10:36:04.244 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.244 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.245 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_CONSENSUS': maxForks=0; fair=false; array=0 Oct-20 10:36:04.260 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RENAME_FASTA_HEADER` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:RENAME_FASTA_HEADER Oct-20 10:36:04.264 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.264 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.265 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:RENAME_FASTA_HEADER': maxForks=0; fair=false; array=0 Oct-20 10:36:04.289 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:QUAST Oct-20 10:36:04.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:.*:CONSENSUS_.*:.*:QUAST` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:QUAST Oct-20 10:36:04.295 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.295 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.296 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:QUAST': maxForks=0; fair=false; array=0 Oct-20 10:36:04.322 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PANGOLIN Oct-20 10:36:04.324 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PANGOLIN` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PANGOLIN Oct-20 10:36:04.329 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.329 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.330 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PANGOLIN': maxForks=0; fair=false; array=0 Oct-20 10:36:04.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PLOT_BASE_DENSITY Oct-20 10:36:04.357 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLOT_BASE_DENSITY` matches process NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PLOT_BASE_DENSITY Oct-20 10:36:04.362 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.362 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.363 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PLOT_BASE_DENSITY': maxForks=0; fair=false; array=0 Oct-20 10:36:04.439 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS Oct-20 10:36:04.441 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS Oct-20 10:36:04.446 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.446 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.447 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS': maxForks=0; fair=false; array=0 Oct-20 10:36:04.594 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_VIRALRECON:ILLUMINA:MULTIQC Oct-20 10:36:04.596 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_VIRALRECON:ILLUMINA:MULTIQC Oct-20 10:36:04.602 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Oct-20 10:36:04.602 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Oct-20 10:36:04.603 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'NFCORE_VIRALRECON:ILLUMINA:MULTIQC': maxForks=0; fair=false; array=0 Oct-20 10:36:04.647 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: MAKE_BED_MASK, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MASKFASTA, NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_FILTER, NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT, MOSDEPTH, BCFTOOLS_CONSENSUS, CAT_FASTQ, GUNZIP, SAMTOOLS_STATS, NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME, NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP, NFCORE_VIRALRECON:ILLUMINA:MULTIQC, GUNZIP_GFF, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PANGOLIN, QUAST, NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS, GUNZIP_GFA, NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_NORM, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:QUAST, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:TABIX_TABIX, NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:SNPEFF_BUILD, BOWTIE2_ALIGN, UNTAR_BLAST_DB, NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:TABIX_TABIX, SAMTOOLS_INDEX, TABIX_TABIX, FASTQC, COLLAPSE_PRIMERS, MULTIQC, UNICYCLER, CUTADAPT, NEXTCLADE_DATASETGET, NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB, KRAKEN2_BUILD, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MERGE, IVAR_TRIM, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PLOT_BASE_DENSITY, UNTAR_BOWTIE2_INDEX, BLAST_MAKEBLASTDB, NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VARIANTS_QC:ASCIIGENOME, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:RENAME_FASTA_HEADER, SAMTOOLS_FLAGSTAT, MAKE_VARIANTS_LONG_TABLE, SAMPLESHEET_CHECK, SNPSIFT_EXTRACTFIELDS, GUNZIP_SCAFFOLDS, GUNZIP_FASTA, PLASMIDID, BCFTOOLS_SORT, RENAME_FASTA_HEADER, BEDTOOLS_MASKFASTA, BCFTOOLS_FILTER, FILTER_BLASTN, BLAST_BLASTN, BCFTOOLS_NORM, PLOT_BASE_DENSITY, BANDAGE_IMAGE, MOSDEPTH_GENOME, FASTQC_TRIM, BCFTOOLS_STATS, SNPEFF_BUILD, IVAR_CONSENSUS, NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2, FASTP, TABIX_BGZIP, NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX, MINIA, PICARD_MARKDUPLICATES, NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP, NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME, GUNZIP_PRIMER_FASTA, KRAKEN2_KRAKEN2, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_CONSENSUS, UNTAR, FASTQC_RAW, NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NEXTCLADE_RUN, NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK, NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES, PLOT_MOSDEPTH_REGIONS_GENOME, MOSDEPTH_AMPLICON, IVAR_VARIANTS, PICARD_COLLECTMULTIPLEMETRICS, BEDTOOLS_GETFASTA, BOWTIE2_BUILD, SPADES, CUSTOM_GETCHROMSIZES, BCFTOOLS_QUERY, GUNZIP_PRIMER_BED, SAMTOOLS_SORT, NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN, NFCORE_VIRALRECON:ILLUMINA:CAT_FASTQ, NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:MAKE_BED_MASK, PANGOLIN, ASCIIGENOME, BCFTOOLS_MPILEUP, NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, SNPEFF_ANN, ABACAS, NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD, NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW, BEDTOOLS_MERGE, NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:BCFTOOLS_STATS, UNTAR_NEXTCLADE_DB, UNTAR_KRAKEN2_DB, PLOT_MOSDEPTH_REGIONS_AMPLICON, IVAR_VARIANTS_TO_VCF, SAMTOOLS_IDXSTATS, CUSTOM_DUMPSOFTWAREVERSIONS, PLOT_MOSDEPTH_REGIONS, NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS Oct-20 10:36:04.753 [main] WARN nextflow.Session - There's no process matching config selector: .*:.*:PREPARE_GENOME:GUNZIP_.* Oct-20 10:36:04.755 [main] WARN nextflow.Session - There's no process matching config selector: .*:.*:.*:.*:SNPEFF_SNPSIFT:.*:TABIX_BGZIP Oct-20 10:36:04.756 [main] WARN nextflow.Session - There's no process matching config selector: .*:.*:.*:.*:SNPEFF_SNPSIFT:.*:.*:TABIX_TABIX Oct-20 10:36:04.756 [main] WARN nextflow.Session - There's no process matching config selector: .*:.*:.*:.*:SNPEFF_SNPSIFT:.*:.*:BCFTOOLS_STATS Oct-20 10:36:04.756 [main] WARN nextflow.Session - There's no process matching config selector: .*:.*:.*:.*:SNPEFF_SNPSIFT:SNPSIFT_EXTRACTFIELDS Oct-20 10:36:04.761 [main] DEBUG nextflow.Session - Igniting dataflow network (107) Oct-20 10:36:04.764 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Oct-20 10:36:04.765 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB Oct-20 10:36:04.765 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD Oct-20 10:36:04.765 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:SNPEFF_BUILD Oct-20 10:36:04.765 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK Oct-20 10:36:04.765 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CAT_FASTQ Oct-20 10:36:04.765 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-20 10:36:04.766 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP Oct-20 10:36:04.766 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-20 10:36:04.766 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 Oct-20 10:36:04.766 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN Oct-20 10:36:04.767 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT Oct-20 10:36:04.767 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX Oct-20 10:36:04.767 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Oct-20 10:36:04.767 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Oct-20 10:36:04.767 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Oct-20 10:36:04.768 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS Oct-20 10:36:04.768 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME Oct-20 10:36:04.768 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME Oct-20 10:36:04.768 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP Oct-20 10:36:04.769 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_NORM Oct-20 10:36:04.769 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:TABIX_TABIX Oct-20 10:36:04.769 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VCF_TABIX_STATS:BCFTOOLS_STATS Oct-20 10:36:04.769 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:VARIANTS_QC:ASCIIGENOME Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_FILTER Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:TABIX_TABIX Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:MAKE_BED_MASK Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MERGE Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BEDTOOLS_MASKFASTA Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:BCFTOOLS_CONSENSUS Oct-20 10:36:04.770 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:RENAME_FASTA_HEADER Oct-20 10:36:04.771 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:QUAST Oct-20 10:36:04.771 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PANGOLIN Oct-20 10:36:04.771 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:PLOT_BASE_DENSITY Oct-20 10:36:04.771 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS Oct-20 10:36:04.772 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_VIRALRECON:ILLUMINA:MULTIQC Oct-20 10:36:04.778 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_392e714dbe8a1df6: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/fastqc/main.nf Script_171f56be792dd032: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/abacas/main.nf Script_e5c8e282196fb75b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/filter_blastn.nf Script_82832e4f78731dc7: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/snpsift_extractfields.nf Script_4ae97b6c4de15968: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/kraken2_build.nf Script_afe2a5128af617ec: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/mosdepth/main.nf Script_5a9d552c62a087ee: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bandage/image/main.nf Script_9eaf890fa8a7af97: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/asciigenome.nf Script_50b41f6826c95502: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bowtie2/build/main.nf Script_cc13f936b26c353f: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/nf-core/bam_sort_stats_samtools/main.nf Script_cff2a19c060594ab: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/variants_qc.nf Script_c51a3e306ca4c7aa: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/bam_trim_primers_ivar.nf Script_1163f0f7340cba96: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/mpileup/main.nf Script_7a3e19921fa26aec: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/pangolin/main.nf Script_cc2526b718012024: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/multiqc_illumina.nf Script_bbf547d8dba4eb76: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/blast/blastn/main.nf Script_98b09c3b35046f13: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/samplesheet_check.nf Script_b99f81f3247c1b22: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/gunzip/main.nf Script_f82ba87ff21585e1: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/plot_base_density.nf Script_1d7f44b8ee00eb23: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/rename_fasta_header.nf Script_813f8bd24f68044c: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/samtools/flagstat/main.nf Script_0e1385d55e695123: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/sort/main.nf Script_212886b35bdb8b3e: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/variants_long_table.nf Script_622d4b2a91e75ea6: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/samtools/index/main.nf Script_7527dacac01b0a6d: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/vcf_tabix_stats.nf Script_0df5d5439880a542: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/assembly_spades.nf Script_eb68c3e575f8fcdb: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/consensus_bcftools.nf Script_e67131615ff8f59b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/nextclade/run/main.nf Script_dd40e7ee19caedbd: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/tabix/tabix/main.nf Script_edfe1f1a3349a1ba: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/prepare_genome_illumina.nf Script_0c5ebca7ad03f851: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/picard/markduplicates/main.nf Script_67767acafb3ca123: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/snpeff_ann.nf Script_f560ba5b2809315b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/custom/dumpsoftwareversions/main.nf Script_d7295afec28f0af7: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/fastq_trim_fastp_fastqc.nf Script_ddee89947b9fac93: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bedtools/getfasta/main.nf Script_0f06d4e9cb0c04fd: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/fastp/main.nf Script_78f752979dec5aaa: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/quast/main.nf Script_c01951670e23583f: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/snpeff_snpsift.nf Script_bc1513495600293b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/make_variants_long_table.nf Script_161e0fc774636b4d: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/filter/main.nf Script_653df7ce942ce029: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/vcf_bgzip_tabix_stats.nf Script_3936c78ef9aedf26: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/ivar/variants/main.nf Script_f9bc8fbc66fea321: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/collapse_primers.nf Script_582e23b0fa8893c0: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/consensus_qc.nf Script_0c90d264a51bc64b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bedtools/merge/main.nf Script_dbeb776b6996f1b0: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/plasmidid/main.nf Script_d049e4333c2db68e: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/norm/main.nf Script_e69457c5a9478b12: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/snpeff_build.nf Script_509677ea22863b9c: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/query/main.nf Script_524f102e8e077dc3: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/input_check.nf Script_747a639779ec3d31: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/stats/main.nf Script_6e7e3ea92560e94a: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/nf-core/bam_stats_samtools/main.nf Script_505ec9861459c120: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/tabix/bgzip/main.nf Script_b7eabc0280d0f6de: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/spades/main.nf Script_6ced4aca7f503e1e: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/minia/main.nf Script_d9f37cc7b6553f2c: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/kraken2/kraken2/main.nf Script_08e8120406c42c87: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/samtools/stats/main.nf Script_9f7e885c36e49ade: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/variants_ivar.nf Script_cb211c549341a328: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/samtools/idxstats/main.nf Script_dd1c43c2a0597b3b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bcftools/consensus/main.nf Script_043409e31d8b9164: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/variants_bcftools.nf Script_a4cc5b311d906ff4: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/assembly_minia.nf Script_0aaf4911c5a2ee55: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/plot_mosdepth_regions.nf Script_c5947f9108c123ff: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/nextclade/datasetget/main.nf Script_dbfcd99b4643d9a2: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/nf-core/bam_markduplicates_picard/main.nf Script_3e99caba1ee271cd: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bedtools/maskfasta/main.nf Script_3da931254dea4372: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/cutadapt.nf Script_f9a3f3717ec9abf7: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/picard/collectmultiplemetrics/main.nf Script_95a000d7314a53ff: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/assembly_qc.nf Script_7ddd67a51b3ad523: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/main.nf Script_c45bc812e1d5f5cb: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/samtools/sort/main.nf Script_91738e59e65f95b5: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/cat/fastq/main.nf Script_cb35c946a46bb082: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/make_bed_mask.nf Script_143639a160311391: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/assembly_unicycler.nf Script_cdf3da412293fa45: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/untar/main.nf Script_bf272342dd9add44: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/blast/makeblastdb/main.nf Script_ae0a281286baa19e: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/local/ivar_variants_to_vcf.nf Script_5e602e6befe4adc6: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/custom/getchromsizes/main.nf Script_fa87eec1e33566a9: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/nf-core/fastq_align_bowtie2/main.nf Script_9542053f40d7b8d9: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/bowtie2/align/main.nf Script_e0924165c0b96bdf: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/ivar/consensus/main.nf Script_9b7486b9ec30328b: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/subworkflows/local/consensus_ivar.nf Script_6a4e2158c1b55792: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/unicycler/main.nf Script_2455faffc6e9a0ac: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/modules/nf-core/ivar/trim/main.nf Script_b5dd8be0b54c663e: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/workflows/illumina.nf Oct-20 10:36:04.778 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Oct-20 10:36:04.778 [main] DEBUG nextflow.Session - Session await Oct-20 10:36:04.779 [Actor Thread 23] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Oct-20 10:36:04.931 [Actor Thread 46] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.9--1; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-python-3.9--1.img Oct-20 10:36:04.931 [Actor Thread 59] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-bowtie2-2.4.4--py39hbb4e92a_0.img Oct-20 10:36:04.931 [Actor Thread 65] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ubuntu:20.04; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-ubuntu-20.04.img Oct-20 10:36:04.931 [Actor Thread 37] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-samtools-1.16.1--h6899075_1.img Oct-20 10:36:04.961 [Actor Thread 44] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/bin/check_samplesheet.py Oct-20 10:36:05.008 [Actor Thread 24] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.022 s; total time: 0.024 s Oct-20 10:36:05.026 [Actor Thread 24] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/collect-file/d3141a430104b097132cedb83b61b294 Oct-20 10:36:05.038 [Actor Thread 24] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-15693389815082041828 Oct-20 10:36:05.093 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:05.096 [Task submitter] INFO nextflow.Session - [d8/13288b] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (LCMVABQS.fasta) Oct-20 10:36:05.114 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:05.114 [Task submitter] INFO nextflow.Session - [39/e04dfa] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD (LCMVABQS.fasta) Oct-20 10:36:05.127 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:05.128 [Task submitter] INFO nextflow.Session - [04/2f4085] Submitted process > NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK (LCMV_ABQ_Sample_sheet_run2.csv) Oct-20 10:36:05.141 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:05.142 [Task submitter] INFO nextflow.Session - [ca/8ec90b] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz) Oct-20 10:36:07.108 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (LCMVABQS.fasta); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/d8/13288bdf39cae319470680828dbfbf] Oct-20 10:36:07.109 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Oct-20 10:36:07.350 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:CUSTOM_GETCHROMSIZES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:36:07.396 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_VIRALRECON:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK (LCMV_ABQ_Sample_sheet_run2.csv); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/04/2f4085703d55420b4ae3f1fa1838ed] Oct-20 10:36:07.418 [TaskFinalizer-2] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=192; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false Oct-20 10:36:07.471 [Actor Thread 44] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img Oct-20 10:36:07.471 [Actor Thread 41] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-fastp-0.23.2--h79da9fb_0.img Oct-20 10:36:07.516 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.517 [Task submitter] INFO nextflow.Session - [2c/4c8dcd] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_8_15) Oct-20 10:36:07.529 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.530 [Task submitter] INFO nextflow.Session - [9c/85fdfe] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_5_23) Oct-20 10:36:07.541 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.542 [Task submitter] INFO nextflow.Session - [90/d15cfc] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_9_4) Oct-20 10:36:07.555 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.556 [Task submitter] INFO nextflow.Session - [7f/d40a08] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_4_28) Oct-20 10:36:07.568 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.569 [Task submitter] INFO nextflow.Session - [05/8890af] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_3_18) Oct-20 10:36:07.585 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.586 [Task submitter] INFO nextflow.Session - [44/08ee41] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_9_4) Oct-20 10:36:07.597 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.597 [Task submitter] INFO nextflow.Session - [c3/5a5555] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_AQS11) Oct-20 10:36:07.607 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:07.608 [Task submitter] INFO nextflow.Session - [c8/255f04] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_3_18) Oct-20 10:36:08.441 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:BOWTIE2_BUILD (LCMVABQS.fasta); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/39/e04dfaccea5579c115ead4edb39cb9] Oct-20 10:36:08.454 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:08.454 [Task submitter] INFO nextflow.Session - [25/16c399] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_4_28) Oct-20 10:36:08.467 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:08.467 [Task submitter] INFO nextflow.Session - [9f/6d244d] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_5_23) Oct-20 10:36:42.175 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/2c/4c8dcda0764198902d948c2ec14415] Oct-20 10:36:42.199 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:42.204 [Task submitter] INFO nextflow.Session - [54/94f4d3] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_AQS11) Oct-20 10:36:42.209 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-20 10:36:42.210 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-20 10:36:42.340 [Actor Thread 63] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a-a0ffedb52808e102887f6ce600d092675bf3528a-0.img Oct-20 10:36:44.479 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/05/8890af3cd15cbf6d289946032c073d] Oct-20 10:36:44.494 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:44.495 [Task submitter] INFO nextflow.Session - [6e/c1af52] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_8_15) Oct-20 10:36:53.626 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/c3/5a55551652b4ea6b180d9c393ac95c] Oct-20 10:36:53.641 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:53.642 [Task submitter] INFO nextflow.Session - [ed/b240d6] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_8_15) Oct-20 10:36:53.645 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-20 10:36:53.646 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-20 10:36:54.652 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/c8/255f04702cb906681e84b775d20e79] Oct-20 10:36:54.668 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:54.669 [Task submitter] INFO nextflow.Session - [34/16fdea] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_AQS11) Oct-20 10:36:54.673 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-20 10:36:54.673 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-20 10:36:56.443 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/44/08ee41af0bfcab50b2e7d895886bf7] Oct-20 10:36:57.137 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:57.138 [Task submitter] INFO nextflow.Session - [48/cedc6b] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_3_18) Oct-20 10:36:57.141 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-20 10:36:57.141 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-20 10:36:57.450 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/25/16c399633893b136d56b003a043e05] Oct-20 10:36:57.465 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:36:57.466 [Task submitter] INFO nextflow.Session - [69/f14dac] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_9_4) Oct-20 10:36:57.475 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-20 10:36:57.476 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-20 10:37:02.541 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/7f/d40a0848268db40ce6fdfaf6ebdbbd] Oct-20 10:37:02.552 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:02.553 [Task submitter] INFO nextflow.Session - [59/6d0b9d] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_4_28) Oct-20 10:37:12.087 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ed/b240d68ae222314f663e5085969f64] Oct-20 10:37:12.369 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/90/d15cfc6db045824aae648c7d72a90f] Oct-20 10:37:12.381 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:12.382 [Task submitter] INFO nextflow.Session - [25/00b75b] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_8_15) Oct-20 10:37:16.327 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/6e/c1af52471ba669cf8c52476929c52c] Oct-20 10:37:20.036 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/48/cedc6b05f696dd44c5e5fee0fa2919] Oct-20 10:37:20.050 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:20.051 [Task submitter] INFO nextflow.Session - [6e/1614ad] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_AQS11) Oct-20 10:37:23.555 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/25/00b75bbe32b04bce8a0158b013c616] Oct-20 10:37:23.572 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:23.572 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:23.578 [Task submitter] INFO nextflow.Session - [dc/b529d6] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_3_18) Oct-20 10:37:26.732 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/34/16fdeae34f2f5678f5afa62c6d336f] Oct-20 10:37:26.746 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:26.747 [Task submitter] INFO nextflow.Session - [6a/dcc9b1] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_8_15) Oct-20 10:37:27.533 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/69/f14dac2c569842d98f09cdcbe992b5] Oct-20 10:37:28.428 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/6a/dcc9b147cb115e10fbcbe406ef2fcc] Oct-20 10:37:28.443 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:28.452 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:28.454 [Task submitter] INFO nextflow.Session - [b4/334ecd] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_9_4) Oct-20 10:37:28.498 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/59/6d0b9d679cee3ec2c59482a4bd3328] Oct-20 10:37:28.510 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:28.511 [Task submitter] INFO nextflow.Session - [07/6bdc52] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_8_15) Oct-20 10:37:30.165 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/07/6bdc52f6748889767262b3ba0a2e44] Oct-20 10:37:30.180 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:30.181 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:37.295 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/dc/b529d6f2890e784f24a0712d219d56] Oct-20 10:37:37.307 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:37.311 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:37.312 [Task submitter] INFO nextflow.Session - [59/80b035] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_4_28) Oct-20 10:37:37.341 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:37.344 [Task submitter] INFO nextflow.Session - [9f/e31785] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_3_18) Oct-20 10:37:39.247 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/9f/e3178536efbb05911c3f8d41bb50ab] Oct-20 10:37:39.261 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:39.299 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:39.300 [Task submitter] INFO nextflow.Session - [6f/7a991c] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_3_18) Oct-20 10:37:40.833 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/6f/7a991ca1598f475737d7f1d49fb4e8] Oct-20 10:37:40.845 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:40.845 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:41.856 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/6e/1614ad918f943cdf2e1d4e0963f1af] Oct-20 10:37:41.872 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:41.902 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:41.903 [Task submitter] INFO nextflow.Session - [73/ccc98f] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_AQS11) Oct-20 10:37:47.019 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/73/ccc98f1b911423839ec368db0ee7c8] Oct-20 10:37:47.031 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:47.063 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:47.064 [Task submitter] INFO nextflow.Session - [f7/64f412] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_AQS11) Oct-20 10:37:49.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/f7/64f412ebfa41c617bd8eea3c90d866] Oct-20 10:37:49.077 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:49.077 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:53.041 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/b4/334ecd06c2b411f0092081303b3593] Oct-20 10:37:53.053 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:53.136 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:53.139 [Task submitter] INFO nextflow.Session - [bd/26fd38] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_9_4) Oct-20 10:37:54.282 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/59/80b035606897b4a9738387b2b8463a] Oct-20 10:37:54.294 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:54.329 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:54.330 [Task submitter] INFO nextflow.Session - [e5/0c1fe1] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_4_28) Oct-20 10:37:54.974 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/bd/26fd3807d3874b330fa5ba6ee56952] Oct-20 10:37:54.986 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:55.040 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:55.041 [Task submitter] INFO nextflow.Session - [21/ae9e50] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_9_4) Oct-20 10:37:55.894 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/e5/0c1fe1b0cf98ad5a1dcf9ebc6a25fc] Oct-20 10:37:55.902 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:55.951 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:37:55.952 [Task submitter] INFO nextflow.Session - [cf/25bc88] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_4_28) Oct-20 10:37:56.551 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/21/ae9e50fb4d2d2d4c271f0f53c38882] Oct-20 10:37:56.560 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:56.560 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:37:57.410 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/cf/25bc8822560eb3f3181b8cc987906d] Oct-20 10:37:57.419 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:37:57.420 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:38:04.918 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/54/94f4d3ce93e65a35a0880df9756058] Oct-20 10:38:21.596 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/9f/6d244dc6a6cbeb6136511d8ba2fc5d] Oct-20 10:38:21.617 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-20 10:38:21.617 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-20 10:38:21.656 [Actor Thread 62] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Oct-20 10:38:21.661 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:38:21.662 [Task submitter] INFO nextflow.Session - [6d/a5f434] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_5_23) Oct-20 10:38:21.677 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:38:21.678 [Task submitter] INFO nextflow.Session - [88/584391] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_5_23) Oct-20 10:40:14.967 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/88/5843917afef40d9b5b8b703179b043] Oct-20 10:40:14.981 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:40:15.008 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:15.009 [Task submitter] INFO nextflow.Session - [4d/42f335] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_5_23) Oct-20 10:40:16.565 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/4d/42f33517ef277fbf62f903f8d34764] Oct-20 10:40:16.574 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:40:16.617 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:16.618 [Task submitter] INFO nextflow.Session - [6d/d2a647] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_5_23) Oct-20 10:40:18.072 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/6d/d2a647de9ae40af6429ed17264ecd3] Oct-20 10:40:18.080 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-20 10:40:18.081 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Oct-20 10:40:18.136 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.137 [Task submitter] INFO nextflow.Session - [93/ef174c] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_5_23) Oct-20 10:40:18.147 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.148 [Task submitter] INFO nextflow.Session - [42/b04ce1] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_4_28) Oct-20 10:40:18.157 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.158 [Task submitter] INFO nextflow.Session - [3e/62527c] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_AQS11) Oct-20 10:40:18.167 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.167 [Task submitter] INFO nextflow.Session - [76/dcd582] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_AQS11) Oct-20 10:40:18.175 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.176 [Task submitter] INFO nextflow.Session - [15/43dead] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_8_15) Oct-20 10:40:18.184 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.185 [Task submitter] INFO nextflow.Session - [64/2ba4d4] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_9_4) Oct-20 10:40:18.196 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.197 [Task submitter] INFO nextflow.Session - [b1/98c2ce] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_8_15) Oct-20 10:40:18.208 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.209 [Task submitter] INFO nextflow.Session - [29/03a459] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_3_18) Oct-20 10:40:18.219 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.219 [Task submitter] INFO nextflow.Session - [82/8801c4] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_9_4) Oct-20 10:40:18.230 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.231 [Task submitter] INFO nextflow.Session - [3a/b0a390] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_3_18) Oct-20 10:40:18.246 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.247 [Task submitter] INFO nextflow.Session - [fd/1aa6f9] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_AQS11) Oct-20 10:40:18.256 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.257 [Task submitter] INFO nextflow.Session - [56/64072d] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_8_15) Oct-20 10:40:18.268 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.269 [Task submitter] INFO nextflow.Session - [68/9b0e79] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_9_4) Oct-20 10:40:18.280 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.281 [Task submitter] INFO nextflow.Session - [63/7d294f] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_4_28) Oct-20 10:40:18.294 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.295 [Task submitter] INFO nextflow.Session - [4a/022b57] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_5_23) Oct-20 10:40:18.308 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.309 [Task submitter] INFO nextflow.Session - [1d/c2c2e1] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_3_18) Oct-20 10:40:18.322 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.323 [Task submitter] INFO nextflow.Session - [85/ccc8f3] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_5_23) Oct-20 10:40:18.384 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:18.385 [Task submitter] INFO nextflow.Session - [70/624b8f] Submitted process > NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_4_28) Oct-20 10:40:24.910 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/76/dcd5826e06086aa8c424170354c816] Oct-20 10:40:24.926 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/93/ef174c096269c400e5ace08f4d4469] Oct-20 10:40:24.956 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-bcftools-1.16--hfe4b78e_1.img Oct-20 10:40:24.959 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-mosdepth-0.3.3--hdfd78af_1.img Oct-20 10:40:24.961 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-picard-3.0.0--hdfd78af_1.img Oct-20 10:40:24.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/15/43deade84b38369a00b71ec70a0e1d] Oct-20 10:40:24.979 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:24.980 [Task submitter] INFO nextflow.Session - [51/bc8aaa] Submitted process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_5_23) Oct-20 10:40:24.993 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:24.994 [Task submitter] INFO nextflow.Session - [35/d4286e] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_5_23) Oct-20 10:40:25.006 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.007 [Task submitter] INFO nextflow.Session - [e6/4960de] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_5_23) Oct-20 10:40:25.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/42/b04ce19325ec811f801c3bee081242] Oct-20 10:40:25.084 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.086 [Task submitter] INFO nextflow.Session - [e7/be6113] Submitted process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_8_15) Oct-20 10:40:25.104 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.105 [Task submitter] INFO nextflow.Session - [d8/ee5e49] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_8_15) Oct-20 10:40:25.123 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.124 [Task submitter] INFO nextflow.Session - [c1/db618b] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_8_15) Oct-20 10:40:25.143 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.144 [Task submitter] INFO nextflow.Session - [32/3d691e] Submitted process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_4_28) Oct-20 10:40:25.160 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.162 [Task submitter] INFO nextflow.Session - [77/d63033] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_4_28) Oct-20 10:40:25.188 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/4a/022b5720f4f8e5324031210778454c] Oct-20 10:40:25.203 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/3e/62527ca1054f222fad9667917dbaac] Oct-20 10:40:25.220 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/29/03a4598f295a2b4608d102fe85c7de] Oct-20 10:40:25.221 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.222 [Task submitter] INFO nextflow.Session - [01/2b67bf] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_4_28) Oct-20 10:40:25.247 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/3a/b0a39026f1fea4b46c9684542ad890] Oct-20 10:40:25.267 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.267 [Task submitter] INFO nextflow.Session - [d9/d23cf6] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_AQS11) Oct-20 10:40:25.308 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/82/8801c4eb03a4b61e06100d7011a1f0] Oct-20 10:40:25.318 [Actor Thread 29] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Oct-20 10:40:25.320 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.320 [Task submitter] INFO nextflow.Session - [40/2c77fe] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_3_18) Oct-20 10:40:25.320 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/b1/98c2ced7533a5aa3a31ea9cc054d83] Oct-20 10:40:25.321 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/56/64072d551530f0664bff1f42478b61] Oct-20 10:40:25.335 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/fd/1aa6f93c04dfd0d5d0327029735ee2] Oct-20 10:40:25.345 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.346 [Task submitter] INFO nextflow.Session - [20/448fe5] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_9_4) Oct-20 10:40:25.384 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/64/2ba4d4a7c45a41b673e79cf31df519] Oct-20 10:40:25.388 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/63/7d294f44aa8bc7d35d95787fb46ef3] Oct-20 10:40:25.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/1d/c2c2e1be7a08e731e46b7c03fb66e2] Oct-20 10:40:25.405 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/70/624b8fef68573694694e64ef5c3ce6] Oct-20 10:40:25.420 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:25.421 [Task submitter] INFO nextflow.Session - [3f/b886ba] Submitted process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_AQS11) Oct-20 10:40:25.457 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/85/ccc8f31207af79f2cca6e67e72c766] Oct-20 10:40:25.567 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/68/9b0e79b6b16fd1b5a664f2abc2ab0a] Oct-20 10:40:30.249 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/35/d4286e611ddc4b4a53fcc9590ba322] Oct-20 10:40:30.288 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:30.289 [Task submitter] INFO nextflow.Session - [99/98c668] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_AQS11) Oct-20 10:40:30.300 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/01/2b67bf7d123a8ab9f8e0908da4809a] Oct-20 10:40:30.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/c1/db618bde4da9ed537c7c47edc3c302] Oct-20 10:40:30.364 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:30.364 [Task submitter] INFO nextflow.Session - [71/c34c10] Submitted process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_3_18) Oct-20 10:40:30.367 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:30.368 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Oct-20 10:40:30.368 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Oct-20 10:40:30.368 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Oct-20 10:40:30.368 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Oct-20 10:40:30.373 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:30.374 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Oct-20 10:40:30.374 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Oct-20 10:40:30.375 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Oct-20 10:40:30.375 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Oct-20 10:40:30.380 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:30.380 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Oct-20 10:40:30.380 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Oct-20 10:40:30.380 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Oct-20 10:40:30.380 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Oct-20 10:40:30.384 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:30.384 [Task submitter] INFO nextflow.Session - [f7/980a8b] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_3_18) Oct-20 10:40:30.613 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/32/3d691e8b824a67effe6ea0f807e26c] Oct-20 10:40:30.625 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:30.626 [Task submitter] INFO nextflow.Session - [2d/4d5d76] Submitted process > NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_9_4) Oct-20 10:40:30.629 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:30.633 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/e7/be611308618c3ad21b4fdbeb9a97b4] Oct-20 10:40:30.644 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:30.646 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:30.647 [Task submitter] INFO nextflow.Session - [35/f7d77f] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_9_4) Oct-20 10:40:30.723 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/51/bc8aaa5bdb67983be3d20531e413fb] Oct-20 10:40:30.733 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:30.810 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/3f/b886ba5bddfc90d5cc95f84370371d] Oct-20 10:40:30.825 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:32.809 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/99/98c668e8ced571e81cbae702976906] Oct-20 10:40:32.890 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:32.892 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Oct-20 10:40:32.892 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Oct-20 10:40:32.892 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Oct-20 10:40:32.892 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Oct-20 10:40:32.999 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/f7/980a8befafd3162ac85aaf426f0806] Oct-20 10:40:33.046 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:33.047 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Oct-20 10:40:33.048 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Oct-20 10:40:33.048 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Oct-20 10:40:33.048 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Oct-20 10:40:33.160 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/35/f7d77f1701f009b66dbc523541832a] Oct-20 10:40:33.194 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:33.194 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/71/c34c10c7acdc1a03704af1660f15b2] Oct-20 10:40:33.194 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Oct-20 10:40:33.194 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Oct-20 10:40:33.195 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<10:1> Oct-20 10:40:33.195 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MOSDEPTH_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<11:1> Oct-20 10:40:33.207 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:33.211 [Actor Thread 51] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7-05678da05b8e5a7a5130e90a9f9a6c585b965afa-0.img Oct-20 10:40:33.215 [Actor Thread 41] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/bin/plot_mosdepth_regions.r Oct-20 10:40:33.233 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 10:40:33.234 [Task submitter] INFO nextflow.Session - [81/9b6a36] Submitted process > NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME Oct-20 10:40:33.507 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/2d/4d5d76e66a382fa6e9903934ddc471] Oct-20 10:40:33.523 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:VARIANTS_BCFTOOLS:BCFTOOLS_MPILEUP > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Oct-20 10:40:39.205 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/d8/ee5e4935ec976a1259e4cad3b8797d] Oct-20 10:40:39.287 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/40/2c77fe44206beb5013a5c9bbe545dd] Oct-20 10:40:39.393 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/77/d63033bd1f600c0f9c05d41eeae637] Oct-20 10:40:39.855 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/d9/d23cf6b0197ed445e9382b96b56158] Oct-20 10:40:40.152 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/e6/4960de40ed446336801a2f4e84ff24] Oct-20 10:40:40.736 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/20/448fe557c3e54eee8125aa550b21eb] Oct-20 10:40:45.789 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME; status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/81/9b6a364b06d02df0f40c3e8926159c] Oct-20 10:40:45.811 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<2> Oct-20 10:40:45.812 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:PLOT_MOSDEPTH_REGIONS_GENOME > Skipping output binding because one or more optional files are missing: fileoutparam<3> Oct-20 10:40:52.307 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/6d/a5f4349b0547e13b381dcbe19fdb59] Oct-20 10:41:03.234 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] ~> TaskHandler[id: 9; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_5_23); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/9c/85fdfeafea6d1707f3972d5dff79e1] Oct-20 10:42:25.297 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/9c/85fdfeafea6d1707f3972d5dff79e1] Oct-20 10:46:03.291 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 10:51:03.373 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 10:56:03.447 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:01:03.541 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:06:03.550 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:11:03.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:16:03.636 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:21:03.663 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:26:03.667 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:31:03.709 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:31:11.071 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_VIRALRECON:ILLUMINA:PREPARE_GENOME:UNTAR_KRAKEN2_DB (k2_pluspf_20240605.tar.gz); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ca/8ec90b8f7b6c715af3b18ad95c7a8b] Oct-20 11:31:11.097 [Actor Thread 58] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98-87fc08d11968d081f3e8a37131c1f1f6715b6542-0.img Oct-20 11:31:11.117 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:31:11.118 [Task submitter] INFO nextflow.Session - [9a/841175] Submitted process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_3_18) Oct-20 11:31:11.127 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:31:11.127 [Task submitter] INFO nextflow.Session - [42/0b7697] Submitted process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_8_15) Oct-20 11:31:11.135 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:31:11.135 [Task submitter] INFO nextflow.Session - [ef/0e7127] Submitted process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_5_23) Oct-20 11:31:11.143 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:31:11.144 [Task submitter] INFO nextflow.Session - [f1/c9cf83] Submitted process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_4_28) Oct-20 11:31:11.152 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:31:11.153 [Task submitter] INFO nextflow.Session - [a5/e772f0] Submitted process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_AQS11) Oct-20 11:31:11.154 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 81; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_9_4); status: NEW; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/36/c3c7f3cd836edc0decaf8f5d21199b] Oct-20 11:32:43.603 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_8_15); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/42/0b769745b8138e535b225fb7cf29ad] Oct-20 11:32:43.633 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:32:43.633 [Task submitter] INFO nextflow.Session - [36/c3c7f3] Submitted process > NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_9_4) Oct-20 11:32:43.792 [Actor Thread 62] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 33; slices: 1; internal sort time: 0.163 s; external sort time: 0.006 s; total time: 0.169 s Oct-20 11:32:43.857 [Actor Thread 62] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/collect-file/3f7dd91af9079bfd37f91d79962ffa0a Oct-20 11:32:43.860 [Actor Thread 62] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8994861355682951333 Oct-20 11:32:43.944 [Actor Thread 62] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0; path=/xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/singularity/depot.galaxyproject.org-singularity-multiqc-1.14--pyhdfd78af_0.img Oct-20 11:32:43.987 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:32:43.987 [Task submitter] INFO nextflow.Session - [56/f9e3bb] Submitted process > NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS (1) Oct-20 11:32:52.192 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: NFCORE_VIRALRECON:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS (1); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/56/f9e3bba072bd8f675f84de4b7501b3] Oct-20 11:33:57.092 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_AQS11); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/a5/e772f08ed30cf21947b1e36589bafd] Oct-20 11:34:00.972 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_3_18); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/9a/84117592adb6d7afcdb0959b348f2f] Oct-20 11:34:03.013 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_4_28); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/f1/c9cf83fe8a6557362dd9a35618f917] Oct-20 11:35:39.607 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_9_4); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/36/c3c7f3cd836edc0decaf8f5d21199b] Oct-20 11:36:03.738 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 83; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_5_23); status: RUNNING; exit: -; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ef/0e7127cbd0cbc89d586920af04265a] Oct-20 11:37:52.782 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: NFCORE_VIRALRECON:ILLUMINA:KRAKEN2_KRAKEN2 (LCMV_ABQ_5_23); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/ef/0e7127cbd0cbc89d586920af04265a] Oct-20 11:37:52.878 [Actor Thread 62] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/assets/multiqc_config_illumina.yml Oct-20 11:37:52.881 [Actor Thread 62] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /users/fmtwohig/.nextflow/assets/nf-core/viralrecon/bin/multiqc_to_custom_csv.py Oct-20 11:37:52.904 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Oct-20 11:37:52.905 [Task submitter] INFO nextflow.Session - [40/db59e5] Submitted process > NFCORE_VIRALRECON:ILLUMINA:MULTIQC (1) Oct-20 11:38:37.485 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: NFCORE_VIRALRECON:ILLUMINA:MULTIQC (1); status: COMPLETED; exit: 0; error: -; workDir: /xena/scratch/fmtwohig/LCMV_Stock_Seq_2/work/40/db59e5a4641743ba0de392d6fb8468] Oct-20 11:38:37.512 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MULTIQC > Skipping output binding because one or more optional files are missing: fileoutparam<3> Oct-20 11:38:37.512 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_VIRALRECON:ILLUMINA:MULTIQC > Skipping output binding because one or more optional files are missing: fileoutparam<4> Oct-20 11:38:37.520 [main] DEBUG nextflow.Session - Session await > all processes finished Oct-20 11:38:37.586 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Oct-20 11:38:37.586 [main] DEBUG nextflow.Session - Session await > all barriers passed Oct-20 11:38:37.591 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) Oct-20 11:38:37.765 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Oct-20 11:38:37.770 [main] INFO nextflow.Nextflow - -[nf-core/viralrecon] 6/6 samples passed Bowtie2 10 mapped read threshold: 40993: LCMV_ABQ_5_23 2708: LCMV_ABQ_8_15 2197: LCMV_ABQ_4_28 7384: LCMV_ABQ_AQS11 489: LCMV_ABQ_3_18 65749: LCMV_ABQ_9_4 ..see pipeline reports for full list - Oct-20 11:38:37.771 [main] INFO nextflow.Nextflow - -[nf-core/viralrecon] Pipeline completed successfully- Oct-20 11:38:37.777 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=85; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=7h 31m 6s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=25; peakCpus=67; peakMemory=402 GB; ] Oct-20 11:38:37.777 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Oct-20 11:38:37.779 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Oct-20 11:38:39.211 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Oct-20 11:38:39.664 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Oct-20 11:38:39.729 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Oct-20 11:38:39.730 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye